Journal of Pathology J Pathol 2014; 232: 485–487 Published online 29 January 2014 in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/path.4326
IN BRIEF
In Brief: Genomic imprinting and imprinting diseases Bernhard Horsthemke* Institut f¨ur Humangenetik, Universit¨atsklinikum Essen, Universit¨at Duisburg-Essen, Germany *Correspondence to: Bernhard Horsthemke, Institut f¨ur Humangenetik, Universit¨atsklinikum Essen, Universit¨at Duisburg-Essen, Hufelandstraße 55, D-45147 Essen, Germany. e-mail: [email protected]
Abstract Genomic imprinting is an epigenetic process by which the male and the female germline confer different DNA methylation marks and histone modifications onto specific gene regions, so that one allele of an imprinted gene is active and the other one is silent. Since the dosage of imprinted genes is important for normal development, growth and behaviour, the loss or duplication of the active allele can cause disease. Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Keywords: genomic imprinting; DNA methylation; epigenetics
Received 19 December 2013; Revised 19 December 2013; Accepted 27 December 2013
No conflicts of interest were declared.
Introduction
Mechanisms of imprinting
In diploid cells, most genes come in two copies: a paternal allele and a maternal allele. Unless one allele is mutated, both alleles behave in a similar way: they are either active or inactive, depending on the identity and state of the cell. In therian mammals including humans, there are two exceptions to this rule: Xchromosomal genes in females and imprinted genes. In both cases, one allele is active and one allele is inactive. Whereas males have only one X-chromosome, females have two. For reasons of dosage compensation, in females one X-chromosome in inactivated. The choice of which X-chromosome is inactivated occurs more or less randomly in each cell of the early embryo. Once made, it is maintained during subsequent cell divisions so that female individuals are somatic mosaics: in ∼50% of cells the paternal X is silenced, whereas in the other ∼50% of cells the maternal allele is silenced. In contrast, imprinted gene silencing occurs in the germline. Approximately 100 human genes, most of which are located on chromosomes 6, 7, 11, 14, 15, and 20, are subject to genomic imprinting. Some of the genes are silenced during oogenesis, whereas others are silenced during spermatogenesis. As a consequence, only the paternal or only the maternal allele of a gene is active in the somatic cells of the offspring. With a few exceptions, this parent-of-origin specific pattern is identical in all somatic cells, and there is no difference between males and females. The pattern is maintained during development and growth of the organism, but erased in the primordial germ cells (Figure 1A).
Although there is still some controversy about the nature of the primary imprint, the parental copies of an imprinted region differ with respect to DNA methylation and histone modification. Typically, a gene-regulatory region is methylated on one chromosome and unmethylated on the other chromosome. When both copies of a differentially methylated region (DMR) are analysed together, approximately 50% methylation is found. The establishment of a DNA methylation imprint in the germline requires the activity of the DNA methyltransferase DNMT3A and its cofactor DNMT3L, which confer a methyl group from S -adenosyl-methionine onto a cytosine residue within a CpG dinucleotide to yield 5-methylcytosine (5mC). These enzymes cannot recognize the DNA sequence of target regions, but appear to be recruited to DMRs by histone modification patterns laid down by transcription through these regions. Probably, the two germlines differ in the presence of transcription factors that bind to sites upstream of the DMRs, so that some DMRs are methylated only in the paternal germline and others are methylated only in the maternal germline. The methylation state of a DMR then determines the activity state of the genes that are under the control of this DMR. After fertilization, methylation patterns are maintained by the DNA methyltransferase DNMT1, which methylates hemimethylated DNA after semiconservative DNA replication, and by additional factors including ZFP57, TRIM28, and NLRP7. Methylation imprints survive the waves of global DNA demethylation and remethylation during early
Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
J Pathol 2014; 232: 485–487 www.thejournalofpathology.com
486
B Horsthemke
Figure 1. Genomic imprinting and imprinting diseases. (A) Imprints are erased in the primordial germ cells, established during gametogenesis and maintained in the embryo. For clarity, only one pair of homologous chromosomes (blue, paternal chromosome; pink, maternal chromosome), a paternally expressed gene (yellow dot), a repressive maternal methylation imprint (red square), and only one of four possible gametes are shown. Although the majority of imprinted loci carry a maternal methylation mark, some carry a paternal methylation mark and are expressed from the maternal chromosome only (not shown). (B) Genetic and epigenetic aberrations affecting an imprinted locus. For simplicity, a mutation (m), a deletion, a maternal uniparental disomy, and an imprinting defect affecting a paternally expressed gene are shown. Reciprocal aberrations may affect a maternally expressed gene. (C) Pedigree showing autosomal-dominant inheritance with parent-of-origin specific penetrance. A mutation in a maternally expressed gene causes disease only after maternal transmission. Filled symbol, affected individual; dotted symbol, healthy mutation carrier.
embryogenesis because they are protected by DPPA3 and other factors. It is not yet clear how imprints are erased in primordial germ cells. They may be lost by several rounds of DNA replication in the absence of DNMT1 activity (passive DNA demethylation) or may be actively removed by AID-mediated 5mC deamination and/or TET-mediated oxygenation, followed by base excision repair.
Wang syndrome (paternal UPD 14 syndrome; 14q32), Angelman syndrome (15q11q13), Prader–Willi syndrome (15q11q13), and pseudohypoparathyroidism type IB (20q13). These diseases are caused by several mechanisms: gene mutation, chromosomal deletion or duplication, uniparental disomy, and imprinting defect (Figure 1B). Some of these mechanisms also contribute to tumourigenesis.
Imprinting in disease
Gene mutation
As a consequence of genomic imprinting, only one of the two parental alleles of an imprinted gene is active. Therefore, the loss of function of the active allele cannot be compensated by the other allele. This makes imprinted loci especially vulnerable to mutations. Furthermore, many imprinted genes are dosage-sensitive, ie the duplication of the active allele can also be harmful. On the other hand, a mutation of the inactive allele is without any consequences to the mutation carrier. At present, eight ‘imprinting diseases’ have been recognized (affected chromosome regions in parentheses): transient neonatal diabetes mellitus (6q24), Beckwith–Wiedemann syndrome (11p15), Russell–Silver syndrome (11p15), Temple syndrome (maternal UPD 14 syndrome; 14q32),
A single loss-of-function mutation affecting the one and only active allele of an imprinted gene leads to a complete loss of function of this gene. A good example for this is mutation of the maternally expressed UBE3A gene, which causes Angelman syndrome. The mutations may occur de novo in the female germline or may be carried by the mother on her paternal chromosome. In the latter case, the mother is healthy because the mutation is on the silent, paternal allele, but she has a 50% risk of transmitting the mutant allele as a maternal, disease-causing allele to her offspring. We know of several families in which a UBE3A mutation has been transmitted through the paternal germline of several generations without doing any harm until it was inherited by a female individual, who gave birth to a child with Angelman syndrome. The mode of inheritance is
Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
J Pathol 2014; 232: 485–487 www.thejournalofpathology.com
In Brief: Genomic imprinting and imprinting diseases
autosomal dominant with parent-of-origin specific penetrance (Figure 1C).
Chromosomal deletion or duplication Chromosomal deletion or duplication affecting the active copy of an imprinted gene leads to a complete loss of function or a double dose of this gene. The majority of patients with Prader–Willi syndrome or Angelman syndrome, for example, have a paternal or maternal deletion of 15q11q13, respectively. A paternal duplication of 11p15, which leads to two active copies of IGF2, is one cause of Beckwith–Wiedemann syndrome.
Uniparental disomy Uniparental disomy (UPD) refers to a situation in which both copies of a chromosome pair are derived from the same parent. Most often, UPD is the result of meiotic and mitotic non-disjunction events. It is associated with advanced maternal age and leads to a complete loss of function or a double dose of an imprinted gene, depending on the parental origin of the two chromosomes and the imprinting status of the gene(s) on this chromosome.
Imprinting defect Defects in imprint erasure, establishment, or maintenance result in a paternal chromosome carrying a maternal imprint or a maternal chromosome carrying a paternal imprint. A wrong imprint leads to activation of an allele that should be silent or silencing of an allele that should be active. Imprinting defects can occur spontaneously without any DNA sequence change (primary imprinting defect) or as the result of a mutation in a cis-regulatory element or a trans-acting
Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
487
factor (secondary imprinting defect). Whereas a mutation in an imprint control element affects only one imprinted domain, a mutation in a trans-acting factor such as ZFP57 often leads to multi-locus methylation defects. Apart from mutations in an imprinted gene, all mechanisms lead to aberrant DNA methylation patterns (more or less than 50% methylation). Therefore, DNA methylation analysis of DMRs is the first-tier clinical diagnostic test for individuals suspected of having an imprinting disease.
Acknowledgments Work in the author’s laboratory was supported by the Bundesministerium f¨ur Bildung und Forschung (grant number 01GM1114A). I thank Jasmin Beygo for critical reading of the manuscript.
Author contribution statement BH wrote the review.
Suggested further reading Ferguson-Smith AC. Genomic imprinting: the emergence of an epigenetic paradigm. Nature Rev Genet 2011; 12: 565–575. Horsthemke B. Mechanisms of imprint dysregulation. Am J Med Genet 2010; 154C: 321–328. Tomizawa S, Nowacka-Woszuk J, Kelsey G. DNA methylation establishment during oocyte growth: mechanisms and significance. Int J Dev Biol 2012; 56: 867–875. Uribe-Lewis S, Woodfine K, Stojic L, et al. Molecular mechanisms of genomic imprinting and clinical implications for cancer. Expert Rev Mol Med 2011; 13: e2.
J Pathol 2014; 232: 485–487 www.thejournalofpathology.com
IN BRIEF
In Brief: Genomic imprinting and imprinting diseases Bernhard Horsthemke* Institut f¨ur Humangenetik, Universit¨atsklinikum Essen, Universit¨at Duisburg-Essen, Germany *Correspondence to: Bernhard Horsthemke, Institut f¨ur Humangenetik, Universit¨atsklinikum Essen, Universit¨at Duisburg-Essen, Hufelandstraße 55, D-45147 Essen, Germany. e-mail: [email protected]
Abstract Genomic imprinting is an epigenetic process by which the male and the female germline confer different DNA methylation marks and histone modifications onto specific gene regions, so that one allele of an imprinted gene is active and the other one is silent. Since the dosage of imprinted genes is important for normal development, growth and behaviour, the loss or duplication of the active allele can cause disease. Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Keywords: genomic imprinting; DNA methylation; epigenetics
Received 19 December 2013; Revised 19 December 2013; Accepted 27 December 2013
No conflicts of interest were declared.
Introduction
Mechanisms of imprinting
In diploid cells, most genes come in two copies: a paternal allele and a maternal allele. Unless one allele is mutated, both alleles behave in a similar way: they are either active or inactive, depending on the identity and state of the cell. In therian mammals including humans, there are two exceptions to this rule: Xchromosomal genes in females and imprinted genes. In both cases, one allele is active and one allele is inactive. Whereas males have only one X-chromosome, females have two. For reasons of dosage compensation, in females one X-chromosome in inactivated. The choice of which X-chromosome is inactivated occurs more or less randomly in each cell of the early embryo. Once made, it is maintained during subsequent cell divisions so that female individuals are somatic mosaics: in ∼50% of cells the paternal X is silenced, whereas in the other ∼50% of cells the maternal allele is silenced. In contrast, imprinted gene silencing occurs in the germline. Approximately 100 human genes, most of which are located on chromosomes 6, 7, 11, 14, 15, and 20, are subject to genomic imprinting. Some of the genes are silenced during oogenesis, whereas others are silenced during spermatogenesis. As a consequence, only the paternal or only the maternal allele of a gene is active in the somatic cells of the offspring. With a few exceptions, this parent-of-origin specific pattern is identical in all somatic cells, and there is no difference between males and females. The pattern is maintained during development and growth of the organism, but erased in the primordial germ cells (Figure 1A).
Although there is still some controversy about the nature of the primary imprint, the parental copies of an imprinted region differ with respect to DNA methylation and histone modification. Typically, a gene-regulatory region is methylated on one chromosome and unmethylated on the other chromosome. When both copies of a differentially methylated region (DMR) are analysed together, approximately 50% methylation is found. The establishment of a DNA methylation imprint in the germline requires the activity of the DNA methyltransferase DNMT3A and its cofactor DNMT3L, which confer a methyl group from S -adenosyl-methionine onto a cytosine residue within a CpG dinucleotide to yield 5-methylcytosine (5mC). These enzymes cannot recognize the DNA sequence of target regions, but appear to be recruited to DMRs by histone modification patterns laid down by transcription through these regions. Probably, the two germlines differ in the presence of transcription factors that bind to sites upstream of the DMRs, so that some DMRs are methylated only in the paternal germline and others are methylated only in the maternal germline. The methylation state of a DMR then determines the activity state of the genes that are under the control of this DMR. After fertilization, methylation patterns are maintained by the DNA methyltransferase DNMT1, which methylates hemimethylated DNA after semiconservative DNA replication, and by additional factors including ZFP57, TRIM28, and NLRP7. Methylation imprints survive the waves of global DNA demethylation and remethylation during early
Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
J Pathol 2014; 232: 485–487 www.thejournalofpathology.com
486
B Horsthemke
Figure 1. Genomic imprinting and imprinting diseases. (A) Imprints are erased in the primordial germ cells, established during gametogenesis and maintained in the embryo. For clarity, only one pair of homologous chromosomes (blue, paternal chromosome; pink, maternal chromosome), a paternally expressed gene (yellow dot), a repressive maternal methylation imprint (red square), and only one of four possible gametes are shown. Although the majority of imprinted loci carry a maternal methylation mark, some carry a paternal methylation mark and are expressed from the maternal chromosome only (not shown). (B) Genetic and epigenetic aberrations affecting an imprinted locus. For simplicity, a mutation (m), a deletion, a maternal uniparental disomy, and an imprinting defect affecting a paternally expressed gene are shown. Reciprocal aberrations may affect a maternally expressed gene. (C) Pedigree showing autosomal-dominant inheritance with parent-of-origin specific penetrance. A mutation in a maternally expressed gene causes disease only after maternal transmission. Filled symbol, affected individual; dotted symbol, healthy mutation carrier.
embryogenesis because they are protected by DPPA3 and other factors. It is not yet clear how imprints are erased in primordial germ cells. They may be lost by several rounds of DNA replication in the absence of DNMT1 activity (passive DNA demethylation) or may be actively removed by AID-mediated 5mC deamination and/or TET-mediated oxygenation, followed by base excision repair.
Wang syndrome (paternal UPD 14 syndrome; 14q32), Angelman syndrome (15q11q13), Prader–Willi syndrome (15q11q13), and pseudohypoparathyroidism type IB (20q13). These diseases are caused by several mechanisms: gene mutation, chromosomal deletion or duplication, uniparental disomy, and imprinting defect (Figure 1B). Some of these mechanisms also contribute to tumourigenesis.
Imprinting in disease
Gene mutation
As a consequence of genomic imprinting, only one of the two parental alleles of an imprinted gene is active. Therefore, the loss of function of the active allele cannot be compensated by the other allele. This makes imprinted loci especially vulnerable to mutations. Furthermore, many imprinted genes are dosage-sensitive, ie the duplication of the active allele can also be harmful. On the other hand, a mutation of the inactive allele is without any consequences to the mutation carrier. At present, eight ‘imprinting diseases’ have been recognized (affected chromosome regions in parentheses): transient neonatal diabetes mellitus (6q24), Beckwith–Wiedemann syndrome (11p15), Russell–Silver syndrome (11p15), Temple syndrome (maternal UPD 14 syndrome; 14q32),
A single loss-of-function mutation affecting the one and only active allele of an imprinted gene leads to a complete loss of function of this gene. A good example for this is mutation of the maternally expressed UBE3A gene, which causes Angelman syndrome. The mutations may occur de novo in the female germline or may be carried by the mother on her paternal chromosome. In the latter case, the mother is healthy because the mutation is on the silent, paternal allele, but she has a 50% risk of transmitting the mutant allele as a maternal, disease-causing allele to her offspring. We know of several families in which a UBE3A mutation has been transmitted through the paternal germline of several generations without doing any harm until it was inherited by a female individual, who gave birth to a child with Angelman syndrome. The mode of inheritance is
Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
J Pathol 2014; 232: 485–487 www.thejournalofpathology.com
In Brief: Genomic imprinting and imprinting diseases
autosomal dominant with parent-of-origin specific penetrance (Figure 1C).
Chromosomal deletion or duplication Chromosomal deletion or duplication affecting the active copy of an imprinted gene leads to a complete loss of function or a double dose of this gene. The majority of patients with Prader–Willi syndrome or Angelman syndrome, for example, have a paternal or maternal deletion of 15q11q13, respectively. A paternal duplication of 11p15, which leads to two active copies of IGF2, is one cause of Beckwith–Wiedemann syndrome.
Uniparental disomy Uniparental disomy (UPD) refers to a situation in which both copies of a chromosome pair are derived from the same parent. Most often, UPD is the result of meiotic and mitotic non-disjunction events. It is associated with advanced maternal age and leads to a complete loss of function or a double dose of an imprinted gene, depending on the parental origin of the two chromosomes and the imprinting status of the gene(s) on this chromosome.
Imprinting defect Defects in imprint erasure, establishment, or maintenance result in a paternal chromosome carrying a maternal imprint or a maternal chromosome carrying a paternal imprint. A wrong imprint leads to activation of an allele that should be silent or silencing of an allele that should be active. Imprinting defects can occur spontaneously without any DNA sequence change (primary imprinting defect) or as the result of a mutation in a cis-regulatory element or a trans-acting
Copyright 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
487
factor (secondary imprinting defect). Whereas a mutation in an imprint control element affects only one imprinted domain, a mutation in a trans-acting factor such as ZFP57 often leads to multi-locus methylation defects. Apart from mutations in an imprinted gene, all mechanisms lead to aberrant DNA methylation patterns (more or less than 50% methylation). Therefore, DNA methylation analysis of DMRs is the first-tier clinical diagnostic test for individuals suspected of having an imprinting disease.
Acknowledgments Work in the author’s laboratory was supported by the Bundesministerium f¨ur Bildung und Forschung (grant number 01GM1114A). I thank Jasmin Beygo for critical reading of the manuscript.
Author contribution statement BH wrote the review.
Suggested further reading Ferguson-Smith AC. Genomic imprinting: the emergence of an epigenetic paradigm. Nature Rev Genet 2011; 12: 565–575. Horsthemke B. Mechanisms of imprint dysregulation. Am J Med Genet 2010; 154C: 321–328. Tomizawa S, Nowacka-Woszuk J, Kelsey G. DNA methylation establishment during oocyte growth: mechanisms and significance. Int J Dev Biol 2012; 56: 867–875. Uribe-Lewis S, Woodfine K, Stojic L, et al. Molecular mechanisms of genomic imprinting and clinical implications for cancer. Expert Rev Mol Med 2011; 13: e2.
J Pathol 2014; 232: 485–487 www.thejournalofpathology.com
