Chromatin remodeler mutations in human cancers: epigenetic implications.

Review For reprint orders, please contact: [email protected]

Chromatin remodeler mutations in human cancers: epigenetic implications

Chromatin remodeler complexes exhibit the ability to alter nucleosome composition and positions, with seemingly divergent roles in the regulation of chromatin architecture and gene expression. The outcome is directed by subunit variation and interactions with accessory factors. Recent studies have revealed that subunits of chromatin remodelers display an unexpectedly high mutation rate and/or are inactivated in a number of cancers. Consequently, a repertoire of epigenetic processes are likely to be affected, including interactions with histone modifying factors, as well as the ability to precisely modulate nucleosome positions, DNA methylation patterns and potentially, higher-order genome structure. However, the true significance of chromatin remodeler genetic aberrations in promoting a cascade of epigenetic changes, particularly during initiation and progression of cancer, remains largely unknown. Keywords: ARID1A • BRG1 • BRM • cancer • chromatin remodeling • epigenetics • nucleosome • SNF5 • SWI/SNF

The molecular events involved in cancer initiation and progression are complex and often the result of widespread genetic and epigenetic reprogramming aberrations that promote uncontrolled proliferative and growth advantages [1,2] . While our understanding of the very first changes that occur– the driving events–are still limited, it is now well established that both genetic and epigenetic defects are hallmarks of cancer cells [3,4] that underpin changes to the gene expression program and disruption of normal cellular processes such as mitotic control, DNA repair and cellular signaling [1,2] . Epigenetic mechanisms encompass DNA methylation, post-translational covalent modification of histones (e.g., acetylation, methylation and phosphorylation), incorporation of histone variants within the nucleosome, nucleosome positioning and remodeling, as well as the overall 3D architecture of chromatin [3,4] . Epigenetic changes are dynamic and must function in concert to attain faithful gene expression. However, we are just begin-

10.2217/EPI.14.37 © 2014 Future Medicine Ltd

Katherine A Skulte1,2, Lisa Phan1,2, Susan J Clark2,3 & Phillippa C Taberlay*,1,2,3 Chromatin Dynamics Group, Cancer Division, Garvan Institute of Medical Research, 394 Victoria Rd, Darlinghurst 2010, New South Wales, Australia 2 Epigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, 394 Victoria Rd, Darlinghurst 2010, New South Wales, Australia 3 St. Vincent’s Clinical School, University of NSW, Sydney 2010, New South Wales, Australia *Author for correspondence: Tel.: +61 2 92958396 Fax: +61 2 92958151 p.taberlay@ garvan.org.au 1

ning to understand how this is achieved and moreover, are far from understanding the interplay between epigenetics and genetics. Interestingly, genetic studies have now revealed that many epigenetic-associated genes exhibit high mutation rates in cancer [5,6] . This raises questions regarding the epigenetic consequences of genetic mutations, or vice versa, and in particular the significance of these mutations in the etiology of cancer. What are chromatin remodelers & why are they important? Nucleosomes form the basic unit of chromatin, which is packaged into a highly ordered and multi-layered structure to facilitate containment within the nucleus [7] . The structure of chromatin naturally represses gene expression, in part by preventing the access of transcription machinery and other associated factors to DNA regulatory elements [8] . Hence, chromatin structure must be altered to allow these factors to control gene expression. To date, there are two known classes of

Epigenomics (2014) 6(4), 397–414

part of

ISSN 1750-1911

397

Review Skulte, Phan, Clark & Taberlay proteins that can alter nucleosomes and in turn, chromatin accessibility (Figure 1) . First, covalent modifiers which are chromatin modifying complexes that add or remove covalent modifications such as methyl- or acetyl- groups to the core histone proteins of nucleosomes and second, ATP-dependent chromatin remodelers that reposition nucleosomes through a sliding or ejecting mechanism [4,5] . Both of these processes must occur with precision at DNA regulatory elements, including promoters, enhancers and insulators and in a highly regulated mode to ensure the dynamic balance between repressive or permissive chromatin structures. Discrete chromatin changes at DNA regulatory elements maintain temporal and regulated transcription programs in a cell-type specific manner, while comparatively gross remodeling of the chromatin structure enables cellular differentiation and the establishment of appropriate gene expression profiles during embryonic development [9–18] . Chromatin remodeling complexes assemble, insert, slide and eject nucleosomes, using ATP hydrolysis to catalyze nucleosome movement [19] . There are four known families of ATP-dependent mammalian remodelers; switch/sucrose nonfermenting (SWI/ SNF), imitation switch (ISWI), inositol requiring 80 (INO80) and those with a NuRD/Mi-2/CHD helicase binding domain [5,6,20–25] (Figure 2) . These share a high affinity for the nucleosome, recognition of covalent histone modifications (active or repressive depending on the domain), similar ATPase domain structures and subunits that enable their interaction with sequence-specific transcription factors [19] . An understanding of the exact processes that chromatin remodelers use to mobilize nucleosomes is far from complete. Studies of DNA movement during remodeling have shown that DNA is either ‘looped’ or ‘bulged out’ from the nucleosome surface, disrupting the histone–DNA interaction and translocating the DNA along the nucleosome; or, DNA can twist causing rotational strain that disrupts histone–DNA interactions forcing the DNA to translocate across the nucleosome [26–34] . Still, the mechanisms that underpin the ability of chromatin remodelers to perform these actions are largely unknown. It is likely that the different chromatin remodeler families utilize alternative means to mobilize nucleosomes, possibly due to structural differences in the ATPase subunit and the combination and/or function of accessory subunits. Research on the ISWI family demonstrates these complexes translocate DNA in a stepwise fashion. DNA is pushed out from the exit point of contact between the nucleosome and the DNA, until there is sufficient strain on the remaining DNA surrounding the nucleosome to pull more DNA in through the entry point of contact between

398

Epigenomics (2014) 6(4)

the DNA and the nucleosome, occurring in three basepair increments [35–37] . Chromatin remodelers also mobilize nucleosomes to assemble and disassemble the histone octamer through loosening the DNA around the nucleosome, disrupting DNA–histone interactions [38] . After loosening the DNA, the SWI/SNF complex is known to remove one H2A/H2B dimer first, followed by the remainder of the nucleosome [39] . As with the nucleosome sliding, little is understood of how chromatin remodelers act to assemble and disassemble nucleosomes Chromatin remodelers interact with each other and transcription factors to coordinate gene expression. The ability of chromatin remodelers to interact with transcription factors is essential for guiding the complexes to their appropriate regions, as they lack DNA sequence specificity [40,41] . Each ATP-dependent chromatin remodeling complex comprised several subunits that complement the ATPase but can be interchanged to create diversity in function [19,42,43] , including maintenance of epigenetic programs for gene expression, and roles in DNA repair, replication and genetic recombination [19] . In addition, the different families of ATP-dependent chromatin remodelers have coordinated activity, but nonredundant and specific roles [44– 46] . The subunits Brahma-related gene 1 (BRG1) from SWI/SNF, SNF2h from ISWI and CHD4 from the CHD helicase family co-localize at promoters and distal regulatory elements [44] , suggesting they function in concert, potentially to add multiple layers of control to prevent spurious gene activity. Conversely, each chromatin remodeler family has its own distinct enrichment patterns across DNA features. However, when multiple remodelers are present, it has been proposed that there is independent sequential binding at these sites [44] , suggesting that order of recruitment as well as the combination of remodelers may be critical for faithful gene transcription. Several studies have linked aberrant expression or action of ATP-dependent chromatin remodelers to cancer [6,20,47,48] . In this review we discuss the key roles of the SWI/SNF chromatin remodeling complex and the epigenetic implications for its dysregulation in cancer. The SWI/SNF chromatin remodeler complex The SWI/SNF chromatin remodeler is a large multisubunit complex that has been extensively studied and shows large evolutionary conservation from yeast to humans [6] . There are several functionally important subunits of the SWI/SNF complex that allow it to have diverse roles, with the ability to both activate and repress expression. The SWI/SNF complex has two mutually exclusive subunits, Brahma (BRM) and Brahma-related gene 1 (BRG1; SWI/SNF complex,

future science group


Figure 2) , both which hydrolyze ATP. BRM and BRG1

share approximately 75% sequence homology [6] and are capable of low levels of nucleosome remodeling activity alone, without the remaining members of the complex [49] . Research into cell cycle progression has also demonstrated that BRM and BRG1 have nonredundant roles as the cell progresses through different

A

stages of the cell cycle [50,51] . Their roles also differ during embryogenesis where BRG1 is essential in development and BRG1 null mice are embryonic lethal, while BRM is considered dispensable and is more highly expressed in differentiated cells [52–55] . In cancer cells, BRM is able to compensate for loss of BRG1 [56] such that BRG1-deficient cancer cells can depend on BRM

B

Covalent modifiers

(e.g. Polycomb repressive complex [PRC2], histone deacetylases [HDACs] or histoneacetyltransferases (KATs)

Review

ATP-dependent chromatin remodellers

Chromatin remodelling complex

Chromatin modifying complex

(e.g. SWI/SNF, INO80, NuRD or ISWI)

Chromatin modifier recruited to chromatin ATP

27me

27me

27me

4me

4me

4me

DNA translocation and loosening of chromatin

4me

Covalent histone modifications

Nucleosome sliding

Nucleosome ejection

Figure 1. An overview of chromatin modifier and remodeler actions.Chromatin modifiers and remodelers act on chromatin to alter DNA accessibility. (A) Chromatin modifying complexes are recruited to chromatin and facilitate the covalent modification (e.g., H3K4me3, green circles; H3K27me3, red circles) of histones (pink). These modifications are recognized by other protein complexes that in turn recruit either co-activators to facilitate chromatin opening, or co-repressors to repress and condense chromatin. (B) Chromatin remodelers bind to, and loosen chromatin in an ATP-dependent manner, which mobilizes nucleosomes for ejection or sliding to increase the linker distance. Sliding and ejection both expose transcription factor binding sites or allow basal transcription machinery to bind. These mechanisms can also function in reverse to compact chromatin.


www.futuremedicine.com

399

Review Skulte, Phan, Clark & Taberlay

SWI/SNF

ISWI

BRG1/BRM

BAF60A

BAZ1A

BRG1/BRM BAF180

BRD7 SNF5

SNF2h

ARID1A/1B/2

INO80

NuRD MBD2/3

HDAC1

les2/6 Tip49a/b YY1

BAZ1A

MTA1/2

INO80 Arp4/5/8

CHD4(Mi-β2)

HDAC2

RbAp48

RbAp46

Figure 2. The ATP-dependent chromatin remodeler families. There are four known ATP-dependent chromatin remodeler families, each of which contains multiple subunits. Core subunits of the SWI/SNF complex include one of either BRM or BRG1, the ATPases (blue), [49] ; the DNA-binding subunits, ARID1A/1B/2 are also shown (green, highlighted). Snf2h is the ATPase (blue) subunit of ISWI complexes, which are much smaller than SWI/SNF and exist as two variants: RSF [24] or hACF (human ATP-utilizing chromatin assembly and remodeling factor), pictured [23] . The ATPase subunit of INO80 (also called INO80) shares homology with Snf2h (blue). More than 15 different subunits of INO80 have been reported and a subset of them are similar to yeast homologs, pictured [21,22] . The NuRD complexes contain CHD4 as the ATPase subunit, as well as histone deacetylases and MBD [25] . CHD4: Chromodomain-helicase-DNA-binding protein 4; MBD: Methyl-CpG-binding domain proteins; RSF: Remodeling and spacing factor; SNF: Sucrose nonfermenting; SWI: Switch nonfermenting.

for growth [57] , although some cancers are deficient in both BRG1 and BRM [6] . These data demonstrate the highly complex nature of SWI/SNF complexes and the fine level of control exerted when subunits are combined, or replaced. The SWI/SNF complex relies on the AT-rich interactive domain (ARID) family of subunits (ARID1A, ARID1B and ARID2; Figure 2) for its interaction with DNA [58–60] . ARID1A and ARID1B share approximately 60% sequence homology, but are mutually exclusive in SWI/SNF complexes and have individual functional roles [58,59] . Interestingly, the expression levels of ARID1A decrease while ARID1B increase during cell cycle progression [58] . This corresponds to observations that ARID1A-containing SWI/SNF complexes repress cell cycle progression genes while ARID1B complexes activate those genes necessary for movement through the cell cycle [61] . Furthermore, ARID1B but not ARID1A is essential for embryonic development and pluripotency [62] .

400


The SWI/SNF chromatin remodeling complex binds a number of complementary proteins in order to mediate finer levels of transcription control and modulate epigenetic signatures at DNA regulatory elements. These include regulatory factors to both activate and repress genes such as steroid receptors, integrins and factors that regulate interferon-inducible genes [6] . Association with transcription factors allows for tissue and gene specificity as the SWI/SNF complex does not recognize sequence-specific DNA. The SWI/SNF complex also interacts with chromatin regulators that covalently modify histones to both activate and repress gene expression [63–70] . The ability of SWI/SNF to interact with these proteins suggests it plays a pivotal role in the more complex higher order chromatin structure. SWI/SNF is frequently mutated in human cancers Disruption of SWI/SNF has been reported in a number of human tumors [5,6,20,71–86] (Figure 3) often



resulting in a loss of heterozygosity, consistent with tumor suppressor inactivation [6,86] ; however, the types of tumors affected, and the specific mutations pertaining to the SWI/SNF subunits have already been extensively reviewed [5,6,20,77,79,86,87] . However, it is interesting to note that the ATPase subunits BRG1 and BRM assist in the proliferation in some cancers, while they are mutated or lost in others [74,76,77,83,88] . Concomitant silencing of both BRG1 and BRM gene expression has been reported in 10–20% of human bladder, colon, breast, melanoma, esophageal, head/neck, pancreas and ovarian cancers [6] . In contrast, BRG1 and BRM expression levels increase during disease progression in prostate cancer and some breast cancers [83,89] ; moreover, BRG1 is essential for proliferation of leukemic cells [74,76] . Other subunits can be affected in addition to BRG1 and BRM, notably ARID1A and SNF5. ARID1A disruption has been observed in a number of primary cancers and a correlation between ARID1A downregulation, tumor progression, the disease-free period after treatment and overall survival has been established [71,72,80,81,84] . Moreover, genetic mutations in the SNF5 subunit have linked a dysfunctional SWI/SNF complex to aberrant epigenetic activity in cancer. A study of malignant rhabdoid tumors and medulloblastomas found that loss of SNF5 does not alter the sensitivity of cells to DNA damaging agents, nor is there an increase in genomic rearrangement and instability compared with tumors that express SNF5, suggesting that epigenetic mechanisms contribute to tumorigenesis [90] . These divergent roles suggest the specific combination of subunits in lineage-specific SWI/SNF complexes and other interacting partners ultimately guide SWI/SNF activity in cancers. Epigenetic alterations linked to SWI/SNF Despite the fact that many mutations in SWI/SNF have been reported, there remains little knowledge as to the epigenetic consequences of these mutations and how they may contribute to cancer initiation and development. In this review, we focus on some of the early epigenetic changes that are associated with SWI/SNF-dependent chromatin remodeling and the implications this may have for disrupting cellular processes leading to tumorigenesis. Changes to nucleosome positioning

Correct nucleosome positions are essential for faithful control of gene expression programs. BRG1 and SNF5 are necessary for maintaining nucleosome positions at transcription start sites (TSS), in particular the −1 and +1 nucleosomes of repressed genes [91] . Loss of either BRG1 or SNF5 results in severe nucleosome depletion at the TSS [91] , suggesting that nucleosomes become


Review

disorganized and gene expression changes due to alterations in local chromatin structure. Indeed, reduced BRG1 or SNF5 binding reduces the internucleosomal distance from 184 to 174 bp either side of the TSS [91] , inferring that nucleosome condensation begins to occur in the absence of SWI/SNF from promoters. While the majority of active enhancers exhibit nucleosome-depleted regions, only a few studies have charted the dynamic changes that occur at distal regulatory elements [10] . Detailed studies on androgen receptor (AR) signaling have provided some clues and indicate that the enhancer cores, containing the AR-binding sites, are devoid of nucleosomes and are flanked by two well-positioned nucleosomes [92] . However, not all cells within a population exhibit a nucleosome-depleted region in the first instance [93] . It is only in response to stimulation that a higher turnover of nucleosomes occurs, facilitating new nucleosomedepleted regions overlapping AR-binding sites [93] . To do so, nucleosomes are shifted outward to increase the linker distance at the AR-binding site, creating more densely packed nucleosomes at the periphery of the enhancer core [92,94] . Nucleosome movement at these AR-associated enhancers is positively correlated with BRG1 binding, implicating SWI/SNF in nucleosome repositioning processes at distal regulatory elements [94] , similar to promoters. As already discussed, the combination of subunits forming an active or repressive complex is likely to be important and it is not yet known whether the full complex, or only some specific subunits are required for nucleosome sliding at enhancers. It is implied that SWI/SNF relies on the presence of both BRG1 and SNF5 at the TSS, as indicated by the effect of both BRG1 and SNF5 deletion [91] , but the same has not yet been demonstrated at enhancers. Changes in DNase I hypersensitive sites

DNase hypersensitive sites (DHS) detect regions of chromatin that are sensitive to nuclease cleavage and can be mapped at single loci or genome wide to provide information on DNA accessibility. Similar to more direct measurements of nucleosome occupancy (discussed above), the repositioning of nucleosomes by SWI/SNF at the TSS and at distal regulatory elements can create or close DHS. Genome-wide changes in the location of DHS have been reported during cellular differentiation [9] and it is important that we understand the role of SWI/SNF in such processes, including the subsequent impact nucleosome remodeling has on the location of DHS. Studies on BRG1 binding suggest that BRG1containing SWI/SNF complexes have a primary role in opening chromatin and maintaining active sites [44,94–96] despite being necessary to retain nucleosomes


401

BAF60A/ SMARCD1

BRD7

BAF180/ PBRM1

SNF5/ SMARCB1

ARID2/ BAF200

ARID1B/ BAF250b

ARID1A/ BAF250a

Reduced expression Mutation unknown consequence (e.g., intron) Loss of function mutations (e.g., truncating) Genomic rearrangement (e.g., gene deletion)

BRM/ SMARCA2

Red Green Purple Blue

BRG1/ SMARCA4

Review Skulte, Phan, Clark & Taberlay

Acute lymphoblastic and chronic myeloid leukaemia/non-hodgkin lymphoma Basal cell carcinoma

Bladder TCC/Colorectal Breast

Cervical cancer Endometriod carcinomas Epithelioid sarcomas/extraskeletal myxoid chondrosarcomas /Undifferentiated sarcomas Familial schwannomatosis/meningioma/ mesothelioma Gastric cancer Malignant rhabdoid tumours

Medulloblastoma

Melanoma

Multiple myeloma

Neuroblastoma

Ovarian clear cell adenocarcinoma Lung cancer

Primary pancreatic adenocarcinomas

Prostate

Renal carcinoma

Small cell heptoblastomas Uterine endometrial carcinoma

402


Figure 3. The known mutations and altered expression state of SWI/SNF subunits in a number of cancers are summarized. SNF: Sucrose nonfermenting; SWI: Switch nonfermenting.

Burkitts lymphoma



at repressed TSS [91] . Indeed, BRG1 presence is necessary for the maintenance of a DHS at the locus control region of the β-globin genes—BRG1 loss occurs concomitant with the disappearance of the DHS and removal of histone acetylation, resulting in the downregulation of β-globin transcription [96] . A similar role for BRG1 in maintaining DHS and in turn, the expression of several other genes (e.g., proliferating cell nuclear antigen, neurotrophin 3 and platelet-derived growth factor subunit A) has also been reported [95] . On a genome-wide scale, BRG1 binding and DHS were shown to overlap at 34,311 sites, 3.4% of which were lost upon BRG1 deletion from the cells and a further 9.4% became less accessible by at least 50% in mammary epithelial cells [44] . However, BRM has the ability to compensate for BRG1 loss [88] and this may mask the apparent total number of DHS affected. In addition, SWI/SNF itself co-localizes with the ATPases CHD4 and Snf2h, subunits from the NuRD and ISWI chromatin remodeler families, respectively (Figure 2) , at more that 20,000 DHS in mouse mammary epithelial cells [44] . Therefore, the number of DHS maintained by SWI/SNF may be substantially underestimated due to alterations masked by DHS cocontrolled by other chromatin remodelers [44] . These data demonstrate a loss in the maintenance and opening of chromatin for a subset of SWI/SNF controlled DHS [44] . It would be interesting to further determine the significance of DHS changes when BRM and BRG1 are simultaneously lost in cancer [6] .

Review

tioning of nucleosomes could ultimately lead to abnormal binding of transcription factors, and potentially change the local epigenetic signatures. SWI/SNF is dependent on sequence-specific transcription factors to direct its localization throughout the genome; yet the sequence-specific transcription factors are also dependent on nucleosome remodeling to expose their recognition sites. This presents a conundrum as to which action precedes the other. It is likely that there are roles for other chromatin remodeler families co-localizing with SWI/SNF [44] potentially directing this action. Understanding the order of events has important implications as several transcription factors functionally associated with SWI/SNF, along with SWI/SNF itself, are also dysregulated in cancer [103–106] . Covalent histone modifiers

In addition to transcription factors, the SWI/SNF complex has been linked to chromatin modifiers that are responsible for the covalent modification of histones, in particular the polycomb group proteins (PcG), histone deacetylases (HDACs) and lysine acetyltransferases (KAT) (Figure 1A) . These covalent modifications, together with DNA methylation, nucleosome positions and expression of small RNA molecules, interact and generate an epigenetic signature that is identified and interpreted by chromatin regulators like SWI/SNF, as well as downstream transcriptional activators and repressors. Repressive histone marks

Altered transcription factor binding

The SWI/SNF complex has been functionally linked to a number of transcription factors that potentially provides the sequence specificity for SWI/SNF localization [6] . For example, the SWI/SNF subunit Bromodomain containing protein 7 (BRD7; Figure 2) binds directly to breast cancer type 1 susceptibility protein (BRCA1) and has a direct role in gene transcription in response to UV DNA damage by upregulating the ataxia telangiectasia mutated protein (ATM) signaling [97] . Likewise, steroid hormone receptors, important for the regulation of genes involved in proliferation and differentiation processes, also depend on SWI/SNF for chromatin remodeling activity for gene transactivation [6,40,41,98–102] . Steroid receptor induced chromatin remodeling is also evident at enhancers as well as at promoters [93] . Interestingly, SWI/SNF can act as both a co-repressor and co-activator at the same promoter depending on the context [103] . As described above, mutations and/or loss of SWI/SNF can alter the precise positioning of nucleosomes and in turn the accessibility of DNA (as detected by DHS, for example). Aberrant movement and posi-


The PcG complex, polycomb repressive complex 2 (PRC2) is essential for normal development [93] and acts as a repressor of transcription by catalyzing the addition of covalent marks such as the trimethylation of Lysine 27 on Histone 3 (H3K27me3). SWI/SNF functions antagonistically with PcG complexes by mediating the eviction of PcG proteins from target gene promoters [63–65] , resulting in the formation of open chromatin. However, genes can become aberrantly repressed by PcG in cancer cells concomitant with altered SWI/SNF binding or when subunit composition is altered [2] . It is possible that normal SWI/SNF binding is disrupted by changes to the local epigenetic signature, while mutations or subunit switching in SWI/SNF could signal atypical recruitment of PcG to gene regulatory regions. This has been demonstrated in part in malignant rhabdoid tumor cells, which lack the SNF5 subunit of SWI/SNF, depicted in Figure 4. In these cells, the ARF-INK4a gene is subsequently silenced; however, the re-introduction of SNF5 results in restored expression of ARF-INK4a (Figure 4) . This was shown to be actioned by the displacement of the PcG complex from the ARF-INK4a promoter by SWI/SNF and was


403

Review Skulte, Phan, Clark & Taberlay also associated with the recruitment of mixed-lineage leukemia, a histone acetyltransferase [63] (Figure 4) . Other genes showing similar antagonism by SWI/ SNF and PcG proteins, include those important for stem cell self-renewal programs that become activated in response to a reduction in SNF5 and in converse, genes necessary for lineage specificity are repressed [65] . EZH2, the catalytic subunit of PcG, is also highly mutated in cancers, where its overexpression can drive proliferation [86] . Interestingly, when both SNF5 and EZH2 are simultaneously inactivated in cancer cells, proliferation reduces at a rapid rate, leading to the suggestion that EZH2 may be a novel target for epigenetic therapies in SNF5-deficient cancers [65] . HDACs remove acetyl groups from histone tail residues, and are proven targets for epigenetic therapies due to their ability to restore tumor suppressor function [107–109] . Less is known of SWI/SNF interactions with HDACs. However, SWI/SNF can inhibit transcription as part of a larger multi-protein repressor complex containing the retinoblastoma protein (Rb) and an HDAC [69] . To the best of our knowledge, SWI/SNF has not been shown to form interactions with any other human HDAC complexes. Given that the SWI/SNF-Rb-HDAC complex has a role in regulating cell cycle progression genes [69] , such interactions would be an interesting line of continued investigation as their identification may provide novel insights into the effectiveness of epigenetic HDAC therapies. Active histone marks

SWI/SNF can also promote gene transcription, which it achieves through recognition of active histone marks and associating with other protein complexes such as lysine acetyltransferases (KATs). For example, BRG1 can recognize lysine 14 acetylation on histone 3 that has been catalyzed by the KAT, p300; yet, a point mutation at lysine 14 on the H3 tail and a consequent lack of acetylation prevents the binding of BRG1 and inhibits nucleosome disassembly in vitro [110,111] . This may, in part, account for altered patterns of gene expression in cancers with atypical BRG1 activity. Target genes of BRG1-H3K14ac nucleosome remodeling activity have not yet been experimentally determined in humans, nor is it known if this interaction occurs more frequently at promoters or distal regulatory sites. Interestingly, BRG1 and BRM containing SWI/SNF complexes have differing roles with respect to recognition and activity with other KAT proteins. For example, BRG1 can form a complex with the Crebbinding protein (CBP) to activate p53, but BRM complexes cannot [112] , even though BRM–CBP complexes can be formed in flies [113] . Similarly, acetylation of Lysine 18 on Histone 3 (H3K18ac) by CBP and p300

404


results in recruitment of BRM to facilitate the repair of double-strand DNA breaks [70] . Loss of H3K18ac prevents the recruitment of BRM and in turn, nonhomologous end joining repair, therefore increasing the sensitivity of cancer cells to radio and chemotherapy [70] . The SWI/SNF subunit, eleven-nineteen leukemia protein (ENL), is a known fusion partner of the KAT mixed-lineage leukemia protein [114] . The mixedlineage leukemia-ENL fusion can be incorporated into the SWI/SNF complex and the HoxA7 gene has been identified as a downstream target in its oncogenic activity [115] . Providing insight as to why SWI/SNF is essential for proliferation in leukemia. Taken together, these experiments have established that SWI/SNF has diverse roles in nucleosome remodeling that again is dependent on context, in this case the specific pattern of histone marks. DNA methylation

DNA methylation is the best-studied epigenetic modification and is traditionally associated with the long-term silencing of genes. Several recent studies have definitively established a link between nucleosome occupancy and DNA methylation [116–122] . Indeed, nucleosome occupancy precedes de novo DNA methylation during differentiation [122] . DNA wrapped around nucleosomes can be more highly methylated than linker DNA [116] ; yet, linker DNA first acts as sites for ‘seeding’ methylation that marks regions for the spread of DNA methylation [123] . The nucleosome is also required to anchor the DNA methyltransferases, DNMT3A and DNMT3B, to genomic regions for the faithful maintenance of DNA methylation marks [121] . This highlights the importance of the nucleosome position for establishing and maintaining the correct DNA methylation patterns and likely, a wider repertoire of epigenetic marks. Despite these clear links, little is known about the signals that initiate and determine how nucleosomes are remodeled to enable changes in DNA methylation and in particular the role of SWI/SNF. The expression of CD44 and E-cadherin is silenced due to hypermethylation in the C33A human cervical cancer cell line, but whose expression can be restored following treatment with 5-aza-2′-deoxycytidine, a DNA methylation inhibitor [124] . Interestingly, C33A cells also lack functional BRG1 and BRM, and expression of CD44 and E-cadherin can also be restored following restoration of BRG1 or BRM in these cells [124] . Song et al. [73] also found an overlap in genes activated by 5-aza-2′-deoxycytidine treatment and those affected by BRG1 restoration in nonsmall cell lung carcinoma. However, the same study also found that the DNA methylation altered by 5-aza-2′-deoxycytidine to be correlated poorly with BRG1-induced gene expression



PRC2 complex binding inhibited by SWI/SNF

Review

Transcription factor recruitment 4me

SWI/SNF

4me

4me NDR

4me

4me

4me

Nucleosome sliding

Nucleosome ejection MLL

NORMAL CELL

Recruitment of chromatin modifying complex (e.g., MLL)

SWI/SNF SNF5

SWI/SNF

Altered SWI/SNF subunit composition and/or binding (e.g., SNF5 loss)

SNF5 CANCER CELL

PRC2 recruitment and gene repression 27me

27me

27me

27me

Normal SWI/SNF subunit composition restored (e.g., SNF5)

Other chromatin remodeller involvement in compaction? 27me

27me

27me

27me

27me

Figure 4. The SWI/SNF chromatin remodeling complex plays a key role in maintaining epigenetic signatures. Actively expressed genes exhibit a nucleosome depleted region, maintained by chromatin remodelers (e.g., SWI/ SNF) sliding or ejecting nucleosomes, at the transcription start site. Active epigenetic marks, for example, H3K4me1/2/3 (green circles), are also present. In cancer cells whereby the SNF5 subunit is inactivated (denoted by the gray cross) and SWI/SNF-dependent chromatin remodeling is dysregulated, the NDR is lost and genes can be silenced by the Polycomb complex (PRC2), which catalyses the addition of the repressive H3K27me3 mark (red circles), as has been demonstrated at the ARF-INK4a locus [63] . The restoration of SNF5 levels in these cancers can re-establish SWI/SNF chromatin remodeling activity, resulting in displacement of PRC2, removal of repressive chromatin marks and in turn, formation of the NDR. At the ARF-INK4a promoter, it is known that SWI/SNF also recruits MLL, a histone acetyltransferase that re-applies active epigenetic chromatin marks. MLL: Mixed-lineage leukemia; NDR: Nucleosome depleted region; SNF: Sucrose nonfermenting; SWI: Switch nonfermenting.



405

Review Skulte, Phan, Clark & Taberlay [73] .

These data are highly suggestive of cooperation between SWI/SNF-directed nucleosome mobilization and DNA methylation dysregulation in cancer. DNA methylation outside of gene regulatory elements such as promoters, enhancers or insulators and the effect that altered nucleosome positions has on gene body methylation must also be considered. Contrary to DNA methylation at regulatory elements, DNA methylation in gene bodies, particularly in exons, appears to occur more heavily in active genes suggesting there is an alternative function [125,126] . Exons are often marked by DNA methylation and the associated genes can be grouped into two classes; those that have equal levels of CpGs in both introns and exons and those that have a higher percentage of CpGs in the exons. Interestingly, the two classes also show different levels of nucleosome density [127] with the former group demonstrating a lower nucleosome density [127] . This suggests that chromatin remodeler exhibits different functions depending on the CpG content and level of DNA methylation in gene bodies. In addition to the DNA methylation that occurs within exons, distinct patterns also occur at intron-exon boundaries and play a role in alternate splicing by slowing transcription elongation and marking constitutive from alternate exons [127–129] . SWI/SNF is known to have a role in splicing, where a loss of SNF5 and BRM leads to altered transcription elongation and splicing [130,131] . It is intriguing to consider the possibility that nucleosome positioning could affect splicing through altered DNA methylation patterns at intron-exon boundaries as a consequence of aberrant nucleosome movement. Considerations for epigenetic therapies

Inhibitors of histone modifiers are currently in clinical trials as epigenetic therapies for cancer. As described above, the link between SWI/SNF nucleosome remodeling and proteins that alter the covalent modifications of histones has been established, but little is known about the specific interactions between the two classes of proteins. Moreover, it is unknown how abnormal SWI/SNF function would impact on other chromatin modifiers or in response to the epigenetic therapies against them. This would be an interesting avenue for further research and may provide information on the responsiveness of patients to these therapies. The two ATPase subunits, BRM and BRG1, of the SWI/SNF complex also present as potential targets for cancer therapies. In a study of 10 cancer cell lines where SMARCA2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, the gene encoding BRM) is silenced, butyrate, a broad spectrum HDAC inhibitor, can upregulate or restore SMARCA2 expression [132] while withdrawal of butyrate then

406


returns SMARCA2 to a silenced state [132] . However, restored expression of SMARCA2 after butyrate treatment was not found to return BRM function in vivo, potentially due to the concomitant deactylation of histone proteins, which BRM can no longer recognize [132] . This has important implications for the use of HDAC inhibitors in clinical trials and stresses the importance of a more specific HDAC inhibitor to restore BRM function. In BRG1-deficient cancer cell lines, subsequent loss of BRM will induce senescence [57] . It is therefore likely that despite being shown to have nonredundant roles, BRM is compensating for BRG1 loss and forming residual SWI/SNF complexes [6,88] . The synthetic lethal relationship indicates BRM as a therapeutic target for BRG1-deficient cells [57] , and further suggests that chromatin remodelers in general are attractive targets for future drug design. Remodeling chromatin to maintain developmental epigenetic states

Many of the molecular mechanisms associated with SWI/SNF nucleosome remodeling and its role in cellular differentiation have been discovered through studies of developmental processes. For example, ARID1A containing SWI/SNF complexes remodel chromatin to regulate the embryonic genes Sox2, Utf1 and Oct4; and loss of ARID1A results in embryonic arrest and compromises cell self-renewal [133] . ARID1A also remodels chromatin during mesodermal lineage differentiation, but is dispensable for the ectodermal lineage [133] , signifying that cell linage specific complexes are important for normal developmental processes. More specifically, this has been shown for cardiac progenitor cell differentiation [134] ; ARID1A binds to, and facilitates the opening of chromatin at the promoters of Nkx2.5, Mef2c and Bmp10, which are key factors necessary for cardiac differentiation, and when ARID1A is lost there is a reduction in their expression [134] . ARID1A knockout murine cardiac cells result in underdeveloped heart and cardiac abnormalities, suggesting ARID1A plays a role in maintaining the epigenetic state of cardiac differentiation genes [134] . However, the molecular changes in the epigenetic signature that occur at these genes during development remain unknown. Understanding the role/s of SWI/SNF nucleosome remodeling in establishing and maintaining epigenetic states of developmental gene expression can also provide insight into the aberrant functions of SWI/SNF in cancer. In B-cell acute lymphoplastic (ALL) and acute myeloid (AML) leukemiae, an SWI/SNF complex containing the subunits BRG1, BAF60b, BAF93a, ARID1A, BAF60a, BAF155 and BAF45d is essential for self-renewal and proliferation of the malignant cells



[74,76] .

Specifically, these leukemiae require BRG1 for nucleosome remodeling of the Myc enhancer such that loss of BRG1 causes a reduction of enhancer–promoter interactions; thus, Myc expression [76] . This highlights that in cancers where BRG1 is necessary for continued proliferation, the SWI/SNF complex may function similarly to the embryonic SWI/SNF complex. In contrast, in cancers where loss of BRG1 promotes cancer progression and development, these SWI/SNF complexes may be lineage specific and are likely not important in self-renewal programs. Implications of SWI/SNF & cancer biology

enhance the activity of SWI/SNF but potentially does not drive this activity [6] . Double-stranded break repair is a normal process required by cells after exposure to DNA damaging agents, but also during homologous recombination for meiosis [50] . Loss of BRG1 impedes meiosis largely through defects in double-stranded break repair because the level of histone variant yH2XA persists through prophase I and cell cycle progression is blocked [50,137] . It is possible that the loss of BRG1 prevents the ejection and replacement of the nucleosome variant yH2XA and the cell does not recognize that the damage has been repaired.

The epigenetic processes linked to SWI/SNF function have implications for other processes important in cancer establishment and progression. This largely pertains to outcomes of SWI/SNF interacting with epigenetic marks for maintaining proper nucleosome occupancy states and faithful gene expression, but also in the local and global structure of chromatin for processes such as DNA repair. Uncontrolled progression through cell cycle checkpoints occurs in cancer. Both BRG1- and BRM-containing SWI/SNF complexes coordinate feedback mechanisms during the cell cycle. To do so, BRG1 and BRM normally bind to the retinoblastoma protein; however, in cells lacking BRG1 and BRM, the retinoblastoma protein alone is not able to induce G1 cell cycle arrest [6] . Furthermore, p53 requires BRG1/BRM complexes to bind to p130 to induce cell cycle arrest [6] . Mutations in SNF5 often result in the upregulation of genes important for cell cycle progression and proliferation including retinoblastoma, p53 and Hedgehog-Gli [5] as well as Cyclin D1 [90] . Together these findings point towards roles for SNF5, BRG1 and BRM subunits for maintaining the canonical nucleosome positioning at gene regulatory elements of cell cycle genes and therefore, preventing uncontrolled cellular proliferation in tumor development. The SWI/SNF complex also contributes to DNA repair processes, although the more detailed molecular mechanisms remain obscure [6,50] , suggesting that these processes necessitate mobilization of nucleosomes. BRG1 directly interacts with DNA repair proteins including BRCA1, which it recruits to sites of UV-induced damage [135,136] . Therefore, the presence or absence of BRG1 can determine how a tumor will respond to DNA damaging agents that cause the above-mentioned lesions. SNF5 has also been shown to localize to sites of DNA damage, but in response to DNA damaging agents SNF5 expression or activity does not alter [90] . It has also been shown that normal SWI/SNF function can be maintained even when SNF5 is downregulated, suggesting that SNF5 can

Conclusion Genomic sequencing has revealed that many subunits of chromatin remodelers are mutated or inactivated across a variety of cancers, revealing an interplay between genetics and epigenetics that remains largely unexplored. Of particular interest here are those affecting SWI/SNF, which has seemingly divergent roles in the regulation of chromatin architecture and gene expression. The data suggest that specificity is key; in other words, specific combination of subunits that generate variance in the SWI/SNF complex guide its activity and the remainder of its function determined by interactions with other chromatin remodeler families and regulatory proteins. However, there remains few studies investigating the importance and complexity of such combinatorial control and epigenetic consequences. Moreover, many studies have typically reported and focused on mutations affecting a lone subunit of the SWI/SNF complex. It would be interesting to re-examine these clinical samples for mutations in other SWI/SNF subunits as this may highlight which SWI/SNF complexes are drivers of epigenetic changes in cancer. SWI/SNF chromatin remodeling has now been linked to a variety of epigenetic processes. As we discussed here, this includes its role in maintaining nucleosome positioning and its interaction with other chromatin modifiers (Figure 5) . Current research into the impact of SWI/SNF mutations or inactivation is still in its infancy and there is little known about the genome-wide implications. However, a clear link between SWI/SNF dysregulation, epigenetic modifications and cancer establishment or progression is becoming apparent. It is worthy to note the potential impact of epigenetic therapies on aberrant SWI/SNF functions. There are many epigenetic therapeutics in clinical trials targeting histone modifiers and DNA methyltransferase inhibitors [1] ; yet the effectiveness of these therapeutics is likely to be dependent on the ability of SWI/SNF to interact with epigenetic modifying



Review

407

Review Skulte, Phan, Clark & Taberlay complexes such as PRC2 or KATs. Finally, it is likely that there are other, unidentified epigenetic changes arising in cancer that are the result of mutations in chromatin remodelers that remain unknown. Future perspective We have highlighted the potential impact of aberrant SWI/SNF activity pertaining to epigenetic reprogramming events evident in cancer, with a clear need for further investigation. As expected, alterations in nucleosome position have been observed concomitant with SWI/SNF dysfunction, and changes in nucleosome phasing have also been identified. However, the broader epigenetic impact (for example, on DNA methylation patterns and the distribution of histone modifications) and the potential as a therapeutic target, has not been extensively investigated. This is notwithstanding that atypical chromatin remodeling simply exposes new transcription factor recognition sites at gene regulatory elements (Figure 5), presumably resulting in abnormal enhancer–promoter interactions. Indeed, it has already been demonstrated that altered nucleosome occupancy at the distal regulatory enhancer element of Myc pre-

vents interactions between the Myc enhancer and promoter in leukemic cells [76] . On a global scale, the effect of SWI/SNF mutations higher-order chromatin structures remains unknown (Figure 5) . The relationship between SWI/SNF mutations and the effectiveness and/or side effects seen with epigenetic therapies should be further explored with the benefits being two fold; first, to obtain a greater understanding of treatment outcomes; and second epigenetic drugs may have broader utility than currently known. Given the range of both known and as yet unidentified epigenetic mechanisms, potential interactions with transcription factors and co-factors, as well as the large number of cancers that have been reported to contain SWI/SNF mutations, SWI/SNF presents itself as a strong candidate as a therapeutic target. However, the diverse and complex role of SWI/SNF must be considered, including that many of its functions are based on a specific combination of subunits. The current difficulty lies in knowing how best to target an atypical SWI/SNF complex, including any complications that may arise due to interactions between the various chromatin remodeler families and how these different fam-

Higher-order chromatin structure

Establishment and maintenance of epigenetic signatures

β-actin Enhancer promoter interactions

BRG1/BRM BAF170

BAF155 SNF5

3D chromatin architecture

ARID

Unknown epigenetic effects

Figure 5. Epigenetic implications for SWI/SNF dysregulation. Mutations affecting SWI/SNF chromatin remodeling activity have wider implication for epigenetic processes. Foremost, SWI/SNF maintains NDR at promoters and enhancers, coordinating genomic accessibility and therefore, dictating exposure of transcription factor binding sites. Moreover, the resultant positions of adjacent nucleosomes provide templates for DNA methylation (black circles) or post-translational covalent histone modifications such as histone acetylation (green triangles) and histone methylation (green circles). Local chromatin packaging is likely to affect the higher-order chromatin structure, as well as the 3D chromatin architecture, such as direct interactions between enhancers and promoters. In addition, it is likely that unknown epigenetic consequences of SWI/SNF disruption are yet to be identified. NDR: nucleosome depleted region; SNF: sucrose nonfermenting; SWI: switch nonfermenting.

408




ilies interact at their sites of action. It is therefore clear that a greater knowledge of these complexes and how they function would aid in the ability to target them directly as part of a potential new cancer treatment program. The rapid development of next-generation sequencing technologies and the subsequent implementation of personalized medicine options for the treatment of cancer will undoubtedly enable the fast-tracked development of specific inhibitors for chromatin modifiers and remodelers. This presents an exciting opportunity in this arena, especially when standard drugs could be combined with gene therapies and cutting-edge epigenetic treatments. For SWI/SNF, there is a very real possibility that it may be a core feature of many, if not all cancers. This may not be restricted to mutations

Review

and deletions as primarily discussed, but also altered activity due to epigenetic defects themselves. Financial & competing interests disclosure We thank members of the Clark Epigenetics Laboratory for helpful discussions and careful reading of the manuscript and our funding sources. KA Skulte is supported by an Australian Postgraduate Award. PC Taberlay is a Cancer Institute NSW Early Career Development Fellow. This work was further supported by Cure Cancer Australia Foundation Project Grant #1060713 to P.C.T and NH&MRC Project Grant #1051757 to S.J.C and P.C.T. The authors have no other relevant affiliations, financial involvement or conflicts of interest with any organization other than those stated. No writing assistance was utilized in the production of this manuscript.

Executive summary Chromatin remodelers • Chromatin remodelers mobilize nucleosomes to alter the configuration of nucleosomes allowing access to DNA for transcription factors and basal transcription machinery. • There are four families of ATP-dependent chromatin remodelers that have independent roles, but can also have coordinated functions, to maintain faithful gene transcription. • Chromatin remodelers utilize ATP to translocate DNA along the nucleosome by either a ‘looping/bulge diffusion’ or ‘twist diffusion’ mechanism, both of which cause a disruption in DNA–histone interactions.

The SWI/SNF remodeler complex & cancer • The SWI/SNF complex is an ATP-dependent chromatin remodeler that can both activate and repress genes by interacting with a variety of transcription factors and other chromatin modifiers. • Loss or inactivation of several SWI/SNF subunits has been reported in a number of cancers. Interestingly, some cancers are dependent on SWI/SNF for their sustained proliferation.

Nucleosome positioning affects the position of DHS & transcription factor binding • SWI/SNF is essential for maintaining correct nucleosome positions, particularly at DNA regulatory elements, and mobilizing nucleosomes to either create or close DHS. • One mechanism of SWI/SNF action is to slide the nucleosomes outward, increasing the linker distance to create a DHS site that exposes a transcription factor recognition sequence. • Alterations in DHS due to disrupted SWI/SNF function can lead to incorrect transcription factor binding and in turn, atypical gene expression patterns.

SWI/SNF interacts with histone modifiers & has implications for epigenetic therapies • The SWI/SNF complex has an antagonistic relationship with PcG group proteins. When EZH2 is specifically inhibited concomitant with a loss of SNF5, cell proliferation decreases. • SWI/SNF has been linked with both HDACs and KATs to repress or activate transcription. Aberrations in SWI/ SNF function may present as a novel cause in the effectiveness and/or resistance to these therapies.

Nucleosomes are important for DNA methylation • The precise positioning of the nucleosome is important to establish and maintain DNA methylation and the binding of DNMT3A and DNMT3B. • The precise role of SWI/SNF in DNA methylation is still known. However, cell lines deficient in BRG1 have demonstrated that the expression of a subset of genes silenced by DNA methylation can have their expression restored with 5-aza-deoxycytidine or re-expression of BRG1. • Aberrant nucleosome positioning in gene bodies and at intron-exon boundaries could disrupt alternate splicing through altered patterns in DNA methylation

Secondary effects of dysregulated nucleosome remodeling in cancer • Alterations in nucleosome positioning due to loss of SWI/SNF can alter the expression of cell cycle progression genes and genes involved in adhesion and migration in cancer. • Loss of BRG1 prevents meiosis by defects in DNA repair and persistence in the yH2XA variant.



409

Review Skulte, Phan, Clark & Taberlay References

19

Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009).

Papers of special note have been highlighted as: • of interest; •• of considerable interest 1

Sharma S, Kelly TK, Jones PA. Epigenetics in cancer. Carcinogenesis 31(1), 27–36 (2010).

20

Wilson BG, Roberts CW. SWI/SNF nucleosome remodellers and cancer. Nat. Rev. Cancer 11(7), 481–492 (2011).

2

Taberlay PC, Jones PA. DNA methylation and cancer. Prog. Drug Res. 67, 1–23 (2011).

21

3

Jones PA, Baylin SB. The epigenomics of cancer. Cell 128(4), 683–692 (2007).

4

Shen H, Laird PW. Interplay between the cancer genome and epigenome. Cell 153(1), 38–55 (2013).

Chen L, Cai Y, Jin J et al. Subunit organization of the human INO80 chromatin remodeling complex: an evolutionarily conserved core complex catalyzes ATP-dependent nucleosome remodeling. J. Biol. Chem. 286(13), 11283– 11289 (2011).

22

5

You JS, Jones PA. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22(1), 9–20 (2012).

Jin J, Cai Y, Yao T et al. A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J. Biol. Chem. 280(50), 41207–41212 (2005).

Reisman D, Glaros S, Thompson EA. The SWI/SNF complex and cancer. Oncogene 28(14), 1653–1668 (2009).

23

6 7

Staynov DZ, Proykova YG. Topological constraints on the possible structures of the 30 nm chromatin fibre. Chromosoma 117(1), 67–76 (2008).

Leroy G, Loyola A, Lane WS, Reinberg D. Purification and characterization of a human factor that assembles and remodels chromatin. J. Biol. Chem. 275(20), 14787–14790 (2000).

24

Allfrey VG, Littau VC, Mirsky AE. On the role of histones in regulation of ribonucleic acid synthesis in the cell nucleus. Proc. Natl Acad. Sci. USA 49, 414–421 (1963).

Loyola A, Huang JY, Leroy G et al. Functional analysis of the subunits of the chromatin assembly factor RSF. Mol. Cell Biol. 23(19), 6759–6768 (2003).

25

Hawkins RD, Larjo A, Tripathi SK et al. Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity 38(6), 1271–1284 (2013).

Vignali M, Hassan AH, Neely KE, Workman JL. ATPdependent chromatin-remodeling complexes. Mol. Cell Biol. 20(6), 1899–1910 (2000).

26

Becker PB, Workman JL. Nucleosome remodeling and epigenetics. Cold Spring Harb. Perspect. Biol. 5(9), pii a017905 (2013).

27

Flaus A, Owen-Hughes T. Mechanisms for nucleosome mobilization. Biopolymers 68(4), 563–578 (2003).

28

Kulic IM, Schiessel H. Chromatin dynamics: nucleosomes go mobile through twist defects. Phys. Rev. Lett. 91(14), 148103 (2003).

29

Richmond TJ, Davey CA. The structure of DNA in the nucleosome core. Nature 423(6936), 145–150 (2003).

30

Langst G, Becker PB. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677(1–3), 58–63 (2004).

31

Lia G, Praly E, Ferreira H et al. Direct observation of DNA distortion by the RSC complex. Mol. Cell 21(3), 417–425 (2006).

32

Lorch Y, Davis B, Kornberg RD. Chromatin remodeling by DNA bending, not twisting. Proc. Natl Acad. Sci. USA 102(5), 1329–1332 (2005).

33

Saha A, Wittmeyer J, Cairns BR. Mechanisms for nucleosome movement by ATP-dependent chromatin remodeling complexes. Results Probl. Cell Differ. (41) 127–148 (2006).

34

Narlikar GJ, Sundaramoorthy R, Owen-Hughes T. Mechanisms and functions of ATP-dependent chromatinremodeling enzymes. Cell 154(3), 490–503 (2013).

35

Schwanbeck R, Xiao H, Wu C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279(38), 39933–39941 (2004).

36

Blosser TR, Yang JG, Stone MD, Narlikar GJ, Zhuang X. Dynamics of nucleosome remodelling by individual ACF complexes. Nature 462(7276), 1022–1027 (2009).

8

9

410

10

Heintzman ND, Hon GC, Hawkins RD et al. Histone modifications at human enhancers reflect global cell-typespecific gene expression. Nature 459(7243), 108–112 (2009).

11

Heinz S, Benner C, Spann N et al. Simple combinations of lineage-determining transcription factors prime cisregulatory elements required for macrophage and B cell identities. Mol. Cell 38(4), 576–589 (2010).

12

Gifford CA, Ziller MJ, Gu H et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153(5), 1149–1163 (2013).

13

Stopka T, Skoultchi AI. The ISWI ATPase Snf2h is required for early mouse development. Proc. Natl Acad. Sci. USA 100(24), 14097–14102 (2003).

14

Curtis CD, Griffin CT. The chromatin-remodeling enzymes BRG1 and CHD4 antagonistically regulate vascular Wnt signaling. Mol. Cell Biol. 32(7), 1312–1320 (2012).

15

Ingram KG, Curtis CD, Silasi-Mansat R, Lupu F, Griffin CT. The NuRD chromatin-remodeling enzyme CHD4 promotes embryonic vascular integrity by transcriptionally regulating extracellular matrix proteolysis. PLoS Genet. 9(12), e1004031 (2013).

16

Neuman SD, Ihry RJ, Gruetzmacher KM, Bashirullah A. INO80-dependent regression of ecdysone-induced transcriptional responses regulates developmental timing in Drosophila. Dev. Biol. 387(2), 229–239 (2014).

17

Chen T, Dent SY. Chromatin modifiers and remodellers: regulators of cellular differentiation. Nat. Rev. Genet. 15(2), 93–106 (2014).

18

Nord AS, Blow MJ, Attanasio C et al. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155(7), 1521–1531 (2013).




37

Deindl S, Hwang WL, Hota SK et al. ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell 152(3), 442–452 (2013).

38

Bruno M, Flaus A, Stockdale C, Rencurel C, Ferreira H, Owen-Hughes T. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol. Cell 12(6), 1599–1606 (2003).

39

Dechassa ML, Sabri A, Pondugula S et al. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol. Cell 38(4), 590–602 (2010).

40

Ichinose H, Garnier JM, Chambon P, Losson R. Liganddependent interaction between the estrogen receptor and the human homologues of SWI2/SNF2. Gene 188(1), 95–100 (1997).

41

King HA, Trotter KW, Archer TK. Chromatin remodeling during glucocorticoid receptor regulated transactivation. Biochim. Biophys. Acta 1819(7), 716–726 (2012).

42

Lessard J, Wu JI, Ranish JA et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55(2), 201–215 (2007).

43

Lickert H, Takeuchi JK, Von Both I et al. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature 432(7013), 107–112 (2004).

44

Morris SA, Baek S, Sung MH et al. Overlapping chromatinremodeling systems collaborate genome wide at dynamic chromatin transitions. Nat. Struct. Mol. Biol. 21(1), 73–81 (2014).

•

45

Demonstrated that different chromatin remodeler families have transient sequential binding at sites they co-localize to co-ordinate DHS sites. Gao H, Lukin K, Ramirez J, Fields S, Lopez D, Hagman J. Opposing effects of SWI/SNF and Mi-2/NuRD chromatin remodeling complexes on epigenetic reprogramming by EBF and Pax5. Proc. Natl Acad. Sci. USA 106(27), 11258–11263 (2009).

46

Moshkin YM, Chalkley GE, Kan TW et al. Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Mol. Cell Biol. 32(3), 675–688 (2012).

47

Neely KE, Workman JL. The complexity of chromatin remodeling and its links to cancer. Biochim. Biophys. Acta 1603(1), 19–29 (2002).

48

Lai AY, Wade PA. Cancer biology and NuRD. a multifaceted chromatin remodelling complex. Nat. Rev. Cancer 11(8), 588–596 (2011).

49

Phelan ML, Sif S, Narlikar GJ, Kingston RE. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3(2), 247–253 (1999).

50

Kim Y, Fedoriw AM, Magnuson T. An essential role for a mammalian SWI/SNF chromatin-remodeling complex during male meiosis. Development 139(6), 1133–1140 (2012).

51

Reisman DN, Strobeck MW, Betz BL et al. Concomitant down-regulation of BRM and BRG1 in human tumor cell lines: differential effects on RB-mediated growth arrest vs CD44 expression. Oncogene 21(8), 1196–1207 (2002).

52

Chandler RL, Brennan J, Schisler JC, Serber D, Patterson C, Magnuson T. ARID1a-DNA interactions are required


Review

for promoter occupancy by SWI/SNF. Mol. Cell Biol. 33(2), 265–280 (2013). 53

Bultman S, Gebuhr T, Yee D et al. A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol. Cell 6(6), 1287–1295 (2000).

54

Sumi-Ichinose C, Ichinose H, Metzger D, Chambon P. SNF2beta-BRG1 is essential for the viability of F9 murine embryonal carcinoma cells. Mol. Cell Biol. 17(10), 5976–5986 (1997).

55

Smith-Roe SL, Bultman SJ. Combined gene dosage requirement for SWI/SNF catalytic subunits during early mammalian development. Mamm. Genome 24(1–2), 21–29 (2013).

•

Show that during development, BRM and BRG1 have non-redundant and overlapping roles.

56

Strobeck MW, Reisman DN, Gunawardena RW et al. Compensation of BRG-1 function by Brm: insight into the role of the core SWI-SNF subunits in retinoblastoma tumor suppressor signaling. J. Biol. Chem. 277(7), 4782–4789 (2002).

57

Oike T, Ogiwara H, Tominaga Y et al. A synthetic lethalitybased strategy to treat cancers harboring a genetic deficiency in the chromatin remodeling factor BRG1. Cancer Res. 73(17), 5508–5518 (2013).

58

Flores-Alcantar A, Gonzalez-Sandoval A, Escalante-Alcalde D, Lomeli H. Dynamics of expression of ARID1A and ARID1B subunits in mouse embryos and in cells during the cell cycle. Cell Tissue Res. 345(1), 137–148 (2011).

59

Wang X, Nagl NG, Wilsker D et al. Two related ARID family proteins are alternative subunits of human SWI/SNF complexes. Biochem. J. 383(Pt 2), 319–325 (2004).

60

Xu F, Flowers S, Moran E. Essential role of ARID2 proteincontaining SWI/SNF complex in tissue-specific gene expression. J. Biol. Chem. 287(7), 5033–5041 (2012).

61

Nagl NG, Jr., Wang X, Patsialou A, Van Scoy M, Moran E. Distinct mammalian SWI/SNF chromatin remodeling complexes with opposing roles in cell-cycle control. EMBO J. 26(3), 752–763 (2007).

62

Yan Z, Wang Z, Sharova L et al. BAF250B-associated SWI/ SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells 26(5), 1155–1165 (2008).

63

Kia SK, Gorski MM, Giannakopoulos S, Verrijzer CP. SWI/SNF mediates polycomb eviction and epigenetic reprogramming of the INK4b-ARF-INK4a locus. Mol. Cell Biol. 28(10), 3457–3464 (2008).

64

Tamkun JW, Deuring R, Scott MP et al. Brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2. Cell 68(3), 561–572 (1992).

65

Wilson BG, Wang X, Shen X et al. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell 18(4), 316–328 (2010).

••

SWI/SNF has an antagonistic relationship with polycomb group proteins.

66

Barrales RR, Korber P, Jimenez J, Ibeas JI. Chromatin modulation at the FLO11 promoter of Saccharomyces


411

Review Skulte, Phan, Clark & Taberlay cerevisiae by HDAC and Swi/Snf complexes. Genetics 191(3), 791–803 (2012). 67

68

69

70

Mitra D, Parnell EJ, Landon JW, Yu Y, Stillman DJ. SWI/ SNF binding to the HO promoter requires histone acetylation and stimulates TATA-binding protein recruitment. Mol. Cell Biol. 26(11), 4095–4110 (2006). Zhang HS, Gavin M, Dahiya A et al. Exit from G1 and S phase of the cell cycle is regulated by repressor complexes containing HDAC-Rb-hSWI/SNF and Rb-hSWI/SNF. Cell 101(1), 79–89 (2000). Ogiwara H, Ui A, Otsuka A et al. Histone acetylation by CBP and p300 at double-strand break sites facilitates SWI/ SNF chromatin remodeling and the recruitment of nonhomologous end joining factors. Oncogene 30(18), 2135–2146 (2011).

Cho H, Kim JS, Chung H, Perry C, Lee H, Kim JH. Loss of ARID1A/BAF250a expression is linked to tumor progression and adverse prognosis in cervical cancer. Hum. Pathol. 44(7), 1365–1374 (2013).

82

Bosse T, Ter Haar NT, Seeber LM et al. Loss of ARID1A expression and its relationship with PI3K-Akt pathway alterations, TP53 and microsatellite instability in endometrial cancer. Mod. Pathol. 26(11), 1525–1535 (2013).

83

Bai J, Mei P, Zhang C et al. BRG1 is a prognostic marker and potential therapeutic target in human breast cancer. PloS One 8(3), e59772 (2013).

84

Katagiri A, Nakayama K, Rahman MT et al. Loss of ARID1A expression is related to shorter progression-free survival and chemoresistance in ovarian clear cell carcinoma. Mod. Pathol. 25(2), 282–288 (2012).

85

Roberts CW, Biegel JA. The role of SMARCB1/INI1 in development of rhabdoid tumor. Cancer Biol. Ther. 8(5), 412–416 (2009).

86

Roy DM, Walsh LA, Chan TA. Driver mutations of cancer epigenomes. Protein Cell 5(4), 265–296 (2014).

71

Zhao J, Liu C, Zhao Z. ARID1A. a potential prognostic factor for breast cancer. Tumour Biol. (2014).

87

72

Yokoyama Y, Matsushita Y, Shigeto T, Futagami M, Mizunuma H. Decreased ARID1A expression is correlated with chemoresistance in epithelial ovarian cancer. J. Gynecol. Oncol. 25(1), 58–63 (2014).

Roberts CW, Orkin SH. The SWI/SNF complex--chromatin and cancer. Nat. Rev. Cancer 4(2), 133–142 (2004).

88

Song S, Walter V, Karaca M et al. Gene silencing associated with SWI/SNF complex loss during NSCLC development. Mol. Cancer Res. 12(4), 560–570 (2014).

Wilson BG, Helming KC, Wang X et al. Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation. Mol. Cell Biol. 34(6), 1136–1144 (2014).

89

Sun A, Tawfik O, Gayed B et al. Aberrant expression of SWI/ SNF catalytic subunits BRG1/BRM is associated with tumor development and increased invasiveness in prostate cancers. Prostate 67(2), 203–213 (2007).

90

Mckenna ES, Sansam CG, Cho YJ et al. Loss of the epigenetic tumor suppressor SNF5 leads to cancer without genomic instability. Mol. Cell Biol. 28(20), 6223–6233 (2008).

91

Tolstorukov MY, Sansam CG, Lu P et al. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc. Natl Acad. Sci. USA 110(25), 10165–10170 (2013).

92

He HH, Meyer CA, Shin H et al. Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 42(4), 343–347 (2010).

93

Andreu-Vieyra C, Lai J, Berman BP et al. Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells. Mol. Cell Biol. 31(23), 4648–4662 (2011).

94

Hu G, Schones DE, Cui K et al. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res. 21(10), 1650–1658 (2011).

95

Li L, Liu D, Bu D et al. Brg1-dependent epigenetic control of vascular smooth muscle cell proliferation by hydrogen sulfide. Biochim. Biophys. Acta 1833(6), 1347–1355 (2013).

96

Bultman SJ, Gebuhr TC, Magnuson T. A Brg1 mutation that uncouples ATPase activity from chromatin remodeling reveals an essential role for SWI/SNF-related complexes in beta-globin expression and erythroid development. Genes Dev. 19(23), 2849–2861 (2005).

97

Harte MT, O’brien GJ, Ryan NM et al. BRD7, a subunit of SWI/SNF complexes, binds directly to BRCA1 and

73

412

Kim JH, Saraf A, Florens L, Washburn M, Workman JL. Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2. Genes Dev. 24(24), 2766–2771 (2010).

81

74

Buscarlet M, Krasteva V, Ho L et al. Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance. Blood 123(11), 1720–1728 (2014).

75

Yan HB, Wang XF, Zhang Q et al. Reduced expression of the chromatin remodeling gene ARID1A enhances gastric cancer cell migration and invasion via downregulation of E-cadherin transcription. Carcinogenesis 35(4) 867–876 (2013).

76

Shi J, Whyte WA, Zepeda-Mendoza CJ et al. Role of SWI/ SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 27(24), 2648–2662 (2013).

••

BRG1 is essential in acute leukaemia by maintaining Myc enhancer-promoter interactions.

77

Shain AH, Pollack JR. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PloS One 8(1), e55119 (2013).

78

Romero OA, Torres-Diz M, Pros E et al. MAX inactivation in small-cell lung cancer disrupts the MYC-SWI/SNF programs and is synthetic lethal with BRG1. Cancer Discov. 4(3), 292–303 (2013).

79

Oike T, Ogiwara H, Nakano T, Yokota J, Kohno T. Inactivating mutations in SWI/SNF chromatin remodeling genes in human cancer. Jpn J. Clin. Oncol. 43(9), 849–855 (2013).

•

A recent thorough review of mutations in the SWI/SNF complex.

80

Mao TL, Ardighieri L, Ayhan A et al. Loss of ARID1A expression correlates with stages of tumor progression in uterine endometrioid carcinoma. Am. J. Surg. Pathol. 37(9), 1342–1348 (2013).




regulates BRCA1-dependent transcription. Cancer Res. 70(6), 2538–2547 (2010). 98

99

Miranda TB, Voss TC, Sung MH et al. Reprogramming the chromatin landscape: interplay of the estrogen and glucocorticoid receptors at the genomic level. Cancer Res. 73(16), 5130–5139 (2013). Fryer CJ, Archer TK. Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex. Nature 393(6680), 88–91 (1998).

subunit BRG1 is a critical regulator of p53 necessary for proliferation of malignant cells. Oncogene 28(27), 2492–2501 (2009). 113 Tie F, Banerjee R, Conrad PA, Scacheri PC, Harte PJ.

Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27. Mol. Cell Biol. 32(12), 2323–2334 (2012). 114 Zeisig DT, Bittner CB, Zeisig BB, Garcia-Cuellar MP, Hess

JL, Slany RK. The eleven-nineteen-leukemia protein ENL connects nuclear MLL fusion partners with chromatin. Oncogene 24(35), 5525–5532 (2005).

100 Li J, Fu J, Toumazou C, Yoon HG, Wong J. A role of the

amino-terminal (N) and carboxyl-terminal (C) interaction in binding of androgen receptor to chromatin. Mol. Endocrinol. 20(4), 776–785 (2006).

115 Nie Z, Yan Z, Chen EH et al. Novel SWI/SNF chromatin-

remodeling complexes contain a mixed-lineage leukemia chromosomal translocation partner. Mol. Cell Biol. 23(8), 2942–2952 (2003).

101 Ostlund Farrants AK, Blomquist P, Kwon H, Wrange O.

Glucocorticoid receptor-glucocorticoid response element binding stimulates nucleosome disruption by the SWI/SNF complex. Mol. Cell Biol. 17(2), 895–905 (1997).

116 Chodavarapu RK, Feng S, Bernatavichute YV et al.

Relationship between nucleosome positioning and DNA methylation. Nature 466(7304), 388–392 (2010).

102 Marshall TW, Link KA, Petre-Draviam CE, Knudsen

KE. Differential requirement of SWI/SNF for androgen receptor activity. J. Biol. Chem. 278(33), 30605–30613 (2003). 103 Zhang B, Chambers KJ, Faller DV, Wang S.

Reprogramming of the SWI/SNF complex for co-activation or co-repression in prohibitin-mediated estrogen receptor regulation. Oncogene 26(50), 7153–7157 (2007). ••

SWI/SNF can act as a repressor or activator at the same promoter, dependent on the composition of subunits within the complex.

117 Choi SH, Heo K, Byun HM, An W, Lu W, Yang AS.

Identification of preferential target sites for human DNA methyltransferases. Nucleic Acids Res. 39(1), 104–118 (2011). 118 Collings CK, Waddell PJ, Anderson JN. Effects of DNA

methylation on nucleosome stability. Nucleic Acids Res. 41(5), 2918–2931 (2013). 119 Jeong S, Liang G, Sharma S et al. Selective anchoring of DNA

methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol. Cell Biol. 29(19), 5366–5376 (2009). 120 Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA.

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22(12), 2497–2506 (2012).

104 Gorski JJ, James CR, Quinn JE et al. BRCA1

transcriptionally regulates genes associated with the basallike phenotype in breast cancer. Breast Cancer Res. Treat. 122(3), 721–731 (2010).

121 Sharma S, De Carvalho DD, Jeong S, Jones PA, Liang G.

Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance. PLoS Genet. 7(2), e1001286 (2011).

105 Mazaris E, Tsiotras A. Molecular pathways in prostate

cancer. Nephrourol. Mon. 5(3), 792–800 (2013). 106 Ung M, Ma X, Johnson KC, Christensen BC, Cheng C.

Effect of estrogen receptor alpha binding on functional DNA methylation in breast cancer. Epigenetics 9(4), 523–532 (2014). 107 Duong V, Bret C, Altucci L et al. Specific activity of class

II histone deacetylases in human breast cancer cells. Mol. Cancer Res. 6(12), 1908–1919 (2008). 108 Feng D, Wu J, Tian Y et al. Targeting of histone

deacetylases to reactivate tumour suppressor genes and its therapeutic potential in a human cervical cancer xenograft model. PloS One 8(11), e80657 (2013). 109 Wang G, He J, Zhao J et al. Class I and class II histone

deacetylases are potential therapeutic targets for treating pancreatic cancer. PloS One 7(12), e52095 (2012). 110 Shen W, Xu C, Huang W et al. Solution structure of human

Brg1 bromodomain and its specific binding to acetylated histone tails. Biochemistry 46(8), 2100–2110 (2007). 111 Luebben WR, Sharma N, Nyborg JK. Nucleosome eviction

and activated transcription require p300 acetylation of histone H3 lysine 14. Proc. Natl Acad. Sci. USA 107(45), 19254–19259 (2010). 112 Naidu SR, Love IM, Imbalzano AN, Grossman SR,

Androphy EJ. The SWI/SNF chromatin remodeling


Review

•

Shows the importance of nucleosomes in the establishment and maintenance of DNA methylation.

122 You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang

G, Jones PA. OCT4 establishes and maintains nucleosomedepleted regions that provide additional layers of epigenetic regulation of its target genes. Proc. Natl Acad. Sci. USA 108(35), 14497–14502 (2011). 123 Hinshelwood RA, Melki JR, Huschtscha LI et al. Aberrant de

novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning. Hum. Mol. Genet. 18(16), 3098–3109 (2009). 124 Banine F, Bartlett C, Gunawardena R et al. SWI/SNF

chromatin-remodeling factors induce changes in DNA methylation to promote transcriptional activation. Cancer Res. 65(9), 3542–3547 (2005). 125 Choi JK. Contrasting chromatin organization of CpG islands

and exons in the human genome. Genome Biol. 11(7), R70 (2010). 126 Ndlovu MN, Denis H, Fuks F. Exposing the DNA

methylome iceberg. Trends Biochem. Sci. 36(7), 381–387 (2011).


413

Review Skulte, Phan, Clark & Taberlay 127 Gelfman S, Cohen N, Yearim A, Ast G. DNA-methylation

effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res. 23(5), 789–799 (2013). 128 Maunakea AK, Chepelev I, Cui K, Zhao K. Intragenic DNA

methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res. 23(11), 1256–1269 (2013). 129 Shukla S, Kavak E, Gregory M et al. CTCF-promoted RNA

polymerase II pausing links DNA methylation to splicing. Nature 479(7371), 74–79 (2011). 130 Batsche E, Yaniv M, Muchardt C. The human SWI/SNF

subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol. 13(1), 22–29 (2006). 131 Zraly CB, Dingwall AK. The chromatin remodeling and

mRNA splicing functions of the Brahma (SWI/SNF) complex are mediated by the SNR1/SNF5 regulatory subunit. Nucleic Acids Res. 40(13), 5975–5987 (2012). 132 Glaros S, Cirrincione GM, Muchardt C, Kleer CG, Michael

133 Gao X, Tate P, Hu P, Tjian R, Skarnes WC, Wang Z. ES

cell pluripotency and germ-layer formation require the SWI/ SNF chromatin remodeling component BAF250a. Proc. Natl Acad. Sci. USA 105(18), 6656–6661 (2008). 134 Lei I, Gao X, Sham MH, Wang Z. SWI/SNF protein

component BAF250a regulates cardiac progenitor cell differentiation by modulating chromatin accessibility during second heart field development. J. Biol. Chem. 287(29), 24255–24262 (2012). 135 Bochar DA, Wang L, Beniya H et al. BRCA1 is associated

with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell 102(2), 257–265 (2000). 136 Zhang L, Chen H, Gong M, Gong F. The chromatin

remodeling protein BRG1 modulates BRCA1 response to UV irradiation by regulating ATR/ATM activation. Front. Oncol. doi:10.3389/fonc.2013.00007 (2013) (Epub ahead of print). 137 Wang J, Gu H, Lin H, Chi T. Essential roles of the

chromatin remodeling factor BRG1 in spermatogenesis in mice. Biol. Reprod. 86(6), 186 (2012).

CW, Reisman D. The reversible epigenetic silencing of BRM: implications for clinical targeted therapy. Oncogene 26(49), 7058–7066 (2007).

414



p53 mutations in human cancers.

Epigenetic Alterations in Human Papillomavirus-Associated Cancers.

Frequent involvement of chromatin remodeler alterations in gastric field cancerization.

Epigenetic silencing of miR-490-3p reactivates the chromatin remodeler SMARCD1 to promote Helicobacter pylori-induced gastric carcinogenesis.

De Novo Mutations in CHD4, an ATP-Dependent Chromatin Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive Dysmorphisms.

Influenza Virus and Chromatin: Role of the CHD1 Chromatin Remodeler in the Virus Life Cycle.

Chromatin Memory in the Development of Human Cancers.

Epigenetic instability of imprinted genes in human cancers.

INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation.

The poly(ADP-ribose)-dependent chromatin remodeler Alc1 induces local chromatin relaxation upon DNA damage.

Human sperm chromatin epigenetic potential: genomics, proteomics, and male infertility.

Epigenetic Alterations in Parathyroid Cancers.

Mutations of Chromatin Structure Regulating Genes in Human Malignancies.

Chromatin regulators: weaving epigenetic nets.

Epigenetic biomarkers: potential applications in gastrointestinal cancers.

The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.

bookmarking function of HNF1B.

Functions of Fun30 chromatin remodeler in regulating cellular resistance to genotoxic stress.

Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair.

Sth1 Potentiates Nucleosome Sliding and Ejection.

Chromatin composition alterations and the critical role of MeCP2 for epigenetic silencing of progesterone receptor-B gene in endometrial cancers.

Chromatin Remodeler Recruitment during Macrophage Differentiation Facilitates Transcription Factor Binding to Enhancers in Mature Cells.

A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions.

The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome.