lncRNAs: insights into their function and mechanics in underlying disorders.

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Contents lists available at ScienceDirect

Mutation Research/Reviews in Mutation Research journal homepage: www.elsevier.com/locate/reviewsmr Community address: www.elsevier.com/locate/mutres

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Review

lncRNAs: Insights into their function and mechanics in underlying disorders Q1 Xiaolei

Li a, Zhiqiang Wu a, Xiaobing Fu a,b,**, Weidong Han a,*

a

Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China Key Laboratory of Wound Healing and Cell Biology, Institute of Burns, The First Affiliated Hospital to the Chinese PLA General Hospital, Trauma Center of Postgraduate Medical School, Beijing 100037, China b

A R T I C L E I N F O

A B S T R A C T

Article history: Received 31 May 2013 Received in revised form 27 April 2014 Accepted 28 April 2014 Available online xxx

Genomes of complex organisms are characterized by the pervasive expression of different types of noncoding RNAs (ncRNAs). lncRNAs constitute a large family of long—arbitrarily defined as being longer than 200 nucleotides—ncRNAs that are expressed throughout the cell and that include thousands of different species. While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown at present. Existing examples suggest that lncRNAs have fulfilled a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass signal, decoy, scaffold and guide capacities, derive from folded modular domains in lncRNAs. Early discoveries support a paradigm in which lncRNAs regulate transcription networks via chromatin modulation, but new functions are steadily emerging. Given the biochemical versatility of RNA, lncRNAs may be used for various tasks, including posttranscriptional processing. In addition, long intergenic ncRNAs (lincRNAs) are strongly enriched for trait-associated SNPs, which suggest a new mechanism by which intergenic trait-associated regions might function. Moreover, multiple lines of evidence increasingly link mutations and dysregulations of lncRNAs to diverse human diseases, especially disorders related to aging. In this article, we review the current state of the knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions and mechanisms of action of these molecules. We highlight the growing evidence for the importance of lncRNAs in diverse human disorders and the indications that their dysregulations and

Keywords: Long noncoding RNAs (lncRNAs) Epigenetics Gene regulation Trancriptional Posttranscriptional Disorders

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Abbreviations: Airn, antisense to insulin-like growth factor 2 receptor; APP, amyloid precursor protein; ADAR, adenosine deaminase acting on RNA; ANRIL, CDKN2B antisense RNA 1; BACE-1, beta-amyloid precursor protein-cleaving enzyme 1; BC RNA, brain cytoplasmic RNA; CDKN1A, cyclin-dependent kinase inhibitor 1A; CCND1, cyclin D1; circRNA, circular RNA; CTCF, CCCTC-binding factor; ceRNA, competing endogeneous RNA; CDR1as, CDR1 antisense; Dlx6os1, Dlx opposite strand transcript 1; DHFR, dihydrofolate reductase; DMPK, myotin protein kinase; EZH, Enhancer of zeste; ESCs, embryonic stem cells; Eed, ectoderm development; endo-siRNAs, endogenous short interfering RNAs; FMR4/ASFMR1, FMR1 antisense RNA 1; GAS5, growth arrest specific 5; GR, glucocorticoid receptor; GWAS, genome-wide association studies; HOTAIR, HOX transcript antisense RNA; HSF1, heat shock factor 1; HSR1, heat shock RNA 1; HULC, highly upregulated in liver cancer; HBEFG, heparin-binding epidermal growth factor [EGF]-like growth factor; HOTTIP, HOXA distal transcript antisense RNA; HAR1, highly accelerated region 1; IPS1, INDUCED BY PHOSPHATE STARVATION 1; Kcnq1ot1, Kcnq1 overlapping transcript 1; LSD1-CoREST/REST, lysine-specific histone demethylase 1A-REST corepressor 1-RE1-silencing transcription factor; LINCMD1, long noncoding RNA, muscle differentiation 1; lincRNA, long intergenic (or intervening) ncRNA; lncRNA, long noncoding RNA; MAML1, mastermind-like 1; MLL1, mixed-lineage leukemia 1; MECP2, methyl-CpG-binding protein 2; MIAT, myocardial infarction-associated transcript; MEF2C, myocyte enhancer factor 2C; miRNAs, microRNAs; mTOR, mammalian target of rapamycin; ncRNA, noncoding RNA; NATs, natural antisense transcripts; NEAT1, nuclear paraspeckle assembly transcript 1; NONO, non-POU domain containing octamer-binding protein; NFAT, nuclear factor of activated T cells; NESPAS, neuroendocrine secretory protein antisense; NESP55, neuroendocrine secretory protein 55; NFYA, nuclear transcription factor Y subunit-a; NRON, non-coding repressor of NFAT; NF-kB, nuclear factor-kB; piRNAs, PIWI-interacting RNAs; PcG, Polycomb group; PRC2, polycomb repressive complex 2; PSPC1, proteins paraspeckle component 1; PANDA, P21-associated ncRNA DNA damage activated; PTENP1, PTEN pseudogene 1; PABP1, poly(A)-binding protein; snoRNAs, small nucleolar RNAs; SNPs, signle-nucleotide polymorphisms; Suz12, Suppressor of zeste 12; SR, serine/arginine-rich; SAL-RNAs, senescence-associated lncRNAs; SYNCRIP, synaptotagmin-binding cytoplasmic RNA interacting protein; SRA1, steroid receptor RNA activator 1; TrxG, Trithorax group; TFIIB, transcription factor II B; Tie-1, tyrosine kinase containing immunoglobulin and epidermal growth factor homology domain-1; Tug1, taurine upregulated 1; TERC, telomerase RNA; UCHL1, ubiquitin carboxyl-terminal esterase L1; UBE3A-AS, ubiquitin protein ligase E3A (UBE3A) antisense RNA; XCI, X chromosome inactivation; Xist, X-inactive specific transcript; YY1, Yin Yang 1; ZEB2, zinc-finger E-box binding homeobox 2. * Corresponding author. Tel.: +86 10 66937463; fax: +86 10 66937516. Q2 ** Corresponding author at: Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China. Tel.: +86 10 68989955; fax: +86 10 68989955. E-mail addresses: [email protected] (X. Fu), [email protected] (W. Han). http://dx.doi.org/10.1016/j.mrrev.2014.04.002 1383-5742/ß 2014 Published by Elsevier B.V.

Please cite this article in press as: X. Li, et al., lncRNAs: Insights into their function and mechanics in underlying disorders, Mutat. Res.: Rev. Mutat. Res. (2014), http://dx.doi.org/10.1016/j.mrrev.2014.04.002

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mutations underlie some aging-related disorders. Finally, we consider the potential medical implications, and future potential in the application of lncRNAs as therapeutic targets and diagnostic markers. ß 2014 Published by Elsevier B.V.

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Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Biological functional diversity of lncRNAs . . . . . . . . . . . . . . . . . . . . . . . . Epigenetic gene regulation by lncRNAs . . . . . . . . . . . . . . . . . . . . . 2.1. Transcriptional gene regulation by lncRNAs . . . . . . . . . . . . . . . . . 2.2. Posttranscriptional gene regulation by lncRNAs . . . . . . . . . . . . . . 2.3. 2.4. Regulation of miRNAs by lncRNAs . . . . . . . . . . . . . . . . . . . . . . . . . Emerging mechanistic themes: signals, decoys, scaffolds, and guides . . Theme I: signals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.1. Theme II: decoys. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.2. Theme III: scaffolds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.3. Theme IV: guides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.4. What are the potential roles of lncRNAs in human disorders, especially lncRNAs: new players in aging. . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.1. Roles of lncRNAs in diseases related to aging . . . . . . . . . . . . . . . . 4.2. lncRNAs in Alzheimer’s and cognitive disorders . . . . . . 4.2.1. lncRNAs in cardiovascular diseases . . . . . . . . . . . . . . . . 4.2.2. lncRNAs in diabetes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.2.3. lncRNAs in cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.2.4. Concluding remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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1. Introduction

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The central dogma of molecular biology posits that genetic information is stored in protein-coding genes [1,2]. This hypothesis considered proteins to be the main protagonists of cellular functions, and RNA to be solely an intermediary between the DNA sequence and its encoded protein. Although the central role of RNA in cellular functions and organismal evolution has been advocated periodically during the past half-century, only recently has RNA received a remarkable level of attention from the scientific community. A growing body of evidence from highthroughput genomic platforms has suggested that developmental processes evolved to regulate the complexity of organisms mainly due to the expansion of the regulatory potential of the genome’s non-coding portions [3,4]. Analyses that compare transcriptomes with genomes of mammalian species have revealed that 50%–70% of genomic DNA is pervasively transcribed, which is in sharp contrast to the 200 nucleotides in size, are


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often poorly conserved at the sequence level, which initially leads to uncertainty as to whether they represent active entities or transcriptional ‘‘noise’’ [18,19]. However, while a growing number of lncRNAs have been characterized, it has been established that orthologs can be identified in other species through synteny. Although these ‘‘syntelogs’’ bear little to no sequence similarity, their location relative to neighboring protein-coding genes has been maintained throughout evolution [12]. Nevertheless, the functions of most of the identified lncRNAs remain largely uncharacterized, and the mechanisms of gene expression regulation at multiple layers by lncRNAs are not fully understood. Although only a small number of functional lncRNAs have been well studied to date, many roles are emerging for lncRNAs in ribonucleoprotein complexes that regulate various stages of gene expression [20,21]. RNAs not only encode primary sequence information, allowing them to directly interact with both DNA and RNAs, but also contain great structural complexity and plasticity. Their intrinsic nucleic acid nature confers on lncRNAs the dual ability to function as ligands for proteins (i.e., those with functional roles in gene regulation processes) and to mediate base-pairing interactions that guide lncRNA-containing complexes to specific RNA or DNA target sites [20–22]. This dual activity is shared with small ncRNAs. However, unlike small ncRNAs, lncRNAs are proposed to function as molecular scaffolds, assembling diverse combinations of regulatory proteins through folding into thermodynamically stable secondary and higherorder structures to provide greater potential and versatility for both protein and target recognition [20–22]. Moreover, their flexible [22–24] and modular [25,26] scaffold nature enables lncRNAs to tether proteins that would not functionally cooperate or interact if they relied only on protein-protein interactions [20,22]. Such combinatorial lncRNA-mediated tethering activity has enhanced gene regulatory networks to facilitate a wide range of gene expression programs to provide an important evolutionary advantage [20–22]. This complexity is likely to be further extended by differential splicing and the use of alternative transcription initiation sites and polyadenylation sites by lncRNAs, thus changing the protein cargo and subsequent function of the resulting protein complex, and increasing the number of tethering-module combinations. The repertoire of roles performed by lncRNAs is growing, because there is now evidence that lncRNAs participate in multiple networks that regulate gene expression and function [27]. For example, they have long been implicated in posttranscriptional gene regulation through controlling processes like protein synthesis, RNA maturation, and transport, and very recently, in transcriptional gene silencing through the regulation of chromatin structure [17]. Structurally different lncRNAs engage diverse functional and mechanistic paradigms that lead to different regulatory outcomes. Although the primary sequence of these lncRNAs is generally less conserved than protein-coding exons, evidence so far indicates that most lncRNAs have several similarities in their mode of action. One theme that has emerged during large-scale characterization efforts is that lncRNAs are commonly involved in mediating chromatin-level gene regulation via interactions with histone modifiers, the DNA methylation machinery, or transcriptional regulators and recruits them to their target regions [27–29]. The exact physical association between these lncRNAs and chromatin modifiers and/or gene promoter chromatin remains to be elucidated, and most lncRNAs remain partially uncharacterized. Additionally, there has been a heavy focus thus far on the ways that lncRNAs regulate chromatin states, and this emphasis probably underrepresents the full repertoire of the lncRNA function. Nonetheless, the rapidly growing lncRNA field is already changing not just our perspective of genomic content, but also the way that we think about genes.

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Considering the wide range of roles that lncRNAs play in cellular networks, it is not surprising that ncRNAs have been implicated in disease. Genome-wide association studies (GWAS) have revealed that only 7% of disease or trait-associated singlenucleotide polymorphisms (SNPs) reside in protein-coding exons, whereas 43% of trait-/disease-associated SNPs are found outside of protein-coding genes [30,31]. In addition, lincRNAs are strongly enriched for trait-associated SNPs, which suggest a novel mechanism by which intergenic trait-associated regions may function [32]. In support of this idea, a number of lncRNAs have been implicated in adult cardiac disease by the analysis of genetic variation among individuals who have cardiac traits [33]. Emerging studies are starting to link distinct types of mutations in lncRNAs genes with diverse diseases [34]. However, the precise mechanism by which mutations in lncRNAs contribute to the pathogenesis of disease remains a mystery. Recognition of the roles of lncRNAs in human disorders is their emergence as key players in the etiology of several disease states and has unveiled new diagnostic and therapeutic opportunities. lncRNAs are expressed in a more tissue-specific fashion than mRNA transcripts, a pattern that has been shown to hold true in pathologic states, such as cancer [35]. Hence, lncRNA measurements can trace cancer metastases or circulating cancer cells to their origins. Recently, a strong connection between lncRNAs and cancer has been clearly established, because many lncRNAs are dysregulated in human cancers [10,27]. Although cancer has been the most studied, it is likely that lncRNAs are involved in the pathogenesis of many other disorders, such as Alzheimer’s [36], aging related declines in cognitive function [37], diabetes [38], and cardiovascular diseases [33,39], which suggests that aberrant lncRNA expression may be a new contributor to aging and aging-associated illnesses. lncRNAs appear to be more structured and stable than mRNA genes, which facilitate their detection as free nucleic acids in body fluid (i.e., blood, urine); this knowledge is already put to good use in clinically approved tests for prostate cancer [40–42]. Notably, aberrant lncRNAs can be knocked down in vivo using oligonucleotide ‘‘drugs’’ [43,44], which should spur advances in lncRNA genetics and therapeutics. In this article, we review our latest understanding of the lncRNA field according to the roles of lncRNA in various cellular processes, discussing what is known about the biological functions and mechanisms of action of lncRNAs. We focus on the functional attributes of lncRNAs and highlight the unconventional, and perhaps underappreciated biological contributions of the lncRNAs, including the diverse mechanisms through which lncRNAs participate in regulating chromatin states and transcription. In addition, we highlight roles beyond transcription whereby lncRNAs function in many cellular contexts, including posttranscriptional regulation, and the organization of protein complexes; then, we highlight how lncRNAs themselves serve key regulatory roles, with a specific focus on functional paradigms. Finally, in this review, we highlight the importance of further studies on lncRNAs in building the framework that is necessary to interpret the effect of mutations on lncRNA function and their direct connection to disease and we also discuss lncRNAs as a new strategy for therapeutic interventions.

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Only a very small portion of identified lncRNAs has been experimentally examined to date, yet an emerging paradigm suggests that lncRNAs function in many biological contexts. Thus far, lncRNAs have been implicated in diverse processes (Fig. 1). In the following sections, we will discuss the evidence that supports the established roles in which lncRNAs function biologically.

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Fig. 1. Genomic locations of lncRNAs and diverse mechanisms of lncRNA function. (A) Gemomic locations of lncRNAs. lncRNAs (shown in orange) mediate a broad array of genomic and cellular functions and are independently transcribed. Schematic diagram illustrates the complexity of interwoven networks of lncRNAs that are associated with a protein-coding gene. lncRNAs can be transcribed from the following: intergenic regions, antisense overlapping, intronic and bidirectional orientations to protein-coding genes (green and purple), gene-regulatory regions, including gene promoters, enhancers and untranslated regions (UTRs), and specific chromosomal regions, including telomeres (arrows indicate direction of transcription). (B) Examples of lncRNAs that regulate transcription by recruiting specific transcriptional regulators onto specific chromosomal loci are shown. Working models of gene regulation by cis- (a) and trans-acting (b) lncRNAs. lncRNAs, such as Xist/RepA, Air, HOTAIR, Tsix, ANRIL, and Kcnq1ot1, can recruit polycomb repressive complex (PRC) via direct interaction with EZH2 or other components to the targeted locus where trimethylation of H3K27 is promoted, leading to silencing of the specific genes. (C) lncRNA in transcriptional regulation. (a) Transcriptional activation. lncRNA transcribed from the ultraconserved region of the gene, Dlx6os1 (or Evf-2), functions as a co-activator of a homeodomain protein (Dlx2), facilitating the Dlx-5/6 gene transcription (above). In addition, enhancer lncRNA


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2.1. Epigenetic gene regulation by lncRNAs

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A hallmark of lncRNA function is their ability to mediate epigenetic regulation. lncRNAs represent a previously hidden layer of information that is necessary for the architectural control of development and function (Fig. 1B). In general, the term ‘‘epigenetics’’ refers to changes that affect gene regulation, including changes in DNA methylation, nucleosome positioning and miRNA expression as well as histone modifications and highorder chromatin remodeling [45,46]. DNA methylation plays a key regulatory role in normal development, and aberrations in epigenetic modifications can cause diseases such as cancer [45]. Many of the identified protein partners of lncRNAs are chromatin modifiers, and 30% of the lincRNAs that are expressed in mouse embryonic stem cells (ESCs) are associated with at least 1 of 12 chromatin complexes that are involved in reading, writing, and erasing histone modifications [47]. In addition, the alteration of epigenetic modifications also changes the pattern of lncRNAs expression, which suggests that lncRNA expression is regulated by the state of the chromatin and feeds back to control the state of the chromatin [48]. Although the diverse functions of lncRNAs are only beginning to be uncovered, their potential ability to interact with and modulate the activity of chromatin regulatory complexes may allow lncRNAs to affect gene expression on a genome-wide scale [17,22]. Recently, it has been reported that many lncRNAs bind to protein complexes of the Trithorax group (TrxG) or Polycomb group (PcG) families, which form molecular modules with a cellular memory mechanism that maintains gene expression states that are established by other regulators, and they guide these protein complexes to their sites of action [49–51]. Generally, TrxG proteins are responsible for maintaining an active expression state [52], whereas PcG proteins act in opposition to maintaining a repressed expression state [53]. A common mark that is associated with active chromatin is the trimethylation of histone 3 (H3) at lysine 4 (K4), or H3K4me3, which is often found at promoters of actively transcribed genes. Conversely, the marks that are associated with silenced heterochromatin include di- and trimethylated H3K9, as well as the trimethylation of H3K27. More than 20% of human lncRNAs are associated with polycomb repressive complex2 (PRC2) [51], which is classically composed of four core components: Enhancer of zeste (EZH), Embryonic ectoderm development (Eed), Suppressor of zeste 12 homolog (Suz12) and RbAp46/48 [54,55]. The Ezh component contains a SET domain that exhibits histone lysine methyltransferase (HMT) activity directed toward histone H3 Lys 27 (H3K27); while Ezh is the catalytic subunit, it functions as such only when contained within PRC2. Eed plays a role as a scaffold protein that, through its N terminal region, physically links PRC2 to its H3 substrates [56,57]. The C terminus of Eed is composed of WD40 repeats that, while represented in a number of other proteins, are arranged in the case of Eed in such a way that an aromatic cage is established that can bind transcriptionally repressive, methylated lysine residues, resulting in an allosteric effect that significantly enhances the PRC2 activity

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[58]. Suz12 is necessary for Ezh stability [59]. Last, the RbAp46/48 components are known to bind histones H3 and H4 [60]. X chromosome inactivation (XCI) is a closely related process that equalizes the gene expression between mammalian males and females by inactivating one X in female cells [61]. The identification of X-inactive specific transcript (XIST) as a regulator of XCI in mammals provided one of the first examples of an lncRNA that is directly involved in the formation of repressive chromatin [62,63]. During female development, Xist RNA is expressed from the inactive X (Xi) and ‘‘coats’’ the X chromosome from which it is transcribed, leading to a chromosome-wide repression of gene expression [64,65]. Importantly, the conditional knockout of Xist has demonstrated that the folding of Xi requires the Xist RNA. After Xist deletion, the Xi chromosome adopts a confirmation that is more similar to that of the active X chromosome (Xa) without reactivation of the Xi gene expression. Therefore, Xist appears to regulate X chromosome structure via mechanisms other than the relocation of active genes to transcriptional factories [66]. Xist is required only for the initiation and not for the maintenance of Xi, and its spatiotemporal expression must be properly controlled. Xist induces the formation of repressive heterochromatin, at least in part, by tethering PRC2 to the Xi chromosome. One intriguing clue is that conditional Xist deletion also led to the loss of PRC2 and H3K27me3 marks. However, the conformations of the two X chromosomes appear to be regulated by distinct mechanisms because PRC2 is dispensable for the topological domains of Xa [67]. Whether one or several Xa-expressed lncRNAs controls the Xa conformation remains to be seen. The interaction between Xist and chromatin may involve, among others, the transcriptional repressor factor Yin Yang 1 (YY1), which is thought to function as a recruitment platform for Xist and to tether Xist to sites in the X chromosome by binding to its DNA and RNA; and its depletion results in a loss of Xist loading on the Xi [68]. These observations suggest that YY1 is the docking factor that is responsible for the cis-acting nature of Xist RNA. Moreover, it has been recently shown that Xist itself is able to recognize the three-dimensional conformation of the X chromosome [69]. Although the regulation of the Xist transcription is not fully understood, it is clear that the Xist expression is itself controlled by other lncRNAs in both a positive and negative manner [62]. An overlapping antisense lncRNA, called Tsix, counteracts Xist expression by inducing repressive epigenetic modifications at the Xist promoter [70]. The loss of the Tsix function in vivo resulted in ectopic Xist expression, aberrant Xi and early embryonic lethality [71,72]. Other lncRNAs, such as Xcite and RepA, also contribute to ensuring that only one X chromosome is inactivated, by enhancing Tsix expression on the Xa and upregulating Xist on the Xi. Furthermore, Xist activation also requires the lncRNA Jpx [73], which induces Xist transcription by the sequestration of transcriptional repressor CCCTC-binding factor (CTCF) [74]. Similar to X inactivation, genomic imprinting is an epigenetic regulatory mechanism that best illustrates the concept of allele specificity. In general, imprinted genes associate in clusters and are

transcribed from gene enhancers can also facilitate gene transcription by cooperating with lineage-specific complexes (below). (b) Transcriptional suppression. Top, lncRNA CCND1 transcribed from the upstream region of the cyclin D1 gene recruits the RNA-binding protein (translocated-in-liposarcoma [TLS]), allosterically to modulate HAT activities of CREB-binding protein (CBP) and p300, resulting in inhibition of gene expression. Bottom, lncRNA transcribed from the dihydrofolate reductase (DHFR) minor promoter can form a triplex at the major promoter to prevent the binding of general transcription factors, such as TFIIB and TFIID, and subsequently silence the expression of DHFR. (D) lncRNA in post-transcriptional regulation. (a) Regulation of alternative splicing. MALAT1 and NEAT1 lncRNAs may be integral components of the nuclear paraspeckle and contribute to posttranscriptional processing of mRNAs. (b) Degradation of mRNA. Gene expression regulation may also occur through direct lncRNA-mRNA interactions, which arise from hybridization of homologous sequences and can serve as a signaling for STAU1-mediated degradation of the mRNA [220]. (c) Stabilization of mRNA. RNA molecules, including mRNAs, pseudogenes, and ncRNAs, can serve as molecular ‘‘sponges’’ for miRNAs. Transcripts of pseudogenes and the counterpart gene (for example, PTENP1 and PTEN, as described in this text) are highly conserved at 30 -UTR. Such transcripts act as competing endogenous RNA and thereby the PTEN mRNA is protected from common miRNA targeting for degradation by binding with PTENP1 transcripts competitively, thus increasing the abundance of PTEN mRNA and protein. (E) lncRNA in protein metabolism. (a) Increase in translational efficiency. Transcripts of the antisense lncRNA (NAT Zeb2) can mask the 50 -splice site of an intron in the 50 -UTR of the zinc finger Hox mRNA Zeb2 by complementary interaction, preventing spliceosome binding to generate an inhibitory sequences for ribosome scanning, resulting in activating polysomes for translation and leading to more efficient translation of Zeb2. Similarly, Uchl1AS increases UCHL1 protein synthesis at a posttranscriptional level (see text for more detail).


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epigenetically marked in sex-dependent manners during male and female gametogenesis. Mammals are diploid organisms that carry two alleles of each autosomal gene, one inherited from the mother and one from the father. Whereas in most cases both parental alleles are expressed equally, a subset of genes show genomic imprinting, in which expression is restricted through an epigenetic mechanism to either the paternal or the maternal allele [75]. Imprinted regions encode different species of ncRNAs, including lncRNAs that, in many cases, bind to imprinted regions and are directly involved in silencing [62]. These lncRNAs are usually long (more than 100 kb) and function in cis. The best-characterized example at both the molecular and the genetic levels are the lncRNAs Kcnq1 overlapping transcript 1 (Kcnq1ot1) and antisense to Igf2r (insulin-like growth factor 2 receptor) RNA (Airn). These lncRNAs are paternally expressed; they function by repressing flanking protein-coding genes in cis and are involved in the early development in mice [62]. Notably, the loss of function of these lncRNAs in the embryo is not lethal: paternal inheritance of a null allele results in a loss of imprinting and in growth defects, whereas maternal inheritance of this allele does not affect imprinting or growth [76–78], which suggests that during development, multiple repressive pathways regulate imprinted gene silencing by lncRNAs and that the extent of silencing along the chromosome varies in different tissues [78–80]. For example, Kcnq1ot1 ncRNA functions by establishing and maintaining of repressive DNA methylation on these surrounding genes during embryonic development, whereas certain genes in the Kcnq1 domain are only imprinted in the placenta because Kcnq1ot1 ncRNA functions by recruiting the repressive histone modifiers PRC2 and the H3K9 methyltransferase G9a (also known as EHMT2) on genes that are located farther away from the imprinted region [78]. Specifically, an interaction between Kcnq1ot1 with G9a and PcG proteins was detected in the placenta, while no interaction was detected in the fetal liver [78]. Additionally, at least in some cases, lncRNA expression may influence epigenetic events by transcriptiondependent mechanisms. It is worthwhile noting that, in the establishment of transcriptional gene silencing by cis-acting lncRNAs, continuous transcription rather than the production of mature lncRNA itself might be more important for silencing. The relationship has been elegantly shown for the mammalian lncRNA Airn, which is expressed from the paternal chromosome. Arin has been suggested to function in cis to silence the paternal Igf2r allele, whereas the maternal Igf2r allele remains expressed. In embryonic tissues, Airn silences paternal Igf2r via a mechanism that does not require a stable RNA product but that is based on continuous Airn transcription, which interferes with the recruitment of RNA polymerase II [81]. In contrast, in the placenta, mature Airn lncRNA recruits G9a to induce the formation of repressive chromatin [77]. In summary, these studies showed that a single lncRNA can work by different mechanisms depending on the cell type, which might reflect the presence of either different interactions or chromatin modifications that affect lncRNA functions in diverse cellular contexts. The above examples also show the advantages of using cis-acting lncRNAs to regulate a gene cluster. The in situ production of regulators at their site of action is intrinsically more robust than in dedicated trans-acting proteins. Therefore, it is tempting to speculate that using cis-acting lncRNAs to silence gene transcription is an evolutionarily conserved mechanism and is not restricted to complex and multicellular organisms, as in the case of yeast cryptic unstable transcripts [82]. In contrast to Kcnq1ot1 and Airn, another example of the tight relationship between time and space is illustrated by two ncRNAs from the mammalian Hox loci. The HOX transcript antisense RNA (HOTAIR) was one of the first trans-acting lncRNAs to be identified [83]. HOTAIR, a 2.1 kb transcript, is derived from the human HOXC gene cluster but acts as a repressor of the HOXD locus, as well as

other targets throughout the genome. HOTAIR can simultaneously bind PRC2 and the LSD1-CoREST/REST (lysine-specific histone demethylase 1A-REST corepressor 1-RE1-silencing transcription factor) histone modifying complexes that reinforce PRC2 repression by catalyzing the demethylation of the active H3K4 me2 histone mark [25,84]. HOTAIR binds EZH2 and is required for PRC2mediated H3K27 trimethylation and the silencing of the HOXD locus in humans [83]. However, HOTAIR may play a different role in mice because a deletion within the HOXC locus that encompasses mHOTAIR has no effect on the expression of the HOXD cluster [85]. Interaction of HOTAIR with PRC2 is mediated through a region in its 50 terminus, while the 30 terminus binds LSD1, a H3K4 demethylase that functions within the CoREST/REST complexes [25]. Overexpression of HOTAIR results in global changes in the PRC2 occupancy and H3K27me3 marks [20]. Conversely, knockdown of HOTAIR alters the chromatin occupancy of PRC2 and LSD1 genome-wide, leading to reduced H3K27me3 and increased H3K4me2 at target loci [25]. Thus, this result, together with the interactions of HOTAIR with a PRC2 subunit and the LSD–CoREST complex, suggests that HOTAIR lncRNA appears to serve as a scaffolding molecule, bridging PRC2 with LSD1, and then, it targets PRC2 to HOXD. Surprisingly, deletion of HOTAIR does not affect the genes of the HOXC cluster in cis because Hox ncRNAs have long been suspected to be involved in cis-regulation. This finding poses a key puzzle for future studies; specifically, can HOTAIR directly target PRC2 to another chromosome, and if so, how? A key mechanism of lncRNA specificity in cis is the higher-order chromosomal configuration. The cis-acting lncRNA HOXA distal transcript antisense RNA (HOTTIP), an enhancer-like lncRNA, which is produced from the 50 end tip of the human HOXA locus upstream of HOXA13, was identified in human primary fibroblasts. The downregulation of HOTTIP levels in primary fibroblasts induced the transcription of several downstream 50 -HOXA genes. HOTTIP is conserved in vertebrates, and its knockdown by short hairpin RNAs in chick embryos altered the limb morphology [86]. The mechanism by which HOTTIP regulates HOXA expression relies on its interaction with the activating histone-modifying complex mixed-lineage leukemia 1 (MLL1), a component of the TrxG complex, and on the formation of chromatin loops that connect distally expressed HOTTIP transcripts with various HOXA gene promoters [86]. The MLL complex is also recruited to the HOX locus by the mistral lncRNA (Mira), which is a mouse-specific lncRNA that is located between the homeotic genes HOXA6 and HOXA7 [87]. Mira directly interacts with MLL1, leading to changes at the chromatin level that activate HOXA6 and HOXA7 [87]. Hence, lncRNA interaction with MLL/TrxG complexes and likely additional proteins will define their function in enforcing activated chromatin states and gene activation.

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2.2. Transcriptional gene regulation by lncRNAs

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We have described how lncRNAs can regulate gene expression via interactions with chromatin-modifying complexes and how they can alter chromatin at the gene promoter to affect the transcriptional output (vide supra). Alternatively, some lncRNAs can also form RNA-protein complexes with transcription factors and modulate transcription factor activity (Fig. 1C). Although the functional mechanisms have not been delineated, increasing evidence suggests that at least some lncRNAs can regulate transcription by serving as ‘ligands’ for transcription factors. In eukaryotes, transcriptional control has many wide-ranging roles in regulating gene expression. The action of transcription factors and polymerases that bind in a sequence-specific manner to promoters is important for gene regulation. Many proteins bind to RNAs through a variety of RNA-binding motifs to modulate the processing, localization, and stability of the bond RNAs; naturally,

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the converse is also true: RNAs can influence the activity and localization of the proteins that they bind. Due to their widespread distribution, lncRNAs can affect the activity of specific transcription factors and polymerases [88,89]. For example, lncRNAs can serve as key co-activators of proteins that are involved in transcriptional regulation, including the regulation of the Dlx genes and the transcription of heat-shock proteins. An alternatively spliced, 3.8-kb polyadenylated lncRNA Dlx6 opposite strand transcript 1 (Dlx6os1; also known as Evf2) is transcribed from an ultraconserved region [88]; it is an antisense RNA to distal-less homeobox 6 (Dlx6) and is located downstream of Dlx5 in mice. Dlx6os1 controls the expression of Dlx5, Dlx6 and the glutamate decarboxylase 1 gene (Gad1; also known as Gad67) via both cis- and trans-acting mechanisms [88]. In cis, the transcription of Dlx6os1 negatively regulates the Dlx6 expression. In contrast, in trans, Dlx6os1 recruits the transcription factors homeobox protein DLX2 (which is an activator) and methyl-CpG-binding protein 2 (MECP2, which is a repressor) to regulate the expression of Dlx5 and Gad1 (which encodes an enzyme that is responsible for g-aminobutyric acid (GABA) synthesis) [88,89]. The loss of Dlx6os1 function in mice produced a specific neural phenotype that had reduced numbers of GABAergic interneurons in the early postnatal hippocampus. Hence, as a co-activator molecule, the Dlx6os1 was required for balanced gene regulation in the development of the ventral forebrain in mice [89]. Moreover, several lncRNAs act directly on specific transcription factors. For example, the lncRNA heat shock RNA 1 (HSR1) could form a complex with heat shock factor 1 (HSF1), and a surprising protein interaction partner and coactivator, translation elongation factor eEF1A, thus enabling the transcription factor to induce the expression of heat-shock proteins during the cellular heat-shock response [90]. Furthermore, an isoform of ncRNA SRA functions as a transcriptional coactivator of steroid receptors [91]. In another example, the growth arrest specific 5 (GAS5) lncRNA folds into a structure that mimics the DNA-binding site of the glucocorticoid receptor (GR), and the resulting interaction represses GR-mediated transcription [92]. More recently, lncRNAs with enhancer-like functions have been reported. Ørom et al. [93] used a GENCODE annotation of the human genome to characterize >1000 lncRNAs that are expressed in multiple cell lines with sizes that ranged from 100 to 9100 nucleotides. In contrast to well-characterized lncRNAs, Ørom et al. [93] reported that some lncRNAs have functional properties of enhancers in human cell lines. These lincRNAs that were transcribed from regions that were located outside of proteincoding loci can increase the expression of specific genes in the immediate surroundings. The ablation of seven of these lincRNAs by siRNA-mediated knockdown resulted in an unexpected, concomitant decrease in the expression of some, but not all, nearby protein-coding genes [93]. Aside from positive regulators of transcription, some lncRNAs can also function as transcription co-repressors. A set of singlestranded, low-abundance lncRNAs produced from the cyclin D1 (CCND1) promoter region has recently been shown to allosterically modulate the activity of an RNA-binding protein (TLS), which is a key transcriptional regulatory sensor of DNA damage signals [94]. Upon binding these lncRNAs, the TLS protein changes from an inactive to an active conformation, in such a way that TLS binds and inhibits the enzymatic activities of the histone acetyltransferases, CBP and p300, thus silencing CCND1 gene expression [94]. Alternative promoters within the same gene are a general phenomenon in gene expression [95]. The mechanisms of selective regulation vary from one gene to another and are only beginning to be uncovered. Martianov et al. [96] reported that the lncRNA that is transcribed from the minor promoter of the human dihydrofolate reductase (DHFR) gene regulates its transcription by forming a stable complex with its major promoter. The lncRNA thereby

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directly interacts with the general transcription factor II B (TFIIB) and dissociation of the pre-initiation complex from the major promoter caused repression of DHFR expression [96]. lncRNAs, therefore, can regulate transcription through several mechanisms. Given the decades of research that have focused on transcriptional control from a transcription factor-centric point of view, it is interesting to speculate about the purpose of this additional layer of lncRNA-based regulation. Notably, the impressive diversity of transcriptional regulatory mechanisms discussed here might be only the tip of the iceberg, with additional means of lncRNAmediated transcriptional regulation to be uncovered in the future.

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2.3. Posttranscriptional gene regulation by lncRNAs

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Aside from the aforementioned mechanisms in diverse cellular contexts, lncRNAs have also been involved in the control of these posttranscriptional events of mRNAs, including alternative splicing, editing, translation, and trafficking (Fig. 1D and E), as summarized below. mRNA transcripts often have a complicated posttranscriptional existence [97]. Immediately in the wake of transcription, nascent pre-mRNAs are spliced and processed into one of potentially many isoforms. Importantly, alternative splicing and editing contribute to increasing the gene isoform diversity. In contrast, rather than directly silencing or activating the transcription of a particular gene, some lncRNAs influence the complement of expressed genes in a cell through posttranscriptional mechanisms. In some cases, lncRNA genes that have an antisense orientation to known proteincoding genes, which are also known as NATs, can form RNA duplexes to mask key cis-regulatory elements in the mRNA of overlapping genes, which leads to alternative splicing patterns of the sense strand. For example, NATs influence splicing patterns of mRNAs at the neuroblastoma MYC [98], Tie-1 (tyrosine kinase containing immunoglobulin and epidermal growth factor homology domain-1) [99], c-ErbAalpha (also known as Thra) [100,101], ZEB2 (zinc-finger E-box binding homeobox 2) [102] and BACE-1 (beta-amyloid precursor protein-cleaving enzyme 1) [36,103] loci in mammalian cells. In the case of neuroblastoma MYC, Tie-1, BACE1 and c-ErbAalpha, the NAT and pre-mRNA were suggested to form RNA-RNA duplexes, which then inhibit the splicing. At the ZEB2 locus, a recent study by Beltran et al. (2008) showed that maintenance of the 50 -UTR ZEB2 intron depends on the expression of the ZEB2 NAT that overlaps the 50 splice site in the intron. Ectopic expression of the ZEB2 NAT in epithelial cells masked the splicing site and prevented splicing of the ZEB2 50 -UTR, thereby increasing the levels of the ZEB2 protein [102]. In contrast, BACE-1AS is transcribed from the opposite strand to BACE-1, which is an aspartylprotease that is responsible for cleaving beta-site amyloid precursor protein (APP). BACE-1AS, which modulates BACE-1 gene expression by promoting the stabilization of BACE-1 mRNA and the up-regulation of BACE-1 protein via a posttranscriptional feedforward mechanism, has been shown to be linked to Alzheimer’s disease [36,103]. Although the mechanism by which NATs influence splicing is unclear, it has been postulated to involve splice-site masking and a subsequent block in spliceosome recruitment. The alternative splicing of pre-mRNA is used to diversify transcriptomes and to increase the proteomic complexities that are frequently observed in higher eukaryotes. Several lines of evidence suggest that alternative splicing is regulated by trans-acting protein factors, which include small nuclear ribonucleoproteins, the serine/arginine-rich (SR) family of nuclear phosphoproteins (SR proteins), SR-related proteins, and heterogeneous nuclear ribonucleoproteins [104,105]. However, the underlying mechanisms that modulate the cellular levels of active SR proteins remain unclear. One of the abundant nuclear lncRNAs in

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mammalian cells is MALAT-1, which is approximately 7 kb in length and is located in nuclear speckles. The MALAT-1 lncRNA also regulates the alternative splicing of pre-mRNAs, but through a more indirect mechanism. This lncRNA, which associates with interchromatin granules, has been implicated in alternative splicing through the modulation of active SR splicing factors, which are named after the characteristic SR domain. MALAT-1 interacts with and influences the distribution and levels of phosphorylated SR proteins. Importantly, the depletion of MALAT-1 alters splicing factor localization and activity, leading to altered patterns of alternative splicing for a set of pre-mRNAs [106]. In addition to modulating the splicing, overlapping antisense lncRNAs have in principle the potential to direct mRNA editing. During editing, adenosine deaminase acting on RNA (ADAR) enzymes catalyze adenosine to inosine conversion in double-stranded RNA (known as A-to-I editing), and this conversion can influence the RNA structure, splicing patterns, coding potential and targeting by the miRNAs [107]. Nuclear paraspeckle assembly transcript 1 (NEAT1) is an lncRNA that localizes to paraspeckles and is essential to their structure; it binds to the proteins paraspeckle component 1 (PSPC1) and the non-POU domain that contains octamer-binding protein (NONO; also known as p54), thereby facilitating A-to-I editing and subsequent mRNA cleavage [108]. While many of these pervasive transcripts anticipate being lncRNAs, lncRNAs are likely to help the diversity of the transcriptome and proteome through the control of RNA editing. Following processing and nuclear export, mRNAs are subjected to a wide range of posttranscriptional regulatory pathways that modulate gene expression levels. For example, the overall level of protein that is produced from an mRNA depends on the translation efficiency, mRNA turnover kinetics and small RNA-mediated translational repression. Recently, lncRNAs have been shown to increase the protein synthesis by directly modulating translation at the posttranscriptional level. The mouse Uchl1AS lncRNA is an antisense transcript to the neuron-specific Uchl1 (ubiquitin carboxyl-terminal esterase L1) gene, which functions in protein ubiquitylation and has roles in brain function and various neurodegenerative diseases [109,110]. Uchl1AS lncRNA was shown to upregulate the translation of Uchl1 mRNA through a repeat element. In this case, the sense and antisense transcripts are oriented in a 50 head-to-head fashion such that the mature lncRNA contains a 73-nucleotide motif that is complementary to the 50 end of the Uchl1 mRNA. The sequence-specific interaction serves to position the effector domain, which is contained in the nonoverlapping 30 region of Uchl1AS and consists of a SINEB2 repeat element that upregulates protein expression without changing the Uchl1 mRNA levels. In particular, upon stress-induced inhibition of mTOR activity and the resulting repression of cap-dependent translation, Uchl1AS is exported from the nucleus to the cytoplasm, where it can base pair with the Uchl1 mRNA and stimulate its capindependent translation. Because this activation of UCHL1 expression does not require de novo RNA synthesis, it provides a rapid response to environmental changes [109]. Notably, lncRNA-mediated translational regulation has also been documented in yeast, in which an antisense KCS1 lncRNA was suggested to regulate the translation of the inositol pyrophosphate synthase KCS1 mRNA that is expressed from the same locus. Although it has an unknown mechanism that is thought to involve base pairing interactions between the antisense and sense RNAs, the expression of KCS1 NAT results in the production of truncated KCS1 protein [111]. lncRNAs have been shown to modulate the activity of proteins by regulating subcellular localization (Fig. 1E, b). A cell-based screen for lncRNAs that modulates the activity of the nuclear factor of activated T cells (NFAT) by regulating subcellular localization

has identified a non-coding repressor of NFAT (NRON) [112]. In response to extracellular signals, the calcium-regulated phosphatase, calcineurin, dephosphorylates the cytoplasmic subunits of NFAT in the nucleus where it becomes transcriptionally active. Intriguingly, one of the key regulators of NFAT trafficking is an ncRNA known as NRON, which shows a tissue-specific pattern of expression and is enriched in lymphoid tissues. Northern blot analysis revealed that NRON can be alternatively spliced to yield transcripts that ranged from 0.8 to 3.7 kb [112]. Surprisingly, NRON does not target the transcriptional activation properties of NFAT. Instead, it appears to disrupt the nuclear localization of NFAT, most likely via interactions with various nuclear transport factors, thereby preventing NFAT from activating the transcription [112]. Strikingly, NRON specifically inhibits the nuclear accumulation of NFAT, but not that of other transcription factors, such as p53 and nuclear factor-kB (NF-kB), which also translocates from the cytoplasm to the nucleus [112]. Thus, further studies are required to understand the precise mechanism by which NRON functions and to reveal the diversity of lncNRAs that might control the nuclear trafficking of the proteins.

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2.4. Regulation of miRNAs by lncRNAs

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Certain lncRNAs can likely base pair with small RNAs to modulate the activities. Aside from competing with small RNAs for binding sites on target mRNAs, lncRNAs can also act as decoys to attenuate small RNA regulation, for example, through the sequestration of proteins or RNA-dependent effectors (Fig. 1D, c). Based on this idea, the competing endogeneous RNA (ceRNA) hypothesis postulates that a widespread network of crosstalk exists between coding and non-coding RNAs that manifests through competition for miRNA binding [113]. This activity was initially described in plants and, subsequently, in mammals, in which it was shown to be relevant in many processes, including tumorigenesis. Examples of potential ceRNAs include IPS1 (INDUCED BY PHOSPHATE STARVATION 1) [114], PTENP1 (PTEN pseudogene 1) [115], LINCMD1 (long noncoding RNA, muscle differentiation 1) [116], HULC (highly upregulated in liver cancer) [117], H19 [118], and CDR1as (CDR1 antisense; as known as ciRS-7) [119,120]. In the plant Arabidopsis thaliana, the lncRNA IPS-1 binds to and sequesters miR399 (which was induced in response to phosphate starvation) away from its target mRNAs [114]. Whereas most miRNAs in plants have perfect complementarity to their targets, which results in mRNA cleavage, IPS1 contains an imperfect binding site for miR399. Thus, miR399 binding to IPS1 does not lead to its cleavage, but instead limits the levels of miR399 that are available for other targets and blunts miR399 action and alters the shoot phosphate content. This ability to evade cleavage is an important aspect of IPS1 regulation, because mutant IPS1 with perfect complementarity to miR399 no longer regulates miR399 [114]. Traditionally, miRNAs function by annealing to complementary sites on the coding sequences or 30 -UTRs of the target gene transcripts, where they promote recruitment of protein complexes that impair translation and/or decrease the stability of the mRNA, which leads to a decrease in the target protein abundance [16,121]. However, recent evidence suggests that the opposing mechanism may also occur. For example, mRNA expression can affect the distribution of miRNAs. Recent work on the tumor suppressor pseudogene PTENP1, which was previously considered to be biologically inconsequential, has introduced the idea that PTENP1 may have a biological function as a decoy by sequestering miRNAs, which affects the regulation of the expressed target genes [115]. Specifically, the 30 -UTR of the PTENP1 lncRNA was shown to bind the same set of regulatory miRNA sequences that normally target the tumor suppressor gene, PTEN, thus reducing the down-regulation of PTEN mRNA and allowing its

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to specific genomic loci to exert effects [49]. Here, we will discuss several mechanisms by which lncRNAs exert effects.

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3.1. Theme I: signals

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lncRNAs show cell type-specific responses to diverse stimuli based on dynamic expression patterns, which suggests that the expression of lncRNAs is under considerable transcriptional control. As such, lncRNAs can serve as molecular signals because the transcription of individual lncRNAs occurs at a very specific time and place to the integrate developmental cues, interpret the cellular context, or respond to diverse stimuli. lncRNAs, such as Airn and Kcnq1ot1, can accumulate at the promoter chromatin of silenced alleles and mediate repressive modifications in an allelespecific manner [79,80]. An extreme example of lncRNA-mediated epigenetic regulation is Xist [62]. During female development, Xist ncRNA is expressed from the Xi and ‘coats’ the X chromosome from which it is transcribed, which leads to chromosome-wide repression of gene expression [61–63,65]. In all three examples (Airn, Kcnq1ot1 and Xist), the presence of the transcribed lncRNA indicates active silencing at the respective genomic locations. Another example of the tight relationship between spatial and temporal aspects is illustrated by the HOTAIR and HOTTIP lncRNAs from the mammalian HOX loci, which serve as signals of the anatomic position. [123] The spatiotemporal pattern of HOX gene expression is often correlated with their genomic location within each locus, which is a property that is called collinearity [124]. Many lncRNAs were found to be transcribed from within the human HOX loci that were expressed in a temporal and sitespecific fashion [83]. These lncRNAs (HOTAIR and HOTTIP) have also been shown to be collinear with the overall anatomic expression pattern of the HOX loci, implying that they most likely used the same enhancers as the HOX genes. In addition, lncRNAs that act to integrate contextual and environmental cues can be found not only during development but also during times of organismal stress. lncRNAs can act as key regulatory nodes in multiple transcriptional pathways, serving as both a signal and a convenient means of tracking the transcriptional activity of the promoters in response to the stimuli. lncRNAs, such as lincRNA-p21 [125], PANDA (P21associated ncRNA DNA damage activated) [126], and Tug1 (taurine upregulated 1) [127], are transcriptionally activated in response to DNA damage via the direct binding of p53 to promoters. Subsequently, these lncRNAs regulate gene expression through distinct pathways. lincRNA-p21, which represses a set of genes in the p53 pathway, requires heterogeneous nuclear ribonucleoprotein (hnRNP) K and other as yet unidentified factors [125]. In contrast, PANDA, which is also induced in a p53-dependent manner, interacts with the nuclear transcription factor Y subunit-a (NF-YA) to limit the expression of pro-apoptotic genes and enables cell-cycle arrest, which suggests potentially widespread roles for lncRNAs in cell growth control [126]. In contrast, Tug1 functions by interacting with the chromatin-modifying complex PRC2 [127].

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3. Emerging mechanistic themes: signals, decoys, scaffolds, and guides

3.2. Theme II: decoys

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lncRNAs, thus far, have been implicated in many biological functions and pathways [9,10]. Despite our limited knowledge from dozens of characterized examples, an elegant framework for categorizing the emerging functions of lncRNAs was recently proposed. lncRNAs are described as follows: signals for integrating spatiotemporal, developmental, and stimulus-specific cellular information; decoys with the ability to sequester a range of RNA-dependent effectors and protein partners, thereby inhibiting their functions; scaffolds for bringing two or more proteins into discrete complexes; and guides for the proper localization of chromatin-modifying complexes as well as other nuclear proteins

This archetype of lncRNAs is transcribed and then binds and titrates away a protein target but does not exert any additional functions. lncRNAs have thus far been shown to act as a ‘‘molecular sink’’ and form ribonucleoprotein complexes with chromatin modifiers, transcription factors, splicing factors, and other classes of proteins. Presumably, lncRNAs that fit into this function archetype would act by negatively regulating an effector. Therefore, lncRNAs can serve as decoys that preclude the access of regulatory proteins to DNA. For example, lncRNA that is initiated from the upstream minor promoter of the human DHFR gene inhibits the assembly of a pre-initiation complex at the major

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translation into protein [115]. Similarly, one of the first lncRNAs that was identified with a role in myogenesis was LINCMD1. This lncRNA is expressed in a specific temporal window during in vitro muscle differentiation of mouse myoblasts and was shown to control the progression from early to late phases to muscle differentiation by functioning as a ceRNA. LINCMD1 can regulate muscle differentiation by binding and sequestering miR133 and miR135 [116]. Normally, these miRNAs negatively regulate the expression of the MAML1 (mastermind-like 1) and MEF2C (myocyte enhancer factor 2C) transcription factors, which drive late-differentiation muscle-specific gene expression. LINCMD1 is conserved between mice and humans [122], and its expression is strongly reduced in the myoblasts of patients who have Duchenne muscular dystrophy [116]. Intriguingly, in these cells, the recovery of LINCMD1 levels rescued the correct timing of ex vivo differentiation, which suggests a relevant conserved role in the control of muscle differentiation. In addition, the HULC lncRNA and the H19 lncRNA have been suggested to act as molecular ‘‘sponges’’ that inhibit miR372 and Let-7 miRNAs, respectively, by sequestering them away from potential mRNA targets [117,118]. Another example of lncRNA-based miRNA sponges has recently been described, but these RNAs are unique in that they have a circular structure [119,120]. In humans, the highly stable circular RNA (circRNA) CDR1as has a large number of miR7 binding sites [119,120]. Zebrafish was used to study the in vivo function of this circRNA because it lost the CDR1 locus while maintaining miR7 expression in the embryonic brain during evolution [120]. Interestingly, embryos that expressed ectopic CDR1as developed brain defects and had a smaller midbrain region, which is similar to the phenotype of the loss of miR7 function that was obtained through treatment with morpholino oligonucleotides [120]. Conspicuously, a similar CDR1as genomic cluster can be found across eutherian mammals, which indicates that, unlike many other lncRNAs, this lncRNA might be conserved [119]. Furthermore, bioinformatic analyses demonstrate that there may be thousands of expressed circRNAs across a broad range of multicellular eukaryotes [120]. Collectively, these findings are very intriguing because they indicate that distinct classes of ncRNAs cooperate with gene regulation. lncRNAs can, therefore, modulate gene expression through diverse posttranscriptional regulatory pathways. It is conceivable that other lncRNAs can also act as ‘‘sponges’’ for miRNAs in a developmental stage- and tissue-specific manner. Whereas some lncRNAs appear to influence the translation, others operate at the RNA level. However, a number of key questions still must to be answered. For example, how do cells regulate the levels of miRNA and lncRNA expression, and how do lncRNAs receive the signal to bind or not bind target miRNAs? As more and more lncRNAs are functionally characterized, we will probably see additional examples of posttranscriptional regulation by lncRNAs.

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promoter by forming a stable ncRNA-DNA complex with promoter sequences and interacting with TFIIB. When the lncRNA was specifically degraded by siRNA knockdown, the occupancy of TFIIB on the major promoter remained high [96]. lncRNA PANDA also appears to possess a decoy function. PANDA is induced temporally ahead of that of P21 (also known as CDKN1A (cyclin-dependent kinase inhibitor 1A)) in response to DNA damage and inhibits the expression of apoptotic genes, which favors cell-cycle arrest via direct binding to and sequestration of NF-YA, a nuclear transcription factor that activates the apoptotic program upon DNA damage, resulting in the promotion of cell survival by repressing apoptotic gene expression profiles in the context of low-level DNA damage. Intriguingly, the ablation of PANDA substantially increases NF-YA occupancy at the target genes, while the concomitant knockdown of PANDA and NF-YA significantly attenuates the induction of apoptotic genes and apoptosis [126]. The lncRNA GAS-5, which is induced upon growth factor starvation, has been identified as a new mechanism by which cells can create a state of relative glucocorticoid resistance. GAS-5 contains a hairpin sequence motif and represses the glucocorticoid receptor of this motif, mimicking the DNA motif that is equivalent to that of hormone response elements found in the promoter regions of glucocorticoidresponsive genes [92]. lncRNA GAS-5 can then compete for binding to the DNA binding motif of the glucocorticoid receptor, acting as a molecular decoy to effectively preclude interaction with the chromosome [92].

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3.3. Theme III: scaffolds

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lncRNAs can also serve as ‘‘fishing nets’’ upon which relevant molecular components are assembled into discrete complexes, in many diverse cellular signaling processes, this characteristic of precise control is vital to the precise control of the dynamics and the specificity of intermolecular interactions and signaling events [128]. Traditionally, proteins were thought to be the major elements in diverse scaffolding complexes [129,130]. Recent evidence, however, raises the possibility that lncRNAs may also play a similar role. lncRNAs can act as adaptors to bring two or more proteins into discrete complexes. This class of lncRNAs is perhaps the most functionally intricate and complex class because the lncRNAs possess different motifs that bind distinct effector molecules. The lncRNA can also bind multiple effector partners and, in doing so, brings the effectors, which may possess transcriptional activating or repressive activities, together in both time and space. A better understanding of the assembly and regulation of these discrete complexes will facilitate design strategies to selectively utilize specific signaling components to reshape cellular behavior. What lncRNAs might belong to this archetype? The answer to this question is that key predictions for this archetype of lncRNAs would include the following: knockdown of lncRNA to tear the ‘‘fishing net’’, which then interferes with the proper localization of the effector molecule or phenocopy and the loss of function of the component effector itself by dismantling the lncRNA-effector scaffold in such a way that the components no longer assemble together. Concomitant knockdown of the lncRNA and the effector(s) is expected to result in phenotype exacerbation instead of rescue, as would be expected from the decoy archetype. The telomerase RNA (TERC) is a classic example of an RNA scaffold that assembles the telomerase complex [23,131,132]. Based on dynamic expression patterns, specific lncRNAs can potentially integrate and direct complex patterns of chromatin states at specific target loci in a spatiotemporal-specific manner during both organismal developmental and disease. Another prime example of lncRNA scaffolds is HOTAIR, which can simultaneously bind two different chromatin-modifying complexes via specific domains of the RNA structure [25,83,84].

This finding shows that multiple chromatin-modifying complexes are targeted by HOTAIR, which implies that this lncRNA acts as a scaffold and bridges between PRC2 and the LSD1-CoREST/REST complex in one package; the HOTAIR-PRC2-LSD1 complex can suppress gene expression by multiple concurrent mechanisms [25,83]. The molecular interplay between lncRNAs and chromatinmodifying complexes can also be found in the transcriptional repression of the well-studied INK4a locus. The antisense ncRNA ANRIL (also known as CDKN2B-AS1, which is CDKN2B antisense RNA 1), which emanates from the INK4b/ARF/INK4a locus, is also important for protein-coding genes expressions in cis. Over the past decades, work has shown a direct interaction between ANRIL and the components from both the PRC1 and PRC2 complexes [133,134]. Binding to ANRIL contributes to the functions of both the PRC1 and PRC2 proteins, and disruption of either interaction impacts the transcriptional repression of both the target INK4a (which is encoded by CDKN2A) and INK4b (which is encoded by CDKN2B) loci. Thus, similar to HOTAIR and Kcnq1ot1, ANRIL represents a prototype of an lncRNA that is always present at the locus and recruits multiple sets of chromatin-modifiers to the target gene for silencing, serving as a molecular scaffold to dynamically modulate the transcriptional activity. Notably, many lncRNAs can interact with PRC2 and LSD1 complexes in several cell types [51]. It is conceivable that other lncRNAs might also contain multiple binding sites where distinct protein complexes can assemble to more specifically induce specific combinations of histone modifications on target gene chromatin.

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3.4. Theme IV: guides

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Cellular identity in an organism is determined by epigenetic factors, such as chromatin-modifying complexes and DNA methyltransferases, which activate and repress specific gene expression programs by enzymatically modifying the chromatin and DNA. One of the most puzzling questions in biology is how do these omnipresent enzymes, which lack DNA binding motifs, recognize the target genes in various cell types. Recent evidence suggests that lncRNA is a guide for chromatin-modifying complex(es) and other nuclear protein(s) that direct their localization to specific targets to exert their effects [50,135,136]. Essentially, some lncRNAs may act as ‘‘global positioning system (GPS)’’ devices to direct other cellular components to the target sites of action. As evident from the discussions thus far, lncRNAs can guide the changes in the gene expression either in cis (on neighboring genes) or in trans (distantly located genes) in a manner that is difficult to identify and that is based on the sequence of lncRNA. Recent work has shed light on the advantages that lncRNA offers in delivering allelic, cis-limited, and locus-specific control (i.e., Xist, Airn, Kcnq1ot1, HOTTIP, CCND1 and Dlx6os1) [20,49]. In contrast, several lncRNAs exert transcriptional effects across chromosomes in trans (i.e., HOTAIR, lincRNA-p21 and Jpx) [20,49]. Currently, the sequence of events that leads to the lncRNA-mediated guidance of a protein complex to chromatin has not been fully elucidated. Guide lncRNAs thereby combines two basic molecular functions (binding of a protein partner plus a mechanism to interface with selective regions of the genome). In support of this model, a recent study that utilizes a novel technology that determines the genomic occupancy of an lncRNA revealed that HOTAIR localizes to chromatin independent of the HOTAIR partner PRC2 [132].

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4. What are the potential roles of lncRNAs in human disorders, especially in diseases related to aging?

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In contrast to the extensive evidence that links dysregulation of miRNAs and protein-coding genes to the onset of human disorders, especially diseases related to aging [137,138], To date, only a few

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lncRNAs have been implicated in aging and diseases related to aging. However, lncRNAs participate in a wide-repertoire of cellular contexts. Almost every step in the life cycle of the genes (from transcription to mRNA splicing, RNA decay, and translation) can be influenced by lncRNAs, as shown above. Given the prevalence of lncRNA expression, molecular studies of diseases should address the possible involvement of lncRNA in various settings. Indeed, in complex diseases, association signals often derive from noncoding regions of the genome. Accumulating reports of dysregulated lncRNA expression in Alzheimer’s [36], aging-related declines in cognitive function [37], diabetes [38], cardiovascular diseases [33,39] and cancer [21,27] imply that lncRNAs are implicated in a variety of disorders, especially those that involve diseases that are related to aging; these relationships underscore their importance in maintaining cellular homeostasis (Fig. 2A). It is reasonable to expect that a concrete, mechanistic understanding of these connections will emerge in the coming years. Because both the role of lncRNA dysregulation and the molecular mechanisms in aging and aging-associated diseases are not fully understood, it is time to ask several important questions: How many lncRNAs are differentially regulated in aging and diseases that are related to aging compared to healthy humans? What are the molecular and biological functions of the lncRNAs that are dysregulated in human diseases that are related to aging?

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How stable are the lncRNAs, and is their stability altered in various disease states? Thus, the immediate goals of lncRNA research are to investigate the mechanisms by which lncRNAs govern aging processes, the utility of the biomarkers for early tissue aging or cellular senescence detection, and the use of lncRNAs as candidate drug targets for intervention in diseases related to aging.

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4.1. lncRNAs: new players in aging

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Analysis of lncRNAs in regulating aging at the level of organism lifespan, tissue aging, or cellular senescence is still in its infancy, and the full impact of this field is yet to be realized. lncRNAs represent another important and emerging subclass of ncRNAs that may also play a role in the aging network and the onset of diseases related to aging. Importantly, lncRNAs are implicated in the development of axonal and dendritic connections, and additionally, in synaptic modulation that is correlated with neural network plasticity and that may also participate in the generation of long-term potentiation that underlies learning and memory [139,140]. Notably, numerous lncRNAs are dysregulated in a wide range of human disorders, including various types of cancers and diseases related to aging [21,27]. Thus, lncRNA may represent a novel molecular mechanism that underlies aging. However, there is still little information with regard to the potential involvement

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Fig. 2. lncRNAs are deregulated in aging-related diseases and serve as potential molecular markers and therapeutic targets. (A) lncRNA that are regulated by transcription factors and epigenetic modifications participate in aging processes. A wide repertoire of studies have now demonstrated that the expression of lncRNAs can be dysregulated in several human diseases, including some aging-associated illnesses, such as Alzheimer’s diseases, cardiovascular diseases, diabetes, and cancer. Therefore, lncRNAs may constitute a non-invasive approach to the diagnosis of aging and the onset of aging-related diseases in the future by collecting patient blood samples, isolating nucleic acids from cells in the blood, and quantifying aging-associated lncRNA expression, CDS, and coding sequences (B). A final goal of lncRNA research on aging and aging-related diseases is to investigate whether lncRNA can serve as a therapeutic target. lncRNA-based therapies may target the lncRNA by utilizing RNAi, which uses sequence homology between the lncRNA and the RNAi therapeutic molecule, or small molecule therapy that interacts with lncRNA. These therapeutic avenues may be appropriate for systemic therapy by intravenous or oral administration (C).


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of lncRNAs in modulating the complex process of cellular senescence. Continuing advances in transcriptomics are resulting in the discovery of a number of novel lncRNAs that involve dynamic changes in aging rat brains, which suggests that these may be of importance in brain aging. In addition to altering the lncRNA expression profiles during aging processes, the precise function of lncRNAs in regulating cellular senescence has recently revealed that lncRNAs may also directly participate in the aging network to regulate aging at the level of tissue aging or cellular senescence. The lncRNA ANRIL has been involved in the repression of INK4a, ARF, and/or INK4b [133,134], which are key effectors of oncogene-induced senescence and are induced during aging [141]. Importantly, in one of the first systematic studies of lncRNAs in aging, researchers have revealed that many senescence-associated lncRNAs (SAL-RNAs) were differentially expressed in the senescent population by deep sequencing of RNA that is expressed in proliferating and senescent fibroblasts [142]. Among these lncRNAs, several SAL-RNAs can modulate the onset of senescence and protect senescent cell viability, which suggests that lncRNAs directly contribute to implementing the senescent phenotype [142]. In addition, the lncRNA MALAT1 was reportedly reduced in senescent fibroblasts, which is in keeping with the observation that lowering MALAT1 triggered cellular senescence in fibroblasts [143]. This effect was attributed in part to the decline in the oncogenic transcription factor b-myb/mybl2 that is caused by B-MYB pre-mRNA splicing when the MALAT1 levels were low. In turn, the reduced levels of bMyb reduced the progression of cells through the G2/M cell cycle compartments and promoted cellular senescence [143]. lncRNAs have been shown to affect the regulation of pathways that are involved in cellular senescence and to exert important effects on the cell cycle progression. Recently, p53, a critical regulator of cellular senescence, has been reported to activate many lncRNAs that have growth-suppressive functions [125]. lncRNAs have been shown to target p53 and components of the p53 pathway, thereby affecting p53 activity. lincRNA-p21 plays a role in apoptosis and acts as a bona fide downstream target of p53, which in turn serves as a key repressor of several important prosurvival genes in the p53 pathway. Specifically, silencing of lncRNA-p21 blocks programmed cell death (i.e., apoptosis) but not cell-cycle arrest [125]. Additionally, the mammalian target of the rapamycin (mTOR) pathway plays a crucial role in the geroconversion from cell-cycle arrest to senescence. mTOR is the catalytic subunit of two cellular complexes (mTORC1 and mTORC2) that have distinct upstream regulatory signals and downstream substrates [144]. Rapamycin, which blocks mTORC1 kinase, suppresses or decelerates geroconversion to maintain quiescence [145,146]. Furthermore, inhibition of the mTOR pathway prolongs the lifespan of model organisms, including mice [147,148]. Intriguingly, the Uchl1AS lncRNA has been reportedly involved in the mTOR-signaling pathway [109]. Furthermore, its function is under the control of stress signaling pathways because mTORC1 inhibition by rapamycin causes an increase in the UCHL1 protein. The mutation of this protein has been linked to an early-onset familial Parkinson’s disease and is downregulated in idiopathic Parkinson’s disease as well as Alzheimer’s disease [149]. From the information above, it can easily be concluded that lncRNAs play a critical role in complex cellular senescence regulatory networks.

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4.2. Roles of lncRNAs in diseases related to aging

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Aging is an inevitable part of life and unfortunately poses the largest risk factor for the onset of age-associated chronic pathologies, such as Alzheimer’s, cognitive disorders, diabetes, cardiovascular diseases, and cancer [150] (Table 1). In contrast to the extensive evidence that links the dysregulation of encoding

genes to aging-related diseases, only a few lncRNAs have to date been implicated in the onset of diseases related to aging. We highlight some examples of lncRNAs that are known or suggested to be involved in diseases that are related to aging. Most of the descriptions are incomplete and only hint at the rich layers of lncRNA function that are yet to be discovered, the new potential biomarkers, and therapeutic targets (Fig. 2B and C).

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4.2.1. lncRNAs in Alzheimer’s and cognitive disorders lncRNAs have been found to be dysregulated in many neurological disorders and lncRNA transcripts that regulate key genes in disease progression have also been described and extensively reviewed [140,191]. We present some examples of lncRNAs that are implicated in the neurological and cognitive disorders below. One of the best-studied examples of an lncRNA regulating a key gene in human neurological disease is b-secretase-1 (BACE1)-AS in Alzheimer’s disease [36]. BACE1 is essential for the generation of beta-amyloid and the consequent amyloid plagues, which are central to the pathophysiology of Alzheimer’s disease. An antisense transcript of BACE1, known as BACE1-AS, has been shown to be capable of upregulating the sense mRNA, by duplexing with BACE1 mRNA and stablizing the mRNA, thereby increasing the BACE1 protein levels. BACE1-AS is elevated in the brain tissues of patients who have Alzheimer’s disease, which suggests that the lncRNA is the driving force behind BACE1 dysregulation in Alzheimer’s disease [36,156]. Understanding the BACE1-AS mechanism may prove to be important in the development of therapeutics for Alzheimer’s disease. Importantly, knockdown of BACE1-AS in vivo by continuous infusion of locked nucleic acid (LNA)-modified small interfering RNAs (siRNAs) into mouse brain resulted in the downregulation of both BACE1-AS and BACE1, as well as in reducing the beta-amyloid synthesis and aggregation in the brain [156]. These findings indicate that BACE1-AS expression is dysregulated, which induces the feed-forward regulation of BACE1, increases the beta-amyloid levels, and thus may promote the pathogenesis of Alzheimer’s disease. Another lncRNA that was found to be dysregulated in Alzheimer’s disease and brain aging was the brain cytoplasmic (BC) RNAs. BC1 RNA in mice and BCYRN1/BC200 RNA in humans are lncRNA transcripts that are transported to dendritic processes as ribonucleoprotein particles, and they modulate gene expression at the translational level [192]. BCYRN1/BC200 levels in Brodmann’s area 9 (the area of the brain that is affected in Alzheimer’s disease) has been found to be consistently higher in age-matched Alzheimer’s disease brains compared with normal brains, and the relative levels of BCYRN1/BC200 RNA in the affected areas increased with the severity of Alzheimer’s disease [152]. BCYRN1/BC200 RNA interacts with several RNA-binding proteins that are involved in mRNA trafficking in neurons, such as poly(A)-binding protein (PABP1), a regulator of translation initiation [192], hnRNPA2, which is implicated in the transport of mRNA in neurons and oligodendrocytes, and Synaptotagmin-binding cytoplasmic RNA interacting protein (SYNCRIP), which is part of an mRNA transport granule and is possibly involved in local protein synthesis at postsynaptic sites in neurons [193]. All of these point to a plausible role of BCYRN1/BC200 in modulating the local protein synthesis at the dendrites, and the overexpression of BCYRN1/BC200 in Alzheimer’s disease and aging brains may be a cause of synaptodendritic deterioration. In addition, BC1, the possible functional analog of BCYRN1/BC200 lncRNA, is localized to synaptic regions; it interacts with key proteins in translational scaffold complexes and contributes to the maintenance of long-term synaptic plasticity through the regulation of synaptic protein synthesis that is critical for synaptic functions. BC1 lncRNA has been shown to negatively regulate dopamine D2 receptor-mediated synaptic transmission in the striatum by derepressing the synaptic

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Table 1 LncRNAs in aging-related disorders outlined here: Alzheimer’s and cognitive disorder, cardiovascular diseases, diabetes, cancer.a Aging-related disorders

Long noncoding RNAs (Refs.b)

Long noncoding RNAs functions/characterization

Dysfunction type

Alzheimer’s and cognitive disorders

BCYRN1/BC200 [151,152]

Increased levels of BC200 were found in brain regions that are preferentially affected in Alzheimer’s disease. Further, in advanced stages of Alzheimer’s disease, BC200 was mislocalized and clustered in the perikaryon. These observations suggest that deregulation of these synaptic lncRNAs is involved in the synaptic and neural network dysfunction that is found in both early and later stages of Alzheimer’s disease Negatively regulates dopamine D2 receptor-mediated synaptic transmission in the striatum, probably by derepressing the synaptic protein that interacts with and downregulates the D2 receptor Upregulates BACE1 mRNA and subsequently BACE1 protein expression in vitro and in vivo. BACE1 mRNA expression is under the control of a regulatory noncoding RNA that may drive Alzheimer’s disease-associated pathophysiology Recent studies showed that single nucleotide polymorphisms mapping in the vicinity of ANRIL are linked to a wide spectrum of conditions, including Alzheimer’s disease HAR1, a deeply conserved genomic region consisting of a cisantisense pair of structured lncRNAs (HAR1F and HAR1R) located 80 kb from the neural microRNA, miR-124-3. HAR1 levels are significantly lower in the striatum of Huntington’s disease patients; Schizophrenia spectrum disorders and Alzheimer’s disease have also been linked with the rheelin (RELN) gene and its antisense transcript HAR1; HAR1 has also been implicated in Huntington’s disease, where the transcriptional repressor RE-1-silencing transcription factor (REST) enters pathologically into the nucleus, leading to the repression of several important neuronal genes. ASFMR1 is silenced in Fragile X syndrome (FXS) patients and upregulated in pre-mutation carriers suggesting that a common process is responsible for regulating the expression these transcripts. UBE3A-AS is a lncRNA transcribed antisense to the maternally expressed UBE3A gene, a candidate gene for Angelman syndrome, suggesting that UBE3A-AS may be responsible for repressing paternal UBE3A expression. An lncRNA embedded in the GABA B receptor 2 (GABBR2) locus is deregulated in brain tissues from patients with Alzheimer’s disease; 17A influences intracellular signaling pathways downstream of the associated GABA receptor by regulating its alternative splicing; 17A is expressed in response to inflammatory stimuli, and it promotes amyloid b (Ab) secretion and increases the pathologic Ab42: Ab40 ratio

Expression

BC1 [153–155]

BACE1-AS [36,103,156]

ANRIL (CDK2BAS/p15AS) [133,134,141,157–160] HAR1 [161]

FMR4/ASFMR1 [151]

UBE3A-AS [162–164]

17A [165]

Cardiovascular diseases

ANRIL (CDK2BAS/p15AS) [158–160] DMPK 30 UTR [166–168]

SRA transcripts [91,169–171]

MIAT (Gomafu/RNCR2) [33,39,172,173]

Diabetes

ANRIL (CDK2BAS/P15AS) [174] HI-LNC25 [38]

IGF2-AS [175] HI-LNC45 [38] PDZRN3-AS1 [176] PVT1 [177,178]

Recent studies showed that single nucleotide polymorphisms mapping in the vicinity of ANRIL are linked to a wide spectrum of conditions, including cardiovascular disease Induction of Nkx2-5; the mutant DMPK transcript causes myotonic dystrophy type 1 (DM1), which is encoded by a protein-coding gene containing a CUG expansion repeat in its 30 -untranslated region. Co-activators of nuclear receptor signaling, muscle differentiation, components of gene insulator complexes; SRA1 results independently in a phenotype of myocardial contractile dysfunction In vitro functional analyses revealed that the minor variant of one SNP in exon 5 increased transcriptional level of MIAT. Moreover, unidentified nuclear protein(s) bound more intensely to risk allele than non-risk allele. These results indicate that the altered expression of MIAT by the SNP may play some roles in the pathogenesis of myocardial infarction Recent studies showed that single nucleotide polymorphisms mapping in the vicinity of ANRIL are linked to a wide spectrum of conditions, including type 2 diabetes Positively regulates GLIS3 mRNA, which encodes an islet transcription factor, mutated in a form of monogenic diabetes, and also contains type 2 diabetes risk variants It is significantly associated with type 1 diabetes identified by GWAS It is significantly decreased in type 2 diabetes islets SNP rs11128347 (C>G) in PDZRN3 is associated with AfricanAmericans with type 2 diabetes There is association between variants (rs2720709, A>G) in the plasmacytoma variant translocation 1 gene (PVT1) and end-stage renal disease (ESRD) attributed to both type 1 and type 2 diabetes

Expression

Expression and interaction

Mutation

Expression and regulation

Expression

Locus

Expression

Mutation

Mutation

N/A

Mutation

Mutation

Expression and mutation Mutation Expression Mutation Mutation


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14 Table 1 (Continued ) Aging-related disorders

Long noncoding RNAs (Refs.b)

Long noncoding RNAs functions/characterization

Dysfunction type

Cancer

HOTAIR [84,179]

Intergenic transcript of HoxC locus, gene silencing in trans through interacting with PCR2 and LSD1 complex, involved in many cancer; Imprinted at the lgf2 locus; controls igf2 expression in cis, implicated in both tumor suppressors and oncogenes Act as a tumor suppressor Alternative splicing of SRA-1, loss of coding frame, an increased expression is associated with tumor metastasis Upregulated in human melanomas compared to melanocytes and keratinocytes, affects cell dynamics, including upon ectopic expression increased rate of wound closure, suggesting that the higher expression of SPRY4-IT1 may pay a crucial role in the molecular etiology of human melanomas Expressed in many cancers, regulates alternative splicing of premRNA and promotes cell motility through transcriptional and posttranscriptional regulation of motility related gene expression Imprinted transcripts, highly expressed in human pituitary, stimulates p53-mediated transactivation and suppresses tumor growth in the absence of p53 GAS5, a ncRNA, controls apoptosis and is downregulated in breast cancer; Gas5 has also been linked with breast cancer because Gas5 transcript levels are significantly reduced compared to unaffected normal breast epithelia; Chromosomal translocations affecting the 1q25 locus containing the Gas5 gene have been detected in melanoma, B-cell lymphoma, and prostate and breast cancer Transcript of PTEN tumor suppressor pseudogene, PTENP1 30 -UTR exerts a tumor suppressive function by acting as a decoy for PTENtargeting miRNAs

Expression and epigenetic Expression and epigenetic Expression Expression and locus Expression

H19 [118,180,181] GAGE6 [182] SRA-1 [170,171] SPRY4-IT1 [183]

MALAT1 [184–187]

MEG3 [188,189]

GAS5 [92,190]

PTENP1 [115]

Expression and interaction Expression, epigenetic and mutation Expression and mutation

Interaction

N/A, not available. a Based on information obtained from http://202.38.126.151/hmdd/html/tools/lncrnadisease.html. b This list indicates representative references for each lncRNA and is not exhaustive.

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protein that interacts with and downregulates the D2 receptor [155]. Notably, BC1/ mice show no overt phenotype or neurologic abnormalities when housed in cages [153,154], but they develop abnormal cognitive and behavioral phenotypes, increased anxiety, and decreased survival rates when kept in an outdoor enclosure [194]. In addition to Alzheimer’s disease, lncRNAs are also associated with cognitive and behavioral disorders. For example, highly accelerated region 1 (HAR1) is primarily expressed during neocortical development in Cajal–Retzius cells, which control radial migration and laminar positioning of pyramidal neurons of the cortical plate. HAR1 is co-expressed with reelin, a critical developmental factor that is implicated in normal cognitive function and in the molecular pathogenesis of diverse cognitive disorders (e.g., neuronal migration defects, autism spectrum disorders, schizophrenia, bipolar disorder, epilepsy, stroke, and Alzheimer’s disease) [195]. Notably, HAR1 expression is decreased in the striatum of patients who have Huntington’s disease, which is mediated again by REST [161]. Additionally, FMR1 antisense RNA 1 (FMR4/ASFMR1) is associated with Fragile X syndrome (FXS; a common cause of autism spectrum disorders) [151]. lncRNAs are also associated with imprinting disorders, such as ubiquitin protein ligase E3A (UBE3A) antisense RNA (UBE3A-AS) in Angelman syndrome. A defect in UBE3A results in this imprinting-related neurodevelopmental disorder. UBE3A is bi-allelically expressed in most tissues, but only the maternal allele contributes to UBE3A expression in the brain [196]. Tellingly, in patients with Angelman syndrome, the maternal UBE3A gene is inactivated or lost, which results in a loss of functional UBE3A in neuronal cells [162]. The lncRNA UBE3A-AS has been shown to regulate epigenetic silencing of the paternal allele [163,164], establishing the importance of this lncRNA in the molecular pathogenesis of Angelman syndrome. This circumstance raises the intriguing possibility that therapeutically targeting UBE3A-AS can increase the expression of paternal UBE3A in the brain and, thus, might constitute a treatment for Angelman syndrome. Intriguingly, lncRNAs that are derived from the

imprinted GNAS locus might have roles in cognitive and behavioral dysfunction that are correlated with GNAS mutations [197]. One possibility is that neuroendocrine secretory protein antisense (NESPAS), an lncRNA that is derived from this locus, modulates neuroendocrine secretory protein 55 (NESP55), a neurosecretory factor that is prominently expressed in the locus coeruleusnoradrenergic system [198]. This system is an important mediator of state-dependent neural network activity and its associated neurodegenerative and neuropsychiatric disorders [199]. In addition, brain aging and related cognitive phenotypes are associated with alterations in synaptic and neural network connectivity, plasticity and stress responses that can be mediated by ncRNAs [89]. One interesting example is the lncRNA HSR1, which plays a key role in promoting the cytoprotective heat shock response that is linked to neural development and brain aging and to the molecular pathogenesis of diverse neurodegenerative disorders [90]. In summary, the transcriptional landscape is particularly complex in the central nervous system, because mRNAs and lncRNAs alike are regulated by neuronal activity, and dysregulation of this intricate regulatory network could result in the disruption of normal brain development and function. Studying lncRNA mechanisms of action will undoubtedly provide valuable insights into the molecular basis of neurological disorders, which might lead to new therapeutics and diagnostics.

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4.2.2. lncRNAs in cardiovascular diseases lncRNA transcript levels are often dynamically altered in a variety of human diseases, and changes in lncRNA expression or structure, as well as the associated chromatin modifiers, are central to several disorders, including cardiovascular diseases [33,39]. Mutations in key core cardiac transcription factors are causative for congenital heart disease and some adult cardiacrelated diseases, such as those that affect the heart muscle as well as the electrical circuits that are required for proper conduction. Given that lncRNAs appear to contribute to the regulation of cardiac networks, these ncRNA transcripts are also expected to

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contribute to cardiac-related pathologies. Because lots of cardiacrelated diseases are heritable, recent efforts to identify potential new disease loci for cardiovascular diseases have relied in part on GWAS. Notably, 93% of GWAS hits fall outside of protein-encoding regions, and emerging evidence indicates that noncoding DNA, including distal regulatory elements as well as lncRNA genes that do not overlap known protein-encoding genes, is enriched for disease SNPs [31]. In support of this idea, a number of lncRNAs have been implicated in adult cardiac disease, including NATs that are transcribed in the opposite direction of critical heart development and structural genes, which suggests that these NATs can impact the expression of key cardiac genes. Other examples of lncRNAs are implicated in adult cardiac disease by the analysis of genetic variations among individuals with cardiac traits. NATs often, but not always, regulate the expression of their corresponding sense RNA and can employ different molecular mechanisms to do so. This mode of regulation is especially important given that the gene dosage is critical for proper heart development and function and has been implicated in aspects of cardiac disease. The strongest genetic susceptibility locus for coronary artery disease is located at the chromosome 9p21 locus, and several SNPs in this region map to the 30 end of an lncRNA (ANRIL), which was discussed above [200]. Approximately 21% of the individuals in the population are homozygous for a risk haplotype and have an approximate 2-fold risk of suffering a myocardial infarction compared to non-carriers. This locus has been linked to other human diseases, including cancer, diabetes, intracranial aneurysms, periodontitis, Alzheimer’s disease, endometriosis, frailty, and glaucoma [159]. ANRIL transcripts are expressed in coronary smooth muscle cells, vascular endothelial cells, and monocyte-derived macrophages, all of which are involved in atherosclerosis. Furthermore, patients who have the risk haplotype exhibit elevated ANRIL expression in peripheral blood mononuclear cells and atherosclerotic plaques [160], with transcript levels that are directly correlated to the severity of atherosclerosis [158]. In contrast to the epigenetic repression of neighboring genes in cis [133,134], overexpression of the 1 ANRIL variant alters the expression of many genes that are involved in nuclear regulation and chromatin architecture, indicating diverse trans-regulatory effects that go beyond the cis-effects that are observed at 9p21 [157]. Recently, 33 enhancers have been described in this region, making 9p21 the second densest gene desert for predicated enhancers [201]. The coronary artery disease risk alleles of the SNPs (rs10811656 and rs10757278) are located in one of these predicated enhancers and disrupt a binding site for the STAT1 transcriptional factor, which results in altered ANRIL expression [201]. STAT1, an effector of the interferon-g inflammatory pathway, is associated with the pathogenesis of atherosclerosis in endothelial tissues [202]. Myotonic muscular dystrophy is a toxic RNA disease in which a CTG triplet repeat in the 30 UTR of the myotin protein kinase (DMPK) gene becomes expanded (50- to >2000-fold) [168]. Part of the disease mechanism involves the accumulation of mutant RNA in the nucleus, where the mutant RNA sequesters RNAbinding proteins that are involved in splicing and other RNAmediated nuclear functions [203]. Intriguingly, mice that carry inducible transgenes that overexpress the 30 UTR harboring 5 CUG repeats within the normal DMPK gene can replicate this disease [166,167]. In this model, abnormal DMPK 30 UTR overexpression results in the down-regulation of connexins 40 and 43, which are gap junction proteins that are essential for the propagation of action potentials. This overexpression also up-regulates the homeodomain transcription factor Nkx2.5, which normally regulates connexin gene expression. Notably, genetic studies have shown that the up-regulation of Nkx2.5 expression in the heart is responsible for progressive heart block. The steroid receptor RNA

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activator 1 (SRA1) gene is a multifunctional gene that generates both steroid receptor RNA activator protein (SRAP) and several non-coding SRA transcripts, depending on the alternative transcription start site usage and alternative splicing [170,171]. SRA1 ncRNA transcripts function as co-activators of nuclear receptor signaling in a ligand-dependent manner and are involved in regulating skeletal muscle differentiation by co-regulation of the muscle development gene MYoD [204]. The identification of genome-wide significant SNPs coupled with linkage disequilibrium mapping implicated three cosegregating genes including heparin-binding epidermal growth factor [EGF]-like growth factor (HBEFG), IK (IK) cytokine, and SRA1 as determinants of human dilated cardiomyopathy. Ablation of any one of these three genes in zebrafish causes myocardial contractile dysfunction predominantly in ventricular heart chambers [169], which is consistent with the role of nuclear receptors in cardiomyocyte maturation and function. In addition, lncRNA variants can also be involved in myocardial infarction and can confer susceptibility. Myocardial infarction-associated transcript (MIAT), which is also known as Gomafu or RNCR is an approximately 9 kb lincRNA that is predominately expressed in the nucleus of developing neural cells and has a known role in retinal cell fate specification during development. This transcript was identified by GWAS as a risk factor that is associated with patients who have suffered myocardial infarction [173]. Several variants were identified as being significantly associated with a higher susceptibility to myocardial infarction compared to controls. In fact, a specific SNP (exon 5 11,741 G>A) was associated with the increased transcription of MIAT. MIAT accumulates in the nucleus in specific nuclear bodies and displays high expression levels in the central nervous system and lower levels in other tissues [172,173,205]. MIAT has also been implicated in retinal cell specification in the mouse [206] and may have a role in splicing regulation [172]; however, the molecular role of MIAT in myocardial infarction remains unknown. In some cases of cardiac disease, such as primary cardiomyopathy, the heart is directly affected, while in other cases, cardiac disease results indirectly from conditions such as inflammation and diabetes, which increase the risk for developing atherosclerosis and coronary artery disease and eventually myocardial infarction. Consequently, the identification and functional validation of lncRNAs that have roles in complex traits will be an added challenge.

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4.2.3. lncRNAs in diabetes The incidence and prevalence of type 2 diabetes mellitus increases with age [207]. Islet cell dysfunction is central to the pathophysiology of type 2 diabetes mellitus, the most prevalent form of diabetes, but the underlying mechanism within beta cells that contributes to this increased susceptibility has not been fully elucidated. A recent study involving GWAS for type 2 diabetes and related traits has revealed >50 susceptibility loci, most of which are not known to carry variants that alter protein-coding sequences [208]. A common hypothesis is that such variants impact regulatory elements of protein-coding genes, even though the variants could equally affect other non-protein-coding elements, such as lncRNAs. Defects in lncRNAs could thus underlie human disease, and cell-specific regulatory lncRNAs might provide therapeutic targets [10,21,209]. Despite the potential implications for human diabetes, information on islet cell lncRNAs is lacking. A more recent study by Moran et al. has integrated sequence-based transcriptome and chromatin maps of human islets and beta cells to uncover >1100 intergenic and antisense islet cell lncRNA genes [38]. This study also found that lncRNAs are an integral component of the dynamic beta cell-specific differentiation program, suggesting a role as a biomarker and potential regulator for programming efforts. Similar to other tissue-specific lncRNAs, islet lncRNAs have

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also been linked to diverse types of functions, frequently involving direct or indirect expression regulation of protein-coding genes. For instance, HI-LNC25, a beta cell-specific lncRNA, positively regulates GLIS3 mRNA, which encodes an islet transcription factor that is mutated in a form of monogenic diabetes and also contains type 2 diabetes risk variants [210]. Conversely, knockdown of HILNC25 down-regulates the level of GLIS3 mRNA expression, thus exemplifying a gene regulatory function of islet lncRNAs. Select lncRNAs are dysregulated in patients with type 2 diabetes mellitus; specifically, two lncRNAs (KCNQ1OT1 and HI-LNC45) are significantly increased or decreased in type 2 diabetes islets [38]. Additionally, some lncRNAs also map to genetic loci underlying diabetes susceptibility, which include a lncRNA in the vicinity of PROX1 and the most significant lncRNA in the MAGENTA analysis near WFS1 [38]. These lncRNAs offer a new class of genomic elements that can be interrogated to dissect the functional etiology of type 2 diabetes mellitus susceptibility and open a new framework to study the pathophysiology of human diabetes.

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4.2.4. lncRNAs in cancer Cancer in the elderly is increasingly common. Cellular senescence, a form of irreversible growth arrest, appears to be an important obstacle that cells must bypass during carcinogenesis [211]. Cancer is a complex disease, involving various changes in gene expression that cause cancer development, including cell proliferation-mediated metastasis, invasion, and angiogenesis. In contrast to miRNAs and protein-coding genes, lncRNAs have provided new insight into cancer biology and provided several lines of evidence to suggest there is a correlation between the expression and promotion of cancers. Until recently, lncRNAs have been shown to be dysregulated in various types of cancers, including breast cancer, colorectal cancer, liver cancer, lung cancer, leukemia, melanoma, and possibly other cancers [10,21,27,34]. On a more mechanistic level, a wide repertoire of studies have now revealed the contribution of lncRNAs as oncogenes, such as HOTAIR [84,179], H19 [180,181], and GAGE6 [182], as tumor suppressor genes, such as p15AS [212], lincRNA-p21 [125], and MEG3 [188,189], as regulators of alternative splicing, such as MALAT1 [106]. Even though the mechanisms of action of most lncRNAs that are dysregulated in cancer have not been fully elucidated, studies have recently begun to investigate more complex questions, including whether lncRNAs cause disease or are altered as a consequence of the disease itself, and whether the deregulated expression of lncRNAs affects the differentiation state, growth rate, or metastatic potential of tumor cells. For example, HOTAIR has been shown to serve as a driver of metastatic transformation, and elevated of HOTAIR expression levels in primary breast tumors is a significant predictor of subsequent metastasis and death [84]. Similarly, high levels of HOTAIR expression are also associated with poorly differentiated histologic grade in oesophageal squamous cell carcinoma and carry a poor prognosis [179]. Another lncRNA, SPRY4-IT1, is upregulated in human melanomas compared to melanocytes and keratinocytes and affects cell dynamics, including ectopic expression. This lncRNA also increases the rate of wound closure, suggesting that the higher expression of SPRY4-IT1 may have a crucial role in the molecular etiology of human melanomas [183]. Another example of a lncRNA involved in tumor cell invasiveness and metastasis is MALAT1, which is widely expressed in normal human tissues and is up-regulated in a variety of human cancers, including those of the lung, breast, prostate, liver, colon, and uterus [185,186,213]. A number of studies have implicated MALAT1 in the regulation of cell mobility. For example, depletion of MALAT1 by siRNAs in lung adenocarcinoma cells impairs migration through concomitant regulation of motilityregulated genes via transcriptional and/or posttranscriptional

mechanisms [184]. Similarly, inhibition of MALAT1 reduces the cell proliferation and invasive potential of cervical cancer cells ex vivo [187]. In contrast to ‘‘onco’’ roles of lncRNAs in cancer, a few recent studies have determined several examples of ‘‘tumor-suppressor’’ lncRNAs. GAS5 represents an example of an lncRNA that regulates the expression of a critical subset of tumor-suppressive genes and is downregulated in breast cancer, perhaps to keep cancer cells active, even under low-nutrient conditions [190]. lincRNA-p21 may be a tumor suppressor gene in mice; although lincRNA-p21 has not been directly associated with diseases. It is tempting to speculate that loss of lincRNA-p21 function could be an important factor that contributes to cancer initiation because lincRNA-p21 triggers cell death by induction of apoptosis in mouse cells [125]. However, unlike the mouse counterpart, human lincRNA-p21 appears not to be involved in the regulation of doxorubicin-induced apoptosis. In addition, under hypoxic conditions, human lincRNA-p21 is specifically upregulated by HIF-1a, but not by HIF-2a and p53, suggesting that human lincRNA-p21 and its mouse counterpart may not be functionally equivalent [214]. In support of this, mouse lincRNA-p21 is predominantly localized in the nucleus while human lincRNA-p21 is maily localized in the cytosol [125,215]. Importantly, a recent study has demonstrated that human lincRNA-p21 acts as an oncogene and could promote glycolysis under hypoxia and promote tumor growth, suggesting that it is an important player in the regulation of the Warburg effect and also implicating it as a valuable therapeutic target for cancer [214]. These association studies have set the stage for follow-up functional studies to reveal how lncRNAs contribute to human disease, opening a new avenue for therapeutic intervention. In summary, the discovery of dysregulated lncRNAs represents a new layer of complexity in the molecular architecture of human aging and aging-related illnesses. Aside from the imminent use of our knowledge of aging-associated lncRNAs for diagnosis, the use of lncRNAs as therapeutic agents is only beginning to be investigated. Although the implementation of therapies targeting ncRNAs is still remote for clinical oncology, the progress in the use of RNAi-mediated gene silencing for the treatment of different diseases is encouraging [216,217] and has been tested in mice, cynomolgus monkeys, and humans [218] as part of a phase I clinical trial for patients with advanced cancer. Systemic administration of RNAi-based therapy was able to effectively localize to human tumors and reduce expression of its target gene mRNA and protein. Ongoing clinical trials are further evaluating the safety and efficacy of RNAi-based therapeutics in patients with a variety of diseases, including aging-associated diseases, and these approaches could be adapted to target lncRNA transcripts (Fig. 2C). Over the past few years, progress in the field of structure-based drug design has indicated that it is pharmacologically possible to disrupt intermolecular interactions with small molecules. Other studies have investigated an intriguing approach that employs modular assembly of small molecules to adapt to aberrant RNA secondary structure motifs in disease [219], which could potentially target aberrant ncRNAs and mutant mRNAs (Fig. 2C). However, most RNA-based research remains in the early stages of development and the potential for RNAi therapies targeting lncRNAs in aging-related diseases is still far from use in clinics.

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5. Concluding remarks

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Continuing advances in transcriptomics are resulting in the discovery of a plethora of novel lncRNAs. The role of lncRNAs in aging, although a relatively new area of research, has already shed light on how aging- and senescence-associated processes are controlled. The involvement of these lncRNAs in genome expression was first met with skepticism. Why would an organism

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generate the universe of RNAs? Rather than reducing lncRNAs to a simple encoding role, it is quickly becoming clear that they could have numerous biological and molecular functions, including modulation of chromatin structure by recruitment of histoneand chromatin-modifying complexes to specific genomic loci, regulation of transcription by the recruitment of transcription factors, formation of nuclear subdomains associated with posttranscriptional RNA processing (i.e., paraspeckles), nuclear-cytoplasmic transport, and translational control (i.e., local protein synthesis). Analyses of lncRNA functions have provided insight into how aging mechanisms are regulated at the cell, tissue, and organism level, yielding a better understanding of the process of aging and its relationship to tumor suppression and the onset of aging-related diseases. With the frequent discovery of new functions for lncRNAs, many more lncRNAs that regulate aging will undoubtedly be found. Nevertheless, many important questions regarding the roles of lncRNAs in aging and aging-related disorders remain. There appear to be discrepancies between reports of general up-regulation, down-regulation, and a mixture of both up- and down-regulation of lncRNAs during aging at the cell, tissue, and organism levels. It will thus be crucial to investigate whether different lncRNAs are activated or repressed in particular settings, such as whether an lncRNA can be globally activated in a tissue or specifically up- or down-regulated at the cellular level. Moreover, it is also important to note that not all lncRNAs whose expression levels are altered during aging or aging-related diseases necessarily play crucial roles during aging. Thus, functional studies of lncRNA knockouts or overexpression are required to provide direct evidence for the role of specific lnRNAs in regulating aging. Nevertheless, studies in mammalian models that constitutively or conditionally lack or overexpress lncRNAs will provide compelling evidence for any conserved aging mechanism mediated by lnRNAs. These studies would elucidate how individual lncRNAs contribute to tissue aging and possibly affect the mammalian lifespan. Additionally, in vivo analyses of knockouts or overexpression of lncRNA processing machinery would illustrate how alteration lncRNA function can affect the transition from replicating to senescent cells in various tissues. One particular challenge of these in vivo models might be to separate an aging phenotype from an aging-related sickness or disease. Nevertheless, a complete understanding of how lncRNAs modulate cellular senescence and affect aging of the entire animal will allow us to determine additional roles of lncRNAs in aging, as well as highlight the potential for therapeutic lncRNA delivery that might modulate aging and aging-related diseases.

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Conflict of interest statement

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The authors have no conflict of interests to declare. Acknowledgments

1511 We are grateful to colleagues in the field for their contributions 1512 to the work discussed here. We thank members of the Fu and Han’s 1513 laboratorys for critical reading and stimulating discussions during 1514 the preparation of this manuscript. We are also grateful to 1515 anonymous reviewers for their helpful and valuable comments on 1516 the manuscript. We regret that space constraints have prevented 1517 the citation of many relevant and important references. This 1518 Q3 research is supported by the Grants from the National Natural 1519 Science Foundation of China (No. 31201033 to XL, No. 31270820 1520 and No. 81230061 to WH, and No. 81121004 to XF) and the Grant 1521 from the Beijing Nova Program (No. Z141107001814104 to XL), 1522 and is partially supported by the Grant from National Basic Science 1523 and Development Programme of China (No. 2012CB518103 to 1524 WH).

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References [1] F.H. Crick, L. Barnett, S. Brenner, R.J. Watts-Tobin, General nature of the genetic code for proteins, Nature 192 (1961) 1227–1232. [2] C. Yanofsky, Establishing the triplet nature of the genetic code, Cell 128 (2007) 815–818. [3] J.S. Mattick, RNA regulation: a new genetics? Nature reviews, Genetics 5 (2004) 316–323. [4] E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J.P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J.C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra, E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin, W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer, L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx, S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J.F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer, J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives, J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D.R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H.M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proctor, R.M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D.R. Cox, M.V. Olson, R. Kaul, C. Raymond, N. Shimizu, K. Kawasaki, S. Minoshima, G.A. Evans, M. Athanasiou, R. Schultz, B.A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W.R. McCombie, M. de la Bastide, N. Dedhia, H. Blocker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J.A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D.G. Brown, C.B. Burge, L. Cerutti, H.C. Chen, D. Church, M. Clamp, R.R. Copley, T. Doerks, S.R. Eddy, E.E. Eichler, T.S. Furey, J. Galagan, J.G. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjakob, K. Hokamp, W. Jang, L.S. Johnson, T.A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W.J. Kent, P. Kitts, E.V. Koonin, I. Korf, D. Kulp, D. Lancet, T.M. Lowe, A. McLysaght, T. Mikkelsen, J.V. Moran, N. Mulder, V.J. Pollara, C.P. Ponting, G. Schuler, J. Schultz, G. Slater, A.F. Smit, E. Stupka, J. Szustakowski, D. Thierry-Mieg, J. Thierry-Mieg, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y.I. Wolf, K.H. Wolfe, S.P. Yang, R.F. Yeh, F. Collins, M.S. Guyer, J. Peterson, A. Felsenfeld, K.A. Wetterstrand, A. Patrinos, M.J. Morgan, P. de Jong, J.J. Catanese, K. Osoegawa, H. Shizuya, S. Choi, Y.J.C. Chen, International Human Genome Sequencing, Initial sequencing and analysis of the human genome, Nature 409 (2001) 860–921. [5] N. Maeda, T. Kasukawa, R. Oyama, J. Gough, M. Frith, P.G. Engstrom, B. Lenhard, R.N. Aturaliya, S. Batalov, K.W. Beisel, C.J. Bult, C.F. Fletcher, A.R. Forrest, M. Furuno, D. Hill, M. Itoh, M. Kanamori-Katayama, S. Katayama, M. Katoh, T. Kawashima, J. Quackenbush, T. Ravasi, B.Z. Ring, K. Shibata, K. Sugiura, Y. Takenaka, R.D. Teasdale, C.A. Wells, Y. Zhu, C. Kai, J. Kawai, D.A. Hume, P. Carninci, Y. Hayashizaki, Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs, PLoS Genet. 2 (2006) e62. [6] S. Djebali, C.A. Davis, A. Merkel, A. Dobin, T. Lassmann, A. Mortazavi, A. Tanzer, J. Lagarde, W. Lin, F. Schlesinger, C. Xue, G.K. Marinov, J. Khatun, B.A. Williams, C. Zaleski, J. Rozowsky, M. Roder, F. Kokocinski, R.F. Abdelhamid, T. Alioto, I. Antoshechkin, M.T. Baer, N.S. Bar, P. Batut, K. Bell, I. Bell, S. Chakrabortty, X. Chen, J. Chrast, J. Curado, T. Derrien, J. Drenkow, E. Dumais, J. Dumais, R. Duttagupta, E. Falconnet, M. Fastuca, K. Fejes-Toth, P. Ferreira, S. Foissac, M.J. Fullwood, H. Gao, D. Gonzalez, A. Gordon, H. Gunawardena, C. Howald, S. Jha, R. Johnson, P. Kapranov, B. King, C. Kingswood, O.J. Luo, E. Park, K. Persaud, J.B. Preall, P. Ribeca, B. Risk, D. Robyr, M. Sammeth, L. Schaffer, L.H. See, A. Shahab, J. Skancke, A.M. Suzuki, H. Takahashi, H. Tilgner, D. Trout, N. Walters, H. Wang, J. Wrobel, Y. Yu, X. Ruan, Y. Hayashizaki, J. Harrow, M. Gerstein, T. Hubbard, A. Reymond, S.E. Antonarakis, G. Hannon, M.C. Giddings, Y. Ruan, B. Wold, P. Carninci, R. Guigo, T.R. Gingeras, Landscape of transcription in human cells, Nature 489 (2012) 101–108. [7] R.J. Taft, M. Pheasant, J.S. Mattick, The relationship between non-protein-coding DNA and eukaryotic complexity, BioEssays 29 (2007) 288–299. [8] V. Ambros, The functions of animal microRNAs, Nature 431 (2004) 350–355. [9] T.R. Mercer, M.E. Dinger, J.S. Mattick, Long non-coding RNAs: insights into functions, Nat. Rev. Genet. 10 (2009) 155–159. [10] X. Li, Z. Wu, X. Fu, W. Han, Long noncoding RNAs: insights from biological features and functions to diseases, Med. Res. Rev. 33 (2013) 517–553. [11] T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, D.G. Knowles, J. Lagarde, L. Veeravalli, X. Ruan, Y. Ruan, T. Lassmann, P. Carninci, J.B. Brown, L. Lipovich, J.M. Gonzalez, M. Thomas, C.A. Davis, R. Shiekhattar, T.R. Gingeras, T.J. Hubbard, C. Notredame, J. Harrow, R. Guigo, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res. 22 (2012) 1775–1789. [12] I. Ulitsky, A. Shkumatava, C.H. Jan, H. Sive, D.P. Bartel, Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution, Cell 147 (2011) 1537–1550.


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[13] M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, E.S. Lander, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature 458 (2009) 223–227. [14] M. Guttman, M. Garber, J.Z. Levin, J. Donaghey, J. Robinson, X. Adiconis, L. Fan, M.J. Koziol, A. Gnirke, C. Nusbaum, J.L. Rinn, E.S. Lander, A. Regev, Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs, Nat. Biotechnol. 28 (2010) 503–510. [15] D.H. Chitwood, M.C. Timmermans, Small RNAs are on the move, Nature 467 (2010) 415–419. [16] D.P. Bartel, MicroRNAs: target recognition and regulatory functions, Cell 136 (2009) 215–233. [17] E. Bernstein, C.D. Allis, RNA meets chromatin, Genes Dev. 19 (2005) 1635–1655. [18] J. Ponjavic, C.P. Ponting, G. Lunter, Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs, Genome Res. 17 (2007) 556–565. [19] R. Louro, A.S. Smirnova, S. Verjovski-Almeida, Long intronic noncoding RNA transcription: expression noise or expression choice? Genomics 93 (2009) 291–298. [20] J.L. Rinn, H.Y. Chang, Genome regulation by long noncoding RNAs, Annu. Rev. Biochem. 81 (2012) 145–166. [21] P.J. Batista, H.Y. Chang, Long noncoding RNAs: cellular address codes in development and disease, Cell 152 (2013) 1298–1307. [22] M. Guttman, J.L. Rinn, Modular regulatory principles of large non-coding RNAs, Nature 482 (2012) 339–346. [23] D.C. Zappulla, T.R. Cech, RNA as a flexible scaffold for proteins: yeast telomerase and beyond, Cold Spring Harb. Symp. Quant. Biol. 71 (2006) 217–224. [24] D.C. Zappulla, T.R. Cech, Yeast telomerase RNA: a flexible scaffold for protein subunits, Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 10024–10029. [25] M.C. Tsai, O. Manor, Y. Wan, N. Mosammaparast, J.K. Wang, F. Lan, Y. Shi, E. Segal, H.Y. Chang, Long noncoding RNA as modular scaffold of histone modification complexes, Science 329 (2010) 689–693. [26] A. Wutz, T.P. Rasmussen, R. Jaenisch, Chromosomal silencing and localization are mediated by different domains of Xist RNA, Nat. Genet. 30 (2002) 167–174. [27] O. Wapinski, H.Y. Chang, Long noncoding RNAs and human disease, Trends Cell Biol. 21 (2011) 354–361. [28] W. Hu, J.R. Alvarez-Dominguez, H.F. Lodish, Regulation of mammalian cell differentiation by long non-coding RNAs, EMBO Rep. 13 (2012) 971–983. [29] C.P. Ponting, P.L. Oliver, W. Reik, Evolution and functions of long noncoding RNAs, Cell 136 (2009) 629–641. [30] L.A. Hindorff, P. Sethupathy, H.A. Junkins, E.M. Ramos, J.P. Mehta, F.S. Collins, T.A. Manolio, Potential etiologic and functional implications of genome-wide association loci for human diseases and traits, Proc. Natl. Acad. Sci. U.S.A. 106 (2009) 9362–9367. [31] M.T. Maurano, R. Humbert, E. Rynes, R.E. Thurman, E. Haugen, H. Wang, A.P. Reynolds, R. Sandstrom, H. Qu, J. Brody, A. Shafer, F. Neri, K. Lee, T. Kutyavin, S. Stehling-Sun, A.K. Johnson, T.K. Canfield, E. Giste, M. Diegel, D. Bates, R.S. Hansen, S. Neph, P.J. Sabo, S. Heimfeld, A. Raubitschek, S. Ziegler, C. Cotsapas, N. Sotoodehnia, I. Glass, S.R. Sunyaev, R. Kaul, J.A. Stamatoyannopoulos, Systematic localization of common disease-associated variation in regulatory DNA, Science 337 (2012) 1190–1195. [32] M.J. Hangauer, I.W. Vaughn, M.T. McManus, Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs, PLoS Genet. 9 (2013) e1003569. [33] J.C. Scheuermann, L.A. Boyer, Getting to the heart of the matter: long non-coding RNAs in cardiac development and disease, EMBO J. 32 (2013) 1805–1816. [34] S.W. Cheetham, F. Gruhl, J.S. Mattick, M.E. Dinger, Long noncoding RNAs and the genetics of cancer, Br. J. Cancer 108 (2013) 2419–2425. [35] A.L. Brunner, A.H. Beck, B. Edris, R.T. Sweeney, S.X. Zhu, R. Li, K. Montgomery, S. Varma, T. Gilks, X. Guo, J.W. Foley, D.M. Witten, C.P. Giacomini, R.A. Flynn, J.R. Pollack, R. Tibshirani, H.Y. Chang, M. van de Rijn, R.B. West, Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers, Genome Biol. 13 (2012) R75. [36] M.A. Faghihi, F. Modarresi, A.M. Khalil, D.E. Wood, B.G. Sahagan, T.E. Morgan, C.E. Finch, G. St Laurent III, Kenny P.J., C. Wahlestedt, Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase, Nat. Med. 14 (2008) 723–730. [37] I.A. Qureshi, M.F. Mehler, Non-coding RNA networks underlying cognitive disorders across the lifespan, Trends Mol. Med. 17 (2011) 337–346. [38] I. Moran, I. Akerman, M. van de Bunt, R. Xie, M. Benazra, T. Nammo, L. Arnes, N. Nakic, J. Garcia-Hurtado, S. Rodriguez-Segui, L. Pasquali, C. Sauty-Colace, A. Beucher, R. Scharfmann, J. van Arensbergen, P.R. Johnson, A. Berry, C. Lee, T. Harkins, V. Gmyr, F. Pattou, J. Kerr-Conte, L. Piemonti, T. Berney, N. Hanley, A.L. Gloyn, L. Sussel, L. Langman, K.L. Brayman, M. Sander, M.I. McCarthy, P. Ravassard, J. Ferrer, Human beta cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes, Cell Metab. 16 (2012) 435–448. [39] N. Schonrock, R.P. Harvey, J.S. Mattick, Long noncoding RNAs in cardiac development and pathophysiology, Circ. Res. 111 (2012) 1349–1362. [40] Y. Fradet, F. Saad, A. Aprikian, J. Dessureault, M. Elhilali, C. Trudel, B. Masse, L.C. Piche, Chypre, uPM3, a new molecular urine test for the detection of prostate cancer, Urology 64 (2004) 311–315, discussion 315–316. [41] S.B. Shappell, Clinical utility of prostate carcinoma molecular diagnostic tests, Rev. Urol. 10 (2008) 44–69.

[42] M. Tinzl, M. Marberger, S. Horvath, C. Chypre, DD3PCA3 RNA analysis in urine—a new perspective for detecting prostate cancer, Eur. Urol. 46 (2004) 182–186, discussion 187. [43] F. Modarresi, M.A. Faghihi, M.A. Lopez-Toledano, R.P. Fatemi, M. Magistri, S.P. Brothers, M.P. van der Brug, C. Wahlestedt, Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation, Nat. Biotechnol. 30 (2012) 453–459. [44] T.M. Wheeler, A.J. Leger, S.K. Pandey, A.R. MacLeod, M. Nakamori, S.H. Cheng, B.M. Wentworth, C.F. Bennett, C.A. Thornton, Targeting nuclear RNA for in vivo correction of myotonic dystrophy, Nature 488 (2012) 111–115. [45] G. Egger, G. Liang, A. Aparicio, P.A. Jones, Epigenetics in human disease and prospects for epigenetic therapy, Nature 429 (2004) 457–463. [46] K. Helin, D. Dhanak, Chromatin proteins and modifications as drug targets, Nature 502 (2013) 480–488. [47] M. Guttman, J. Donaghey, B.W. Carey, M. Garber, J.K. Grenier, G. Munson, G. Young, A.B. Lucas, R. Ach, L. Bruhn, X. Yang, I. Amit, A. Meissner, A. Regev, J.L. Rinn, D.E. Root, E.S. Lander, lincRNAs act in the circuitry controlling pluripotency and differentiation, Nature 477 (2011) 295–300. [48] S.C. Wu, E.M. Kallin, Y. Zhang, Role of H3K27 methylation in the regulation of lncRNA expression, Cell Res. 20 (2010) 1109–1116. [49] K.C. Wang, H.Y. Chang, Molecular mechanisms of long noncoding RNAs, Mol. Cell 43 (2011) 904–914. [50] J.S. Mattick, P.P. Amaral, M.E. Dinger, T.R. Mercer, M.F. Mehler, RNA regulation of epigenetic processes, BioEssays 31 (2009) 51–59. [51] A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, A. van Oudenaarden, A. Regev, E.S. Lander, J.L. Rinn, Many human large intergenic noncoding RNAs associate with chromatinmodifying complexes and affect gene expression, Proc. Natl. Acad. Sci. U.S.A. 106 (2009) 11667–11672. [52] B. Schuettengruber, A.M. Martinez, N. Iovino, G. Cavalli, Trithorax group proteins: switching genes on and keeping them active, Nat. Rev. Mol. Cell Biol. 12 (2011) 799–814. [53] A.P. Bracken, K. Helin, Polycomb group proteins: navigators of lineage pathways led astray in cancer, Nat. Rev. Cancer 9 (2009) 773–784. [54] R. Cao, L. Wang, H. Wang, L. Xia, H. Erdjument-Bromage, P. Tempst, R.S. Jones, Y. Zhang, Role of histone H3 lysine 27 methylation in Polycomb-group silencing, Science 298 (2002) 1039–1043. [55] A. Kuzmichev, K. Nishioka, H. Erdjument-Bromage, P. Tempst, D. Reinberg, Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein, Genes Dev. 16 (2002) 2893–2905. [56] N.D. Montgomery, D. Yee, A. Chen, S. Kalantry, S.J. Chamberlain, A.P. Otte, T. Magnuson, The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation, Curr. Biol. 15 (2005) 942–947. [57] F. Tie, C.A. Stratton, R.L. Kurzhals, P.J. Harte, The N terminus of Drosophila ESC binds directly to histone H3 and is required for E(Z)-dependent trimethylation of H3 lysine 27, Mol. Cell. Biol. 27 (2007) 2014–2026. [58] R. Margueron, N. Justin, K. Ohno, M.L. Sharpe, J. Son, W.J. Drury III, P. Voigt, S.R. Martin, W.R. Taylor, V. De Marco, V. Pirrotta, D. Reinberg, S.J. Gamblin, Role of the polycomb protein EED in the propagation of repressive histone marks, Nature 461 (2009) 762–767. [59] D. Pasini, A.P. Bracken, M.R. Jensen, E. Lazzerini Denchi, K. Helin, Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity, EMBO J. 23 (2004) 4061–4071. [60] F.W. Schmitges, A.B. Prusty, M. Faty, A. Stutzer, G.M. Lingaraju, J. Aiwazian, R. Sack, D. Hess, L. Li, S. Zhou, R.D. Bunker, U. Wirth, T. Bouwmeester, A. Bauer, N. Ly-Hartig, K. Zhao, H. Chan, J. Gu, H. Gut, W. Fischle, J. Muller, N.H. Thoma, Histone methylation by PRC2 is inhibited by active chromatin marks, Mol. Cell 42 (2011) 330–341. [61] B. Payer, J.T. Lee, X chromosome dosage compensation: how mammals keep the balance, Annu. Rev. Genet. 42 (2008) 733–772. [62] J.T. Lee, M.S. Bartolomei, X-inactivation, imprinting, and long noncoding RNAs in health and disease, Cell 152 (2013) 1308–1323. [63] D. Lessing, M.C. Anguera, J.T. Lee, X chromosome inactivation and epigenetic responses to cellular reprogramming, Annu. Rev. Genomics Hum. Genet. 14 (2013) 85–110. [64] J.T. Lee, Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome, Genes Dev. 23 (2009) 1831–1842. [65] J.T. Lee, Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control, Nat. Rev. Mol. Cell Biol. 12 (2011) 815–826. [66] E. Splinter, E. de Wit, E.P. Nora, P. Klous, H.J. van de Werken, Y. Zhu, L.J. Kaaij, W. van Ijcken, J. Gribnau, E. Heard, W. de Laat, The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA, Genes Dev. 25 (2011) 1371–1383. [67] E.P. Nora, B.R. Lajoie, E.G. Schulz, L. Giorgetti, I. Okamoto, N. Servant, T. Piolot, N.L. van Berkum, J. Meisig, J. Sedat, J. Gribnau, E. Barillot, N. Bluthgen, J. Dekker, E. Heard, Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature 485 (2012) 381–385. [68] Y. Jeon, J.T. Lee, YY1 tethers Xist RNA to the inactive X nucleation center, Cell 146 (2011) 119–133. [69] J.M. Engreitz, A. Pandya-Jones, P. McDonel, A. Shishkin, K. Sirokman, C. Surka, S. Kadri, J. Xing, A. Goren, E.S. Lander, K. Plath, M. Guttman, The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome, Science 341 (2013) 1237973. [70] J. Zhao, B.K. Sun, J.A. Erwin, J.J. Song, J.T. Lee, Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome, Science 322 (2008) 750–756.


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[71] J.T. Lee, Disruption of imprinted X inactivation by parent-of-origin effects at Tsix, Cell 103 (2000) 17–27. [72] T. Sado, Z. Wang, H. Sasaki, E. Li, Regulation of imprinted X-chromosome inactivation in mice by Tsix, Development 128 (2001) 1275–1286. [73] D. Tian, S. Sun, J.T. Lee, The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation, Cell 143 (2010) 390–403. [74] S. Sun, B.C. Del Rosario, A. Szanto, Y. Ogawa, Y. Jeon, J.T. Lee, Jpx RNA activates Xist by evicting CTCF, Cell 153 (2013) 1537–1551. [75] F.M. Pauler, M.V. Koerner, D.P. Barlow, Silencing by imprinted noncoding RNAs: is transcription the answer? Trends Genet. 23 (2007) 284–292. [76] G.V. Fitzpatrick, P.D. Soloway, M.J. Higgins, Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1, Nat. Genet. 32 (2002) 426–431. [77] F. Sleutels, R. Zwart, D.P. Barlow, The non-coding Air RNA is required for silencing autosomal imprinted genes, Nature 415 (2002) 810–813. [78] D. Mancini-Dinardo, S.J. Steele, J.M. Levorse, R.S. Ingram, S.M. Tilghman, Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes, Genes Dev. 20 (2006) 1268–1282. [79] T. Nagano, J.A. Mitchell, L.A. Sanz, F.M. Pauler, A.C. Ferguson-Smith, R. Feil, P. Fraser, The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin, Science 322 (2008) 1717–1720. [80] R.R. Pandey, T. Mondal, F. Mohammad, S. Enroth, L. Redrup, J. Komorowski, T. Nagano, D. Mancini-Dinardo, C. Kanduri, Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation, Mol. Cell 32 (2008) 232–246. [81] P.A. Latos, F.M. Pauler, M.V. Koerner, H.B. Senergin, Q.J. Hudson, R.R. Stocsits, W. Allhoff, S.H. Stricker, R.M. Klement, K.E. Warczok, K. Aumayr, P. Pasierbek, D.P. Barlow, Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing, Science 338 (2012) 1469–1472. [82] J. Colin, D. Libri, O. Porrua, Cryptic transcription and early termination in the control of gene expression, Genet. Res. Int. 2011 (2011) 653494. [83] J.L. Rinn, M. Kertesz, J.K. Wang, S.L. Squazzo, X. Xu, S.A. Brugmann, L.H. Goodnough, J.A. Helms, P.J. Farnham, E. Segal, H.Y. Chang, Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs, Cell 129 (2007) 1311–1323. [84] R.A. Gupta, N. Shah, K.C. Wang, J. Kim, H.M. Horlings, D.J. Wong, M.C. Tsai, T. Hung, P. Argani, J.L. Rinn, Y. Wang, P. Brzoska, B. Kong, R. Li, R.B. West, M.J. van de Vijver, S. Sukumar, H.Y. Chang, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature 464 (2010) 1071–1076. [85] P. Schorderet, D. Duboule, Structural and functional differences in the long noncoding RNA hotair in mouse and human, PLoS Genet. 7 (2011) e1002071. [86] K.C. Wang, Y.W. Yang, B. Liu, A. Sanyal, R. Corces-Zimmerman, Y. Chen, B.R. Lajoie, A. Protacio, R.A. Flynn, R.A. Gupta, J. Wysocka, M. Lei, J. Dekker, J.A. Helms, H.Y. Chang, A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression, Nature 472 (2011) 120–124. [87] S. Bertani, S. Sauer, E. Bolotin, F. Sauer, The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin, Mol. Cell 43 (2011) 1040–1046. [88] J. Feng, C. Bi, B.S. Clark, R. Mady, P. Shah, J.D. Kohtz, The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator, Genes Dev. 20 (2006) 1470–1484. [89] A.M. Bond, M.J. Vangompel, E.A. Sametsky, M.F. Clark, J.C. Savage, J.F. Disterhoft, J.D. Kohtz, Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry, Nat. Neurosci. 12 (2009) 1020–1027. [90] I. Shamovsky, M. Ivannikov, E.S. Kandel, D. Gershon, E. Nudler, RNA-mediated response to heat shock in mammalian cells, Nature 440 (2006) 556–560. [91] R.B. Lanz, N.J. McKenna, S.A. Onate, U. Albrecht, J. Wong, S.Y. Tsai, M.J. Tsai, B.W. O’Malley, A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex, Cell, 97 (1999) 17–27. [92] T. Kino, D.E. Hurt, T. Ichijo, N. Nader, G.P. Chrousos, Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor, Sci. Signal. 3 (2010) ra8. [93] U.A. Ørom, T. Derrien, M. Beringer, K. Gumireddy, A. Gardini, G. Bussotti, F. Lai, M. Zytnicki, C. Notredame, Q. Huang, R. Guigo, R. Shiekhattar, Long noncoding RNAs with enhancer-like function in human cells, Cell 143 (2010) 46–58. [94] X. Wang, S. Arai, X. Song, D. Reichart, K. Du, G. Pascual, P. Tempst, M.G. Rosenfeld, C.K. Glass, R. Kurokawa, Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription, Nature 454 (2008) 126–130. [95] T.A. Ayoubi, W.J. Van De Ven, Regulation of gene expression by alternative promoters, FASEB J. 10 (1996) 453–460. [96] I. Martianov, A. Ramadass, A. Serra Barros, N. Chow, A. Akoulitchev, Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript, Nature 445 (2007) 666–670. [97] M.J. Moore, From birth to death: the complex lives of eukaryotic mRNAs, Science 309 (2005) 1514–1518. [98] G.W. Krystal, B.C. Armstrong, J.F. Battey, N-myc mRNA forms an RNA–RNA duplex with endogenous antisense transcripts, Mol. Cell. Biol. 10 (1990) 4180–4191. [99] K. Li, Y. Blum, A. Verma, Z. Liu, K. Pramanik, N.R. Leigh, C.Z. Chun, G.V. Samant, B. Zhao, M.K. Garnaas, M.A. Horswill, S.A. Stanhope, P.E. North, R.Q. Miao, G.A. Wilkinson, M. Affolter, R. Ramchandran, A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo, Blood 115 (2010) 133–139. [100] S.H. Munroe, M.A. Lazar, Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA, J. Biol. Chem. 266 (1991) 22083–22086. [101] M.L. Hastings, C. Milcarek, K. Martincic, M.L. Peterson, S.H. Munroe, Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative

[102]

[103]

[104] [105] [106]

[107] [108]

[109]

[110]

[111]

[112]

[113] [114]

[115]

[116]

[117]

[118]

[119]

[120]

[121] [122]

[123]

[124] [125]

[126]

[127]

[128]

19

mRNA processing is independent of differentiation but correlates with antisense RNA levels, Nucleic Acids Res. 25 (1997) 4296–4300. M. Beltran, I. Puig, C. Pena, J.M. Garcia, A.B. Alvarez, R. Pena, F. Bonilla, A.G. de Herreros, A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial–mesenchymal transition, Genes Dev. 22 (2008) 756–769. Y. Jiang, K.A. Mullaney, C.M. Peterhoff, S. Che, S.D. Schmidt, A. Boyer-Boiteau, S.D. Ginsberg, A.M. Cataldo, P.M. Mathews, R.A. Nixon, Alzheimer’s-related endosome dysfunction in Down syndrome is Abeta-independent but requires APP and is reversed by BACE-1 inhibition, Proc. Natl. Acad. Sci. U.S.A. 107 (2010) 1630–1635. B.J. Blencowe, Alternative splicing: new insights from global analyses, Cell 126 (2006) 37–47. J.C. Long, J.F. Caceres, The SR protein family of splicing factors: master regulators of gene expression, Biochem. J. 417 (2009) 15–27. V. Tripathi, J.D. Ellis, Z. Shen, D.Y. Song, Q. Pan, A.T. Watt, S.M. Freier, C.F. Bennett, A. Sharma, P.A. Bubulya, B.J. Blencowe, S.G. Prasanth, K.V. Prasanth, The nuclearretained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation, Mol. Cell 39 (2010) 925–938. H.A. Hundley, B.L. Bass, ADAR editing in double-stranded UTRs and other noncoding RNA sequences, Trends Biochem. Sci. 35 (2010) 377–383. C.M. Clemson, J.N. Hutchinson, S.A. Sara, A.W. Ensminger, A.H. Fox, A. Chess, J.B. Lawrence, An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles, Mol. Cell 33 (2009) 717–726. C. Carrieri, L. Cimatti, M. Biagioli, A. Beugnet, S. Zucchelli, S. Fedele, E. Pesce, I. Ferrer, L. Collavin, C. Santoro, A.R. Forrest, P. Carninci, S. Biffo, E. Stupka, S. Gustincich, Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat, Nature 491 (2012) 454–457. Y. Liu, L. Fallon, H.A. Lashuel, Z. Liu, P.T. Lansbury Jr., The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson’s disease susceptibility, Cell 111 (2002) 209–218. M. Nishizawa, T. Komai, Y. Katou, K. Shirahige, T. Ito, E.A. Toh, Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast, PLoS Biol. 6 (2008) 2817–2830. A.T. Willingham, A.P. Orth, S. Batalov, E.C. Peters, B.G. Wen, P. Aza-Blanc, J.B. Hogenesch, P.G. Schultz, A strategy for probing the function of noncoding RNAs finds a repressor of NFAT, Science 309 (2005) 1570–1573. L. Salmena, L. Poliseno, Y. Tay, L. Kats, P.P. Pandolfi, A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146 (2011) 353–358. J.M. Franco-Zorrilla, A. Valli, M. Todesco, I. Mateos, M.I. Puga, I. Rubio-Somoza, A. Leyva, D. Weigel, J.A. Garcia, J. Paz-Ares, Target mimicry provides a new mechanism for regulation of microRNA activity, Nat. Genet. 39 (2007) 1033–1037. L. Poliseno, L. Salmena, J. Zhang, B. Carver, W.J. Haveman, P.P. Pandolfi, A codingindependent function of gene and pseudogene mRNAs regulates tumour biology, Nature 465 (2010) 1033–1038. M. Cesana, D. Cacchiarelli, I. Legnini, T. Santini, O. Sthandier, M. Chinappi, A. Tramontano, I. Bozzoni, A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA, Cell 147 (2011) 358–369. J. Wang, X. Liu, H. Wu, P. Ni, Z. Gu, Y. Qiao, N. Chen, F. Sun, Q. Fan, CREB upregulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer, Nucleic Acids Res. 38 (2010) 5366–5383. A.N. Kallen, X.B. Zhou, J. Xu, C. Qiao, J. Ma, L. Yan, L. Lu, C. Liu, J.S. Yi, H. Zhang, W. Min, A.M. Bennett, R.I. Gregory, Y. Ding, Y. Huang, The imprinted H19 lncRNA antagonizes let-7 microRNAs, Mol. Cell 52 (2013) 101–112. T.B. Hansen, T.I. Jensen, B.H. Clausen, J.B. Bramsen, B. Finsen, C.K. Damgaard, J. Kjems, Natural RNA circles function as efficient microRNA sponges, Nature 495 (2013) 384–388. S. Memczak, M. Jens, A. Elefsinioti, F. Torti, J. Krueger, A. Rybak, L. Maier, S.D. Mackowiak, L.H. Gregersen, M. Munschauer, A. Loewer, U. Ziebold, M. Landthaler, C. Kocks, F. le Noble, N. Rajewsky, Circular RNAs are a large class of animal RNAs with regulatory potency, Nature 495 (2013) 333–338. D. Baek, J. Villen, C. Shin, F.D. Camargo, S.P. Gygi, D.P. Bartel, The impact of microRNAs on protein output, Nature 455 (2008) 64–71. S. Twayana, I. Legnini, M. Cesana, D. Cacchiarelli, M. Morlando, I. Bozzoni, Biogenesis and function of non-coding RNAs in muscle differentiation and in Duchenne muscular dystrophy, Biochem. Soc. Trans. 41 (2013) 844–849. K.C. Wang, J.A. Helms, H.Y. Chang, Regeneration, repair and remembering identity: the three Rs of Hox gene expression, Trends Cell Biol. 19 (2009) 268–275. D. Lemons, W. McGinnis, Genomic evolution of Hox gene clusters, Science 313 (2006) 1918–1922. M. Huarte, M. Guttman, D. Feldser, M. Garber, M.J. Koziol, D. Kenzelmann-Broz, A.M. Khalil, O. Zuk, I. Amit, M. Rabani, L.D. Attardi, A. Regev, E.S. Lander, T. Jacks, J.L. Rinn, A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response, Cell 142 (2010) 409–419. T. Hung, Y. Wang, M.F. Lin, A.K. Koegel, Y. Kotake, G.D. Grant, H.M. Horlings, N. Shah, C. Umbricht, P. Wang, Y. Wang, B. Kong, A. Langerod, A.L. Borresen-Dale, S.K. Kim, M. van de Vijver, S. Sukumar, M.L. Whitfield, M. Kellis, Y. Xiong, D.J. Wong, H.Y. Chang, Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters, Nat. Genet. 43 (2011) 621–629. L. Yang, C. Lin, W. Liu, J. Zhang, K.A. Ohgi, J.D. Grinstein, P.C. Dorrestein, M.G. Rosenfeld, ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs, Cell 147 (2011) 773–788. R.C. Spitale, M.C. Tsai, H.Y. Chang, RNA templating the epigenome: long noncoding RNAs as molecular scaffolds, Epigenetics 6 (2011) 539–543.


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[129] M.C. Good, J.G. Zalatan, W.A. Lim, Scaffold proteins: hubs for controlling the flow of cellular information, Science 332 (2011) 680–686. [130] A. Zeke, M. Lukacs, W.A. Lim, A. Remenyi, Scaffolds: interaction platforms for cellular signalling circuits, Trends Cell Biol. 19 (2009) 364–374. [131] K. Collins, Physiological assembly and activity of human telomerase complexes, Mech. Ageing Dev. 129 (2008) 91–98. [132] C. Chu, K. Qu, F.L. Zhong, S.E. Artandi, H.Y. Chang, Genomic maps of long noncoding RNA occupancy reveal principles of RNA–chromatin interactions, Mol. Cell 44 (2011) 667–678. [133] K.L. Yap, S. Li, A.M. Munoz-Cabello, S. Raguz, L. Zeng, S. Mujtaba, J. Gil, M.J. Walsh, M.M. Zhou, Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a, Mol. Cell 38 (2010) 662–674. [134] Y. Kotake, T. Nakagawa, K. Kitagawa, S. Suzuki, N. Liu, M. Kitagawa, Y. Xiong, Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene, Oncogene 30 (2011) 1956–1962. [135] A.M. Khalil, J.L. Rinn, RNA–protein interactions in human health and disease, Semin. Cell Dev. Biol. 22 (2011) 359–365. [136] M.J. Koziol, J.L. Rinn, RNA traffic control of chromatin complexes, Curr. Opin. Genet. Dev. 20 (2010) 142–148. [137] F.J. Liu, T. Wen, L. Liu, MicroRNAs as a novel cellular senescence regulator, Ageing Res. Rev. 11 (2012) 41–50. [138] C.W. Gourlay, K.R. Ayscough, The actin cytoskeleton: a key regulator of apoptosis and ageing? Nat. Rev. Mol. Cell Biol. 6 (2005) 583–589. [139] M.F. Mehler, J.S. Mattick, Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease, Physiol. Rev. 87 (2007) 799–823. [140] I.A. Qureshi, M.F. Mehler, Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease, Nat. Rev. Neurosci. 13 (2012) 528–541. [141] F. Aguilo, M.M. Zhou, M.J. Walsh, Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression, Cancer Res. 71 (2011) 5365–5369. [142] K. Abdelmohsen, A. Panda, M.J. Kang, J. Xu, R. Selimyan, J.H. Yoon, J.L. Martindale, S. De, W.H. Wood III, K.G. Becker, M. Gorospe, Senescence-associated lncRNAs: senescence-associated long noncoding RNAs, Aging Cell 12 (2013) 890–900. [143] V. Tripathi, Z. Shen, A. Chakraborty, S. Giri, S.M. Freier, X. Wu, Y. Zhang, M. Gorospe, S.G. Prasanth, A. Lal, K.V. Prasanth, Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB, PLoS Genet. 9 (2013) e1003368. [144] R. Zoncu, A. Efeyan, D.M. Sabatini, mTOR: from growth signal integration to cancer, diabetes and ageing, Nat. Rev. Mol. Cell Biol. 12 (2011) 21–35. [145] B. Gan, E. Sahin, S. Jiang, A. Sanchez-Aguilera, K.L. Scott, L. Chin, D.A. Williams, D.J. Kwiatkowski, R.A. DePinho, mTORC1-dependent and -independent regulation of stem cell renewal, differentiation, and mobilization, Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 19384–19389. [146] C. Chen, Y. Liu, R. Liu, T. Ikenoue, K.L. Guan, Y. Liu, P. Zheng, TSC-mTOR maintains quiescence and function of hematopoietic stem cells by repressing mitochondrial biogenesis and reactive oxygen species, J. Exp. Med. 205 (2008) 2397–2408. [147] D.E. Harrison, R. Strong, Z.D. Sharp, J.F. Nelson, C.M. Astle, K. Flurkey, N.L. Nadon, J.E. Wilkinson, K. Frenkel, C.S. Carter, M. Pahor, M.A. Javors, E. Fernandez, R.A. Miller, Rapamycin fed late in life extends lifespan in genetically heterogeneous mice, Nature 460 (2009) 392–395. [148] I. Bjedov, J.M. Toivonen, F. Kerr, C. Slack, J. Jacobson, A. Foley, L. Partridge, Mechanisms of life span extension by rapamycin in the fruit fly Drosophila melanogaster, Cell Metab. 11 (2010) 35–46. [149] J. Choi, A.I. Levey, S.T. Weintraub, H.D. Rees, M. Gearing, L.S. Chin, L. Li, Oxidative modifications and down-regulation of ubiquitin carboxyl-terminal hydrolase L1 associated with idiopathic Parkinson’s and Alzheimer’s diseases, J. Biol. Chem. 279 (2004) 13256–13264. [150] T.A. Rando, H.Y. Chang, Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock, Cell 148 (2012) 46–57. [151] I.A. Qureshi, J.S. Mattick, M.F. Mehler, Long non-coding RNAs in nervous system function and disease, Brain Res. 1338 (2010) 20–35. [152] E. Mus, P.R. Hof, H. Tiedge, Dendritic BC200 RNA in aging and in Alzheimer’s disease, Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 10679–10684. [153] J. Zhong, S.C. Chuang, R. Bianchi, W. Zhao, H. Lee, A.A. Fenton, R.K. Wong, H. Tiedge, BC1 regulation of metabotropic glutamate receptor-mediated neuronal excitability, J. Neurosci. 29 (2009) 9977–9986. [154] B.V. Skryabin, V. Sukonina, U. Jordan, L. Lewejohann, N. Sachser, I. Muslimov, H. Tiedge, J. Brosius, Neuronal untranslated BC1 RNA: targeted gene elimination in mice, Mol. Cell. Biol. 23 (2003) 6435–6441. [155] D. Centonze, S. Rossi, I. Napoli, V. Mercaldo, C. Lacoux, F. Ferrari, M.T. Ciotti, V. De Chiara, C. Prosperetti, M. Maccarrone, F. Fezza, P. Calabresi, G. Bernardi, C. Bagni, The brain cytoplasmic RNA BC1 regulates dopamine D2 receptor-mediated transmission in the striatum, J. Neurosci. 27 (2007) 8885–8892. [156] F. Modarresi, M.A. Faghihi, N.S. Patel, B.G. Sahagan, C. Wahlestedt, M.A. LopezToledano, Knockdown of BACE1-AS nonprotein-coding transcript modulates beta-amyloid-related hippocampal neurogenesis, Int. J. Alzheimer’s Dis. 2011 (2011) 929042. [157] K. Sato, H. Nakagawa, A. Tajima, K. Yoshida, I. Inoue, ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1, Oncol. Rep. 24 (2010) 701–707. [158] L.M. Holdt, F. Beutner, M. Scholz, S. Gielen, G. Gabel, H. Bergert, G. Schuler, J. Thiery, D. Teupser, ANRIL expression is associated with atherosclerosis risk at chromosome 9p21, Arterioscler. Thromb. Vasc. Biol. 30 (2010) 620–627.

[159] A. Congrains, K. Kamide, T. Katsuya, O. Yasuda, R. Oguro, K. Yamamoto, M. Ohishi, H. Rakugi, CVD-associated non-coding RNA, ANRIL, modulates expression of atherogenic pathways in VSMC, Biochem. Biophys. Res. Commun. 419 (2012) 612–616. [160] H.M. Broadbent, J.F. Peden, S. Lorkowski, A. Goel, H. Ongen, F. Green, R. Clarke, R. Collins, M.G. Franzosi, G. Tognoni, U. Seedorf, S. Rust, P. Eriksson, A. Hamsten, M. Farrall, H. Watkins, PROCARDIS consortium, Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p, Hum. Mol. Genet. 17 (2008) 806–814. [161] R. Johnson, N. Richter, R. Jauch, P.M. Gaughwin, C. Zuccato, E. Cattaneo, L.W. Stanton, The human accelerated region 1 noncoding RNA is repressed by REST in Huntington’s disease, Physiol. Genomics (2010). [162] K. Yamasaki, K. Joh, T. Ohta, H. Masuzaki, T. Ishimaru, T. Mukai, N. Niikawa, M. Ogawa, J. Wagstaff, T. Kishino, Neurons but not glial cells show reciprocal imprinting of sense and antisense transcripts of Ube3a, Hum. Mol. Genet. 12 (2003) 837–847. [163] L. Meng, R.E. Person, A.L. Beaudet, Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a, Hum. Mol. Genet. 21 (2012) 3001–3012. [164] M. Landers, M.A. Calciano, D. Colosi, H. Glatt-Deeley, J. Wagstaff, M. Lalande, Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans, Nucleic Acids Res. 33 (2005) 3976–3984. [165] S. Massone, I. Vassallo, G. Fiorino, M. Castelnuovo, F. Barbieri, R. Borghi, M. Tabaton, M. Robello, E. Gatta, C. Russo, T. Florio, G. Dieci, R. Cancedda, A. Pagano, 17A, a novel non-coding RNA, regulates GABA B alternative splicing and signaling in response to inflammatory stimuli and in Alzheimer disease, Neurobiol. Dis. 41 (2011) 308–317. [166] R.S. Yadava, C.D. Frenzel-McCardell, Q. Yu, V. Srinivasan, A.L. Tucker, J. Puymirat, C.A. Thornton, O.W. Prall, R.P. Harvey, M.S. Mahadevan, RNA toxicity in myotonic muscular dystrophy induces NKX2-5 expression, Nat. Genet. 40 (2008) 61–68. [167] M.S. Mahadevan, R.S. Yadava, Q. Yu, S. Balijepalli, C.D. Frenzel-McCardell, T.D. Bourne, L.H. Phillips, Reversible model of RNA toxicity and cardiac conduction defects in myotonic dystrophy, Nat. Genet. 38 (2006) 1066–1070. [168] M. Mahadevan, C. Tsilfidis, L. Sabourin, G. Shutler, C. Amemiya, G. Jansen, C. Neville, M. Narang, J. Barcelo, K. O’Hoy, et al., Myotonic dystrophy mutation: an unstable CTG repeat in the 30 untranslated region of the gene, Science 255 (1992) 1253–1255. [169] F. Friedrichs, C. Zugck, G.J. Rauch, B. Ivandic, D. Weichenhan, M. Muller-Bardorff, B. Meder, N.E. El Mokhtari, V. Regitz-Zagrosek, R. Hetzer, A. Schafer, S. Schreiber, J. Chen, I. Neuhaus, R. Ji, N.O. Siemers, N. Frey, W. Rottbauer, H.A. Katus, M. Stoll, HBEGF, SRA1, and IK: three cosegregating genes as determinants of cardiomyopathy, Genome Res. 19 (2009) 395–403. [170] C. Cooper, D. Vincett, Y. Yan, M.K. Hamedani, Y. Myal, E. Leygue, Steroid receptor RNA activator bi-faceted genetic system: heads or tails? Biochimie 93 (2011) 1973–1980. [171] S.M. Colley, P.J. Leedman, Steroid receptor RNA activator—a nuclear receptor coregulator with multiple partners: insights and challenges, Biochimie 93 (2011) 1966–1972. [172] H. Tsuiji, R. Yoshimoto, Y. Hasegawa, M. Furuno, M. Yoshida, S. Nakagawa, Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1, Genes Cells 16 (2011) 479–490. [173] N. Ishii, K. Ozaki, H. Sato, H. Mizuno, S. Saito, A. Takahashi, Y. Miyamoto, S. Ikegawa, N. Kamatani, M. Hori, S. Saito, Y. Nakamura, T. Tanaka, Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction, J. Hum. Genet. 51 (2006) 1087–1099. [174] L.J. Scott, K.L. Mohlke, L.L. Bonnycastle, C.J. Willer, Y. Li, W.L. Duren, M.R. Erdos, H.M. Stringham, P.S. Chines, A.U. Jackson, L. Prokunina-Olsson, C.J. Ding, A.J. Swift, N. Narisu, T. Hu, R. Pruim, R. Xiao, X.Y. Li, K.N. Conneely, N.L. Riebow, A.G. Sprau, M. Tong, P.P. White, K.N. Hetrick, M.W. Barnhart, C.W. Bark, J.L. Goldstein, L. Watkins, F. Xiang, J. Saramies, T.A. Buchanan, R.M. Watanabe, T.T. Valle, L. Kinnunen, G.R. Abecasis, E.W. Pugh, K.F. Doheny, R.N. Bergman, J. Tuomilehto, F.S. Collins, M. Boehnke, A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants, Science 316 (2007) 1341–1345. [175] J.A. Todd, N.M. Walker, J.D. Cooper, D.J. Smyth, K. Downes, V. Plagnol, R. Bailey, S. Nejentsev, S.F. Field, F. Payne, C.E. Lowe, J.S. Szeszko, J.P. Hafler, L. Zeitels, J.H. Yang, A. Vella, S. Nutland, H.E. Stevens, H. Schuilenburg, G. Coleman, M. Maisuria, W. Meadows, L.J. Smink, B. Healy, O.S. Burren, A.A. Lam, N.R. Ovington, J. Allen, E. Adlem, H.T. Leung, C. Wallace, J.M. Howson, C. Guja, C. IonescuTirgoviste, F. Genetics of Type 1 Diabetes in, M.J. Simmonds, J.M. Heward, S.C. Gough, C. Wellcome Trust Case Control, D.B. Dunger, L.S. Wicker, D.G. Clayton, Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes, Nat. Genet. 39 (2007) 857–864. [176] M. Murea, L. Lu, L. Ma, P.J. Hicks, J. Divers, C.W. McDonough, C.D. Langefeld, D.W. Bowden, B.I. Freedman, Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes, Am. J. Nephrol. 33 (2011) 502–509. [177] R.L. Hanson, D.W. Craig, M.P. Millis, K.A. Yeatts, S. Kobes, J.V. Pearson, A.M. Lee, W.C. Knowler, R.G. Nelson, J.K. Wolford, Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study, Diabetes 56 (2007) 975–983. [178] M.L. Alvarez, J.K. DiStefano, Functional characterization of the plasmacytoma variant translocation 1 gene (PVT1) in diabetic nephropathy, PLoS ONE 6 (2011) e18671.


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[179] X. Li, Z. Wu, Q. Mei, X. Li, M. Guo, X. Fu, W. Han, Long non-coding RNA HOTAIR, a driver of malignancy, predicts negative prognosis and exhibits oncogenic activity in oesophageal squamous cell carcinoma, Br. J. Cancer 109 (2013) 2266–2278. [180] S. Lottin, A.S. Vercoutter-Edouart, E. Adriaenssens, X. Czeszak, J. Lemoine, M. Roudbaraki, J. Coll, H. Hondermarck, T. Dugimont, J.J. Curgy, Thioredoxin posttranscriptional regulation by H19 provides a new function to mRNA-like noncoding RNA, Oncogene 21 (2002) 1625–1631. [181] D. Barsyte-Lovejoy, S.K. Lau, P.C. Boutros, F. Khosravi, I. Jurisica, I.L. Andrulis, M.S. Tsao, L.Z. Penn, The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis, Cancer Res. 66 (2006) 5330–5337. [182] L. Li, T. Feng, Y. Lian, G. Zhang, A. Garen, X. Song, Role of human noncoding RNAs in the control of tumorigenesis, Proc. Natl. Acad. Sci. U.S.A. 106 (2009) 12956–12961. [183] D. Khaitan, M.E. Dinger, J. Mazar, J. Crawford, M.A. Smith, J.S. Mattick, R.J. Perera, The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion, Cancer Res. 71 (2011) 3852–3862. [184] K. Tano, R. Mizuno, T. Okada, R. Rakwal, J. Shibato, Y. Masuo, K. Ijiri, N. Akimitsu, MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes, FEBS Lett. 584 (2010) 4575–4580. [185] R. Lin, S. Maeda, C. Liu, M. Karin, T.S. Edgington, A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas, Oncogene 26 (2007) 851–858. [186] P. Ji, S. Diederichs, W. Wang, S. Boing, R. Metzger, P.M. Schneider, N. Tidow, B. Brandt, H. Buerger, E. Bulk, M. Thomas, W.E. Berdel, H. Serve, C. Muller-Tidow, MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer, Oncogene 22 (2003) 8031–8041. [187] F. Guo, Y. Li, Y. Liu, J. Wang, Y. Li, G. Li, Inhibition of metastasis-associated lung adenocarcinoma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferation and invasion, Acta Biochim. Biophys. Sin. 42 (2010) 224–229. [188] Y. Zhou, X. Zhang, A. Klibanski, MEG3 noncoding RNA: a tumor suppressor, J. Mol. Endocrinol. 48 (2012) R45–R53. [189] V. Balik, J. Srovnal, I. Sulla, O. Kalita, T. Foltanova, M. Vaverka, L. Hrabalek, M. Hajduch, MEG3: a novel long noncoding potentially tumour-suppressing RNA in meningiomas, J. Neurooncol. 112 (2013) 1–8. [190] M. Mourtada-Maarabouni, M.R. Pickard, V.L. Hedge, F. Farzaneh, G.T. Williams, GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer, Oncogene 28 (2009) 195–208. [191] S.Y. Ng, L. Lin, B.S. Soh, L.W. Stanton, Long noncoding RNAs in development and disease of the central nervous system, Trends Genet. 29 (2013) 461–468. [192] R. Muddashetty, T. Khanam, A. Kondrashov, M. Bundman, A. Iacoangeli, J. Kremerskothen, K. Duning, A. Barnekow, A. Huttenhofer, H. Tiedge, J. Brosius, Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles, J. Mol. Biol. 321 (2002) 433–445. [193] K. Duning, F. Buck, A. Barnekow, J. Kremerskothen, SYNCRIP, a component of dendritically localized mRNPs, binds to the translation regulator BC200 RNA, J. Neurochem. 105 (2008) 351–359. [194] L. Lewejohann, B.V. Skryabin, N. Sachser, C. Prehn, P. Heiduschka, S. Thanos, U. Jordan, G. Dell’Omo, A.L. Vyssotski, M.G. Pleskacheva, H.P. Lipp, H. Tiedge, J. Brosius, H. Prior, Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice, Behav. Brain Res. 154 (2004) 273–289. [195] Y. Tamura, H. Kunugi, J. Ohashi, H. Hohjoh, Epigenetic aberration of the human REELIN gene in psychiatric disorders, Mol. Psychiatry 12 (519) (2007) 593–600. [196] S.J. Chamberlain, M. Lalande, Angelman syndrome, a genomic imprinting disorder of the brain, J. Neurosci. 30 (2010) 9958–9963. [197] S. Krechowec, A. Plagge, Physiological dysfunctions associated with mutations of the imprinted Gnas locus, Physiology 23 (2008) 221–229. [198] A. Plagge, A.R. Isles, E. Gordon, T. Humby, W. Dean, S. Gritsch, R. Fischer-Colbrie, L.S. Wilkinson, G. Kelsey, Imprinted Nesp55 influences behavioral reactivity to novel environments, Mol. Cell. Biol. 25 (2005) 3019–3026. [199] C.W. Berridge, B.D. Waterhouse, The locus coeruleus-noradrenergic system: modulation of behavioral state and state-dependent cognitive processes, Brain Res. Brain Res. Rev. 42 (2003) 33–84.

21

[200] A. Helgadottir, G. Thorleifsson, A. Manolescu, S. Gretarsdottir, T. Blondal, A. 2191 Jonasdottir, A. Jonasdottir, A. Sigurdsson, A. Baker, A. Palsson, G. Masson, D.F. 2192 Gudbjartsson, K.P. Magnusson, K. Andersen, A.I. Levey, V.M. Backman, S. Mat2193 thiasdottir, T. Jonsdottir, S. Palsson, H. Einarsdottir, S. Gunnarsdottir, A. Gylfason, 2194 V. Vaccarino, W.C. Hooper, M.P. Reilly, C.B. Granger, H. Austin, D.J. Rader, S.H. 2195 Shah, A.A. Quyyumi, J.R. Gulcher, G. Thorgeirsson, U. Thorsteinsdottir, A. Kong, K. 2196 Stefansson, A common variant on chromosome 9p21 affects the risk of myocar2197 dial infarction, Science 316 (2007) 1491–1493. 2198 [201] O. Harismendy, D. Notani, X. Song, N.G. Rahim, B. Tanasa, N. Heintzman, B. Ren, 2199 X.D. Fu, E.J. Topol, M.G. Rosenfeld, K.A. Frazer, 9p21 DNA variants associated 2200 with coronary artery disease impair interferon-gamma signalling response, 2201 Nature 470 (2011) 264–268. 2202 [202] R. Ross, Atherosclerosis is an inflammatory disease, Am. Heart J. 138 (1999) 2203 S419–S420. 2204 [203] A. Ravel-Chapuis, G. Belanger, R.S. Yadava, M.S. Mahadevan, L. DesGroseillers, J. 2205 Cote, B.J. Jasmin, The RNA-binding protein Staufen1 is increased in DM1 skeletal 2206 muscle and promotes alternative pre-mRNA splicing, J Cell Biol. 196 (2012) 2207 699–712. 2208 [204] G. Caretti, R.L. Schiltz, F.J. Dilworth, M. Di Padova, P. Zhao, V. Ogryzko, F.V. Fuller2209 Pace, E.P. Hoffman, S.J. Tapscott, V. Sartorelli, The RNA helicases p68/p72 and the 2210 noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentia2211 tion, Dev. Cell 11 (2006) 547–560. 2212 [205] M. Sone, T. Hayashi, H. Tarui, K. Agata, M. Takeichi, S. Nakagawa, The mRNA-like 2213 noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of 2214 neurons, J. Cell Sci. 120 (2007) 2498–2506. 2215 [206] N.A. Rapicavoli, E.M. Poth, S. Blackshaw, The long noncoding RNA RNCR2 directs 2216 mouse retinal cell specification, BMC Dev. Biol. 10 (2010) 49. 2217 [207] U. Gunasekaran, M. Gannon, Type 2 diabetes and the aging pancreatic beta cell, 2218 Aging (Milano) 3 (2011) 565–575. 2219 [208] M.I. McCarthy, Genomics, type 2 diabetes, and obesity, N. Engl. J. Med. 363 2220 (2010) 2339–2350. 2221 [209] C. Wahlestedt, Targeting long non-coding RNA to therapeutically upregulate 2222 gene expression, Nat. Rev. Drug Discov. 12 (2013) 433–446. 2223 [210] V. Senee, C. Chelala, S. Duchatelet, D. Feng, H. Blanc, J.C. Cossec, C. Charon, M. 2224 Nicolino, P. Boileau, D.R. Cavener, P. Bougneres, D. Taha, C. Julier, Mutations in 2225 GLIS3 are responsible for a rare syndrome with neonatal diabetes mellitus and 2226 congenital hypothyroidism, Nat. Genet. 38 (2006) 682–687. 2227 [211] T. Sperka, J. Wang, K.L. Rudolph, DNA damage checkpoints in stem cells, ageing 2228 and cancer, Nat. Rev. Mol. Cell Biol. 13 (2012) 579–590. 2229 [212] W. Yu, D. Gius, P. Onyango, K. Muldoon-Jacobs, J. Karp, A.P. Feinberg, H. Cui, 2230 Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA, Nature 2231 451 (2008) 202–206. 2232 [213] D.S. Perez, T.R. Hoage, J.R. Pritchett, A.L. Ducharme-Smith, M.L. Halling, S.C. 2233 Ganapathiraju, P.S. Streng, D.I. Smith, Long, abundantly expressed non-coding 2234 transcripts are altered in cancer, Hum. Mol. Genet. 17 (2008) 642–655. 2235 [214] F. Yang, H. Zhang, Y. Mei, M. Wu, Reciprocal regulation of HIF-1alpha and Q42236 LincRNA-p21 modulates the Warburg effect, Mol. Cell (2013). 2237 [215] J.H. Yoon, K. Abdelmohsen, S. Srikantan, X. Yang, J.L. Martindale, S. De, M. Huarte, 2238 M. Zhan, K.G. Becker, M. Gorospe, LincRNA-p21 suppresses target mRNA trans2239 lation, Mol. Cell 47 (2012) 648–655. 2240 [216] C.D. Novina, M.F. Murray, D.M. Dykxhoorn, P.J. Beresford, J. Riess, S.K. Lee, R.G. 2241 Collman, J. Lieberman, P. Shankar, P.A. Sharp, siRNA-directed inhibition of HIV-1 2242 infection, Nat. Med. 8 (2002) 681–686. 2243 [217] N.S. Lee, T. Dohjima, G. Bauer, H. Li, M.J. Li, A. Ehsani, P. Salvaterra, J. Rossi, 2244 Expression of small interfering RNAs targeted against HIV-1 rev transcripts in 2245 human cells, Nat. Biotechnol. 20 (2002) 500–505. 2246 [218] M.E. Davis, J.E. Zuckerman, C.H. Choi, D. Seligson, A. Tolcher, C.A. Alabi, Y. Yen, 2247 J.D. Heidel, A. Ribas, Evidence of RNAi in humans from systemically administered 2248 siRNA via targeted nanoparticles, Nature 464 (2010) 1067–1070. 2249 [219] M.M. Lee, J.L. Childs-Disney, A. Pushechnikov, J.M. French, K. Sobczak, C.A. 2250 Thornton, M.D. Disney, Controlling the specificity of modularly assembled small 2251 molecules for RNA via ligand module spacing: targeting the RNAs that cause 2252 myotonic muscular dystrophy, J. Am. Chem. Soc. 131 (2009) 17464–17472. 2253 [220] C. Gong, L.E. Maquat, lncRNAs transactivate STAU1-mediated mRNA decay by 2254 duplexing with 3’ UTRs via Alu elements, Nature 470 (2011) 284–288. 2255


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