Epigenetic Mechanisms of Human Imprinting Disorders

CHAPTER

13

Epigenetic Mechanisms of Human Imprinting Disorders Richard H. Scott1, 2, Gudrun E. Moore1 Institute of Child Health, University College London, London, UK 2 Great Ormond Street Hospital, London, UK

1

CHAPTER OUTLINE 13.1 Introduction 254 13.2 Chromatin Structure Reflects Epigenetic Modifications 254 13.2.1 DNA Methylation

255

13.3 DNA Methylation and Transcriptional Silencing 255 13.4 Maintenance and Establishment of DNA Methylation During Development 255 13.4.1 Histone Modifications 256 13.4.2 Non-Histone DNA-Binding Proteins 257 13.4.3 Non-Coding RNAs 257 13.4.4 Cross-Talk Between Epigenetic Systems 257

13.5 Genomic Imprinting

13.5.6 Imprinted Domain 2 262 KvDMR1 Controls Imprinting at Imprinted Domain 2 263 13.5.7 Establishment of Imprinting at the 11p15 GRR 263 13.5.8 Abnormalities at Imprinted Loci 263

257

13.5.1 Imprinted Loci 258 13.5.2 Imprinting Centers Control Imprinting in cis 258 13.5.3 Establishment of DNA Methylation at Imprinted Loci During Development 260 13.5.4 The 11p15 Imprinted Region 260 13.5.5 Imprinted Domain 1 261 H19 DMR Controls Imprinted Domain 1 262 Chromatin Looping in the Control of Imprinted Domain 1 262 The IGF2 Differentially Methylated Regions 262

13.6 13.7 13.8 13.9

Uniparental Disomy 263 Epimutations 264 Imprinting Center Mutations 264 Mutations in Imprinted Genes 264 13.10 Copy Number Abnormalities Encompassing Imprinted Genes 264 13.11 Mutations in Imprinting Establishment or Maintenance Machinery 264 13.11.1 Phenotypes Associated with Constitutional Abnormalities at Imprinted Loci 265

13.12 13.13 13.14 13.15 13.16 13.17 13.18

Chromosome 6q24 265 Chromosome 7 265 Chromosome 11p15 265 Chromosome 14q32.2 267 Chromosome 15q11-q13 268 Chromosome 20q13.32 268 Hypomethylation at Multiple Imprinted Loci 268 13.19 Conclusion 269 References 269

T. Tollefsbol (Ed): Epigenetics in Human Disease. DOI: 10.1016/B978-0-12-388415-2.00013-5 Copyright Ó 2012 Elsevier Inc. All rights reserved.

253

Epigenetics in Human Disease

13.1 INTRODUCTION Epigenetics literally means “above genetics” and refers to the biological mechanisms other than alterations in DNA sequence that influence gene expression and that are stable through cell division [1,2]. The word epigenetics was originally coined by Waddington in 1942 as a portmanteau of “epigenesis” and “genetics” to describe the process by which the genotypes give rise to phenotypes during development [3]. Nowadays, Waddington’s definition would be considered to apply to the field of developmental biology in general whereas the meaning of the word epigenetics has narrowed to specifically refer to non-genetic factors that influence gene expression. There are three widely accepted and closely interacting epigenetic mechanisms: (1) DNA methylation; (2) histone modifications; (3) DNA binding of Polycomb/Trithorax proteins (Table 13.1). Many other specific factors as well as general alterations in chromatin structure also correlate with different states of gene activity but are not considered primary epigenetic modifications as they are not stable through cell division independent of their initial trigger. This caveat eliminates, for example, the DNA binding of transcription factors from consideration as truly epigenetic. However, it also leads some to question the use of the term for systems widely referred to as epigenetic such as histone modification, whose independent heritability through cell division is uncertain.

13.2 CHROMATIN STRUCTURE REFLECTS EPIGENETIC MODIFICATIONS

254

Chromatin is the complex of DNA, histones, and other DNA-binding proteins and RNA that together make up chromosomes. Differences in chromatin structure are seen between genes in active and inactive states and reflect underlying epigenetic modifications. At its most extreme, chromatin can be considered to be either in an open, active conformation (euchromatin) or TABLE 13.1 Features of Transcriptionally Active and Inactive Chromatin Feature

Active

Inactive

Chromatin structure DNA methylation at promoter Histone methylation e H3K4 mono-/ trimethylation e H3K4 dimethylation e H3K9 monomethylation e H3K9 trimethylation e H3K27 monomethylation e H3K27 trimethylation Histone acetylation e H3K9 acetylation e H3K14 acetylation Polycomb complex binding

Open, extended No

Closed, condensed Yes

Yes

No

No

Yes

Yes

No

No

Yes

Yes

No

No

Yes

Yes Yes No

No No Yes

H3K4, Histone 3 lysine 4; H3K9, Histone 3 lysine 9; H3K14, Histone 3 lysine 14; H3K27, Histone 3 lysine 27.

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

a closed, inactive conformation (heterochromatin). Other alterations observed include changes in large-scale chromatin conformation and physical interactions between normally distant regions of chromatin.

13.2.1 DNA Methylation DNA methylation was the first epigenetic modification to be identified and is perhaps the best studied. In mammals, it is well established to have a mitotically stable silencing effect on genes when present at CpG dense promoter sequences [4]. In mammals, DNA methylation occurs at cytosine residues to form 5-methylcytosine and almost exclusively affects CpG dinucleotides [4]. DNA methylation affects the large majority of CpG dinucleotides in the genome and is found broadly across inter- and intragenic sequences including the gene bodies of active genes. Unmethylated domains account for only 1e2% of the genome, the majority of which are CpG islands, short CG-rich stretches of sequence found preferentially at gene promoter regions. Genetic knock-out experiments have demonstrated that DNA methylation is essential for embryonic development, genomic imprinting and X-inactivation and may be involved in the silencing of transposons [5e10].

13.3 DNA METHYLATION AND TRANSCRIPTIONAL SILENCING DNA methylation can directly reduce binding of transcription factors, but its principal means of transcriptional repression is thought to be via the recruitment of methyl-CpG binding domain (MBD) proteins which effect alterations in chromatin conformation, for example MBD1 and MECP2, which both result in histone modification [11]. The silencing effect of DNA methylation is well established when it is present in CpG dense promoter regions. However, the large majority of silent genes do not have a methylated CpG island at their promoter, indicating that other means of epigenetic control must exist. The effect of methylation at promoters with low CpG density is not established. Furthermore, in most tissue types, DNA methylation is normally stably present through cell division and relatively uniform between most cell types. The contribution of dynamic/tissue-specific changes in methylation in the control of gene expression remains unclear [12,13].

13.4 MAINTENANCE AND ESTABLISHMENT OF DNA METHYLATION DURING DEVELOPMENT DNA methylation is maintained through cell division by the DNA methyltransferase, DNMT1. The symmetry of the CpG sequence means that both strands of DNA have a CpG dinucleotide. The two strands typically share the same methylation status and this is crucial to the maintenance of stable DNA methylation through mitotic division. Following DNA replication, the two daughter double-stranded DNA molecules are hemimethylated (i.e. methylated on one strand only). Methylation of the new strand of each daughter molecule is then performed by DNMT1 [14]. In contrast to its relative stability in differentiated cells, dramatic changes in DNA methylation occur during mammalian development. This epigenetic reprogramming occurs in two stages; (1) reprogramming of germ cells; and (2) reprogramming of early embryonic cells (Figure 13.1). Each stage involves a round of demethylation and a round of de novo methylation. De novo methylation is carried out by a variety of DNA methyltransferases including DNMT1, DNMT3A, and DNMT3B, some of which have germ cell and sex-specific isoforms [15]. Primordial germ cells undergo genome-wide demethylation early in development, like other post-zygotic cell types and are largely demethylated until gonadal differentiation. After gonadal differentiation, de novo methylation occurs and leads to substantial methylation in both sperm and eggs, principally targeting transposons and repeat sequences but also

255

Epigenetics in Human Disease

(A)

(B)

FIGURE 13.1 256

Changes in the overall level of DNA methylation during mammalian development. (A) Changes in DNA methylation in germ cells. (B) Changes in DNA methylation following fertilization. In both panels the level of DNA methylation is shown on the vertical axis and developmental time on the horizontal axis. Adapted from [16]. This figure is reproduced in the color plate section.

imprinted loci [15,16]. The overall level of methylation is somewhat higher in sperm than eggs and sex-specific differences occur at imprinted loci. The timing of de novo methylation also differs between the sexes. It occurs before meiosis in male germ cells and during meiotic prophase arrest I in female germ cells. After fertilization a further round of genome-wide demethylation then occurs. Shortly before gastrulation, de novo methylation occurs. Following this, somatic embryonic cells show the high level of methylation at sequences other than CpG islands that are seen in maturity. Trophoblast cells undergo de novo methylation but remain relatively less methylated. Primordial germ cells remain largely unmethylated until after gastrulation [16].

13.4.1 Histone Modifications Histones are the chief protein component of chromatin and are assembled as octameric particles made up of two copies of each of the four classes of core histone molecule, H2A, H2B, H3, and H4. One hundred and forty-six base-pairs of DNA are wound around each histone octamer forming the basic building block of chromatin e the nucleosome. Many posttranslational modifications involve histones, often in combination with one another, and exert epigenetic control on gene expression. Foremost amongst these are the methylation and acetylation of lysine residues in the N-terminal tails of histones H3 and H4 (Table 13.1).

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

Modifications most commonly associated with active gene expression include monomethylation at H3K9 and H3K27 (i.e. H3 lysine 9 and H3 lysine 27), trimethylation of H3K4, and acetylation at H3K9 and H3K14. Repressive modifications include dimethylation of H3K4 and trimethylation of H3K9, H3K27. Control of these modifications is exerted by a wide variety of histone methyltransferase, histone demethylase, histone acetylase, and histone deacetylase enzymes [17,18]. Several models have been proposed to explain the heritability of histone modifications through cell division, but none is proven (reviewed in [19]). Indeed it is unclear whether histone modifications themselves are transmitted to daughter chromatin strands following DNA replication or if this is transmitted via a separate system, for example DNA methylation or the binding of non-histone proteins. While this uncertainty remains, some authors argue that histone modifications should not be regarded as true epigenetic modifications.

13.4.2 Non-Histone DNA-Binding Proteins A variety of non-histone proteins also bind to DNA to affect chromatin structure and exert epigenetic control on gene expression. The best established of these are the Polycomb and Trithorax group proteins which promote transcriptional repression and activation respectively, and both of which act stably through cell division. The two systems interact closely with one another and with other epigenetic systems and have been implicated in the regulation of genes in early development and stem cell renewal. They are also involved in X-inactivation and genomic imprinting [20,21]. The Polycomb system consists of two protein complexes. The Polycomb repressor complex 2, the so-called initiation complex, binds to target DNA sequences and, through the action of its component protein EZH2, results in the repressive histone modification H3K27 trimethylation (Table 13.1). The Polycomb repressor complex 1, the so-called maintenance complex, recognizes this repressive mark and is crucial in the resultant transcriptional repression. The mechanism by which the complex causes repression is unknown [21]. The Trithorax system also acts through histone modification with the Trithorax protein MLL causing the activating histone modification H3K4 methylation. Polycomb/Trithorax-induced epigenetic states are stable through cell division, and the Polycomb repressor complex 1 has recently been shown to remain bound to DNA during DNA replication [22].

13.4.3 Non-Coding RNAs Non-coding RNAs have been shown to contribute to epigenetic control of gene expression, for example the Xist non-coding RNA which is central to X-inactivation [23,24].

13.4.4 Cross-Talk Between Epigenetic Systems There is extensive correlation between activating and repressive modifications in different epigenetic systems so that they often appear to work in a concerted manner rather than as separate systems (Table 13.1). In addition to simple correlations, an increasing number of specific interactions are being identified between the systems, for example between DNA methylation and histone deacetylation through the recruitment of methyl cytosine binding proteins such as MECP2 and MBD1 and through the inhibition of binding of DNMT3A and its co-factor DNMT3L to H3 by trimethylation at H3K4. A detailed exposition of these interactions is beyond the scope of this chapter. They are reviewed by Reik [25] and Cedar and Bergman [11].

13.5 GENOMIC IMPRINTING Genomic imprinting is an epigenetic phenomenon observed in mammals, seeded plants, and some insects in which certain genes show parent-of-origin-specific patterns of expression.

257

Epigenetics in Human Disease

Around 60 genes have been shown to be consistently imprinted in man (Geneimprint database 2008; Catalogue of Parent of Origin Effects 2009) [74,75]. Some are imprinted in all cell types examined, while others show tissue-specific imprinting, or are only imprinted at certain stages of development. Imprinted genes are often arranged in clusters, each cluster spanning up to several megabases (Table 13.2). One theory that perhaps best explains the evolution of imprinting is that of parental genome conflict. This theory suggests that there is a conflict of evolutionary advantage between the paternal genome with the maternal genome which is as a result of the mother carrying the offspring in utero. The maternal genome must preserve herself and resources for future offspring so limits supplies to the baby, whereas the paternal genome only needs to consider the baby and encourages growth. Proponents of the theory point to the existence of a number of imprinted genes that regulate growth and the tendency for paternally expressed genes to promote growth and for maternally expressed genes to suppress growth [26,27].

13.5.1 Imprinted Loci Formal demonstration of imprinting requires demonstration of parent-of-origin-specific gene expression. This can be technically challenging as human tissues are difficult to obtain, limiting systematic expression analysis of the human genes. Instead, known imprinted loci have often been identified following the observation of features suggestive of imprinting, including:

258

1. Phenotypic abnormality resulting from uniparental disomy (UPD) 2. Parent-of-origin-specific effects of mutation, copy number abnormality or chromosomal rearrangement 3. Parent-of-origin effects of allelic loss in cancers 4. Parent-of-origin-specific epigenetic modifications in the region (for example differential methylation) 5. DNA sequence characteristics similar to other imprinted loci 6. Evidence of imprinting in other species, e.g. mouse. Major clusters of imprinted genes have been identified at 7q21.3, 7q32.2, 11p15, 15q11.2, 19q13.4, and 20q13.32 (Table 13.2).

13.5.2 Imprinting Centers Control Imprinting in cis Imprinting is controlled by epigenetic modifications at cis-acting regulatory sequence elements termed imprinting centers. The mechanism of control has been elucidated only in a subset of imprinted loci. Even in this small number of loci, the variety of different mechanisms operating is striking. A shared feature is the presence of areas of parent-of-origin-specific DNA methylation termed differentially methylated regions (DMRs). These DMRs are CpG-rich sequences located either at the promoter of an imprinted gene or in a more distant regulatory sequence called an imprinting center. This differential methylation is associated with maintenance of differential (i.e. imprinted) expression of genes in the region. A single differentially methylated imprinting center often appears to control imprinting of multiple genes in a cluster. This is sometimes termed a primary DMR. Differential methylation is sometimes seen at other nearby “secondary” DMRs which are established as a result of the action of the imprinting center/primary DMR and which in some cases have been shown to be involved in the maintenance of imprinting in the region [28]. At some loci, differences in other epigenetic modifications have been demonstrated between the two parental alleles including differential histone modification, Polycomb complex binding as well as the differential binding of the CCCTC-binding factor CTCF and differences in high-order chromatin structure such as looping of chromatin to allow access of genes to distant enhancer elements. A further feature shared by a number of loci is the presence of multiple overlapping, often untranslated, transcripts that may play a regulatory function.

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

TABLE 13.2 Genes/Transcripts Reported to Show Imprinted Expression in Man Gene

Location

Expressed Allele

TP73 DIRAS3 LRRTM1 NAP1L5 PRIM2 PLAGL1 HYMAI IGF2R SLC22A2 SLC22A3 DDC GRB10 CALCR TFPI2 SGCE PEG10 PPP1R9A DLX5 CPA4 MEST MESTIT1 COPG2 COPG2IT1 KLF14 DLGAP2 KCNK9 INPP5F V2 H19 IGF2 IGF2AS INS KCNQ1 KCNQ1OT1 KCNQ1DN CDKN1C SLC22A18AS SLC22A18 PHLDA2 OSBPL5 ZNF215 AWT1 WT1-AS WIF1 DLK1 MEG3 RTL1 RTLas MKRN3 MAGEL2 NDN W89101 SNRPN SNURF SNORD107 SNORD64 SNORD108

1p36.3 1p31.3 2p12 4q22.1 6p11.2 6q24.2 6q24.2 6q25.3 6q25.3 6q25.3 7p12.2 7p12.2 7q21.3 7q21.3 7q21.3 7q21.3 7q21.3 7q21.3 7q32.2 7q32.2 7q32.2 7q32.2 7q32.2 7q32.2 8p23.3 8q24.3 10q26.11 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.5 11p15.4 11p15.4 11p13 11p13 12q14.3 14q32.2 14q32.2 14q32.2 14q32.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2

Maternal Paternal Paternal Paternal Maternal Paternal Paternal Maternal Maternal Maternal Isoform dependent Isoform dependent Maternal Maternal Paternal Paternal Maternal Maternal Maternal Paternal Paternal Paternal Paternal Maternal Paternal Maternal Paternal Maternal Paternal Paternal Paternal Maternal Paternal Maternal Maternal Maternal Maternal Maternal Maternal Maternal Paternal Paternal Paternal Paternal Maternal Paternal Maternal Paternal Paternal Paternal Paternal Paternal Paternal Paternal Paternal Paternal Continued

259

Epigenetics in Human Disease

TABLE 13.2

Genes/Transcripts Reported to Show Imprinted Expression in Mandcontinued

Gene

Location

Expressed Allele

SNORD109A PWCR1 SNORD115 cluster SNORD116 SNORD109B UBE3A ATP10A H73492 ZNF597 TCEB3C ZNF331 ZIM2 PEG3 ITUP1 ZNF264 PSIMCT-1 NNAT BLCAP L3MBTL GNAS GNAS Exon A/B GNASXL NESP NESPAS

15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q11.2 15q13 16p13.3 18q21.1 19q13.41 19q13.43 19q13.43 19q13.43 19q13.43 20q11.21 20q11.23 20q11.2 20q13.12 20q13.32 20q13.32 20q13.32 20q13.32 20q13.32

Paternal Paternal Paternal Paternal Paternal Maternal Maternal Paternal Maternal Maternal Maternal Paternal Paternal Paternal Maternal Paternal Paternal Isoform dependent Paternal Maternal Paternal Paternal Maternal Paternal

260

13.5.3 Establishment of DNA Methylation at Imprinted Loci During Development The establishment of imprinting also involves DNA methylation, histone modification, and/or Polycomb gene binding, although it should be noted that many of the data in this area derive from analyses in the mouse and are assumed to apply also in man. As with other sequences, DNA methylation at imprinted loci is reprogrammed during germ cell development. However, the pattern of methylation differs between the male and female germ cells, resulting in the establishment of primary DMRs and therefore of imprinting. A further difference from reprogramming of non-imprinted loci is that DMRs escape the second round of demethylation and de novo remethylation in early embryonic development. Imprinted regions undergo DNA demethylation similar to that at non-imprinted regions in primordial germ cells and are almost entirely demethylated when they enter the gonads shortly after gastrulation. Methylation of imprinted genes in the male germline occurs at only a small number of loci, the best-studied being the H19 DMR at 11p15. As with non-imprinted loci, methylation at paternally methylated DMRs such as H19 occurs before meiosis [29]. Methylation at a larger number of imprinted loci occurs in the female germline. As with methylation at other loci, this occurs after meiosis I [30]. Unlike the majority of other sequences, imprinted loci appear to escape the genome-wide demethylation that occurs after fertilization, allowing them to retain the differential methylation of the paternal and maternal alleles established during germ cell development.

13.5.4 The 11p15 Imprinted Region The detailed description of the structure and control mechanisms of each of the known imprinted regions is beyond the scope of this chapter. However, in order to illustrate a number

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

of the shared features of imprinted regions, we set out the normal structure and function of the 11p15 imprinted region. The region has been studied extensively in man and is disrupted in the human disorders BeckwitheWiedemann syndrome and SilvereRussell syndrome. In the simplest terms, the paternal 11p15 allele promotes growth through the expression of growth-promoting genes and the silencing of growth-suppressing genes and the maternal 11p15 allele suppresses growth through the expression of growth-suppressing genes and the silencing of growth-promoting genes. In fact, the 11p15 Growth Regulatory Region (GRR) consists of two, apparently independent, imprinted domains each controlled in cis by its own differentially methylated imprinting center (Figure 13.2). Each domain contains a cluster of imprinted genes which include growth promoters and growth suppressors.

13.5.5 Imprinted Domain 1 Imprinted domain 1 is the more telomeric of the two domains and contains the paternally expressed growth promoter IGF2 (insulin-like growth factor 2) and the maternally expressed non-coding H19 (Figure 13.2) [31]. Imprinting at H19 and IGF2 is observed in both placental and embryonic tissues and is maintained in maturity in many differentiated tissues. Imprinting in the domain is controlled by a paternally methylated imprinting center immediately upstream of H19, known as the H19 DMR. It is also referred to as imprinting center 1 or imprinting control region 1 and is thought to act as a physical insulator, controlling access of

(A)

261

(B)

FIGURE 13.2 Schematic diagram of the normal 11p15 GRR. (A) The maternal and paternal alleles at the normal 11p15 growth-regulatory region. The region is arranged in two imprinted domains, the more telomeric imprinted domain 1 and the more centromeric imprinted domain 2. Each imprinted domain is controlled by an imprinting center containing a differentially methylated region (DMR). Imprinted domain 1 is controlled by the H19 DMR. This is methylated on the paternal allele (filled lollipops) and unmethylated on the paternal allele (open lollipops). Imprinted domain 2 is controlled by KvDMR1. This is methylated on the maternal allele and unmethylated on the paternal allele. At imprinted domain 1, IGF2 is expressed (solid outline and arrow at 50 end) from the paternal allele but silent (gray dashed outline and bar at 50 end) on the maternal allele while the non-coding H19 transcript is expressed from the maternal allele and silent on the paternal allele. At imprinted domain 2, a number of genes including CDKN1C are expressed from the maternal allele but silent form the paternal allele, while KCNQ1OT1 is expressed from the paternal allele but silent from the maternal allele. (B) Detailed view of the structure of the H19 DMR, which is arranged in two repeat blocks each containing one A- and three or four B-repeat elements. Six of the B-repeat elements containing target sites for the CTCF zinc-finger protein (numbered above the repeat blocks) and a seventh CTCF target site lies between the repeat blocks and the H19 transcription start site.

Epigenetics in Human Disease

the competing H19 and IGF2 genes to telomeric enhancer elements [32]. On the normal maternal allele, the H19 DMR is unmethylated allowing H19 access to these enhancers. This results in expression of H19 and silencing of IGF2. On the normal paternal allele, the H19 DMR is methylated, allowing IGF2 access to the enhancers. This results in expression of IGF2 and silencing of H19.

H19 DMR CONTROLS IMPRINTED DOMAIN 1 In man, differential methylation at the H19 DMR extends for at least 5.5 kb upstream from the 50 end of the H19 gene. At its core is a, 3.8-kb span of repeated sequence elements which contain multiple target sites for CTCF (Figure 13.2) [33,34]. These are arranged in two repeat blocks containing A- and B-repeat elements. Six CTCF target sites are present within B-repeat elements and a seventh lies between the repeat blocks and the H19 transcription start site. Binding of CTCF at these sites occurs preferentially to the unmethylated maternal allele and may protect it from abnormal methylation and/or mediate its function as a chromatin insulator [35]. The functional importance of these CTCF target sites is supported by the H19 hypermethylation and IGF2 loss of imprinting seen with their deletion or disruption of the maternal allele in model organisms and in man [31,34e37].

CHROMATIN LOOPING IN THE CONTROL OF IMPRINTED DOMAIN 1

262

In the mouse, parent-of-origin-specific chromatin loops have been found at imprinted domain 1 and are thought to be important in the control of imprinting. These physical alterations in chromatin conformation mediate what is often referred to as the chromatin insulator function of the H19 DMR. The chromatin loops are formed by the physical interaction of the H19 DMR with differentially methylated regions at IGF2 and the different loops formed on each parental allele probably result in imprinting at H19 and IGF2 by altering their access to enhancer elements [38]. The unmethylated maternal H19 DMR is bound by CTCF and physically interacts with IGF2 DMR1. This creates two chromatin domains, with H19 in an active domain with its enhancers and IGF2 in an inactive domain away from the enhancers. The methylated paternal H19 DMR is not bound by CTCF and interacts with IGF2 DMR2. This results in IGF2 lying in the active domain, with access to the enhancers telomeric of H19. H19 is in the active domain but silenced, probably by the presence DNA methylation at its promoter (which is within the H19 DMR). It is presumed that a similar mechanism operates in man, though this is yet to be demonstrated and the role of the human IGF2 DMRs is uncertain.

THE IGF2 DIFFERENTIALLY METHYLATED REGIONS Three differentially methylated regions at IGF2 have been identified in the mouse (IGF2 DMR0, DMR1, and DMR2). As described above, IGF2 DMR1 and DMR2 have been demonstrated to be involved in the formation of parent-of-origin-specific chromatin loops. In man, only two IGF2 DMRs have been identified, the paternally methylated IGF2 DMR0 and IGF2 DMR2 [38]. Their roles are not known and understanding of the region was hindered by initial reports which incorrectly assigned the parent-of-origin of the methylated allele at IGF2 DMR0 [39,40].

13.5.6 Imprinted Domain 2 Imprinted domain 2 contains the paternally expressed non-coding KCNQ1OT1 (KCNQ1overlapping transcript 1) and a number of maternally expressed genes including the growth suppressor CDKN1C (Cyclin dependent kinase inhibitor 1C; Figure 13.2) [64]. KCNQ1OT1 and CDKN1C maintain imprinted expression in embryonic and many differentiated tissues. By contrast a number of maternally expressed genes in the region other than CDKN1C are imprinted only in the placenta or in a subset of embryonic or differentiated tissues [41].

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

Imprinting in the domain is controlled in cis by an imprinting center at the promoter of KCNQ1OT1 known as KvDMR1, which is also referred to as KCNQ1OT1, LIT1, imprinting center 2, or imprinting control region 2. On the normal maternal allele KvDMR1 is methylated, resulting in silencing of KCNQ1OT1 and expression of CDKN1C. On the normal paternal allele KvDMR1 is unmethylated, resulting in expression of KCNQ1OT1 and silencing of CDKN1C.

KVDMR1 CONTROLS IMPRINTING AT IMPRINTED DOMAIN 2 KvDMR1 may control imprinting in domain 2 through more than one mechanism. Two main mechanisms have been proposed: (1) a non-coding RNA mediated mechanism; and (2) an enhancer competition-mediated mechanism. On the paternal allele, many of the maternally expressed genes show imprinted expression in the placenta in the absence of differential DNA methylation at their promoters [42]. This is similar to that seen in the process of X inactivation and it has been proposed that silencing of these genes on the paternal allele occurs by a similar process to that seen on the inactive X: through repressive histone H3K27 methylation mediated by Polycomb group proteins. This repressive histone modification is observed in placental tissues across the domain and may be targeted to the paternal allele by coating of the region in cis by the paternally expressed noncoding RNA KCNQ1OT1, a mechanism parallel to that mediated by the Xist transcript on the inactive X [43]. The enhancer-competition mechanism similar to that seen at imprinted domain 1 has also been proposed to explain the maintenance of imprinting in the domain that may be central to the maintenance of imprinting at KCNQ1OT1, CDKN1C, and other genes that are imprinted in embryonic tissues [44]. There is currently limited evidence to provide mechanistic understanding of this model [45]. 263

13.5.7 Establishment of Imprinting at the 11p15 GRR Differential methylation is observed in the germline at the imprinting centers in both domains: at the H19 DMR in imprinted domain 1 and at KvDMR1 in imprinted domain 2 [42,44]. It is thought that this germline differential methylation is the driver of the establishment of post-zygotic imprinting at each domain. At imprinted domain 1 this model predicts that differential methylation at the H19 DMR is the first event in a cascade that involves differential binding of CTCF and possibly other factors, differential methylation at the IGF2 DMRs, establishment of parent-of-origin-specific chromatin loops, and therefore the differential access to enhancers that mediate imprinting in the region. At imprinted domain 2, the model predicts that differential methylation at KvDMR1 is the first event in a cascade that involves imprinted expression of the non-coding KCNQ1OT1 transcript, which in turn is crucial to the establishment of parent-of-origin-specific histone modifications and other epigenetic modifications that mediate imprinting at other genes.

13.5.8 Abnormalities at Imprinted Loci A variety of classes of molecular defects can result in disruption at imprinted loci. These include both epigenetic and genetic defects.

13.6 UNIPARENTAL DISOMY Uniparental disomy (UPD) results when both chromosomes of a pair are inherited from the same parent. When UPD encompasses an imprinted locus, both alleles show the characteristics of the retained allele. For example, in a region of paternal UPD (pUPD), paternally expressed genes are expressed from both alleles and maternally expressed genes are silenced. Uniparental disomy can occur by a variety of mechanisms, either prezygotic (usually errors of

Epigenetics in Human Disease

meiosis) or postzygotic (errors of mitosis) and can affect whole chromosomes or be segmental [46].

13.7 EPIMUTATIONS Epimutations are isolated epigenetic defects that result in disruption of the normal pattern of expression. This can result in the silencing of the normally active allele or expression of a normally silent allele. At imprinted loci, the activation of a normally silent allele is termed loss of imprinting and results in biallelic expression of a normally monoallelically expressed gene. Disrupted expression is frequently associated with disruption of differential DNA methylation, resulting in hypomethylation or hypermethylation at a DMR. The primary defect underlying epimutations is not known. One possibility is that they result from the stochastic loss or gain of DNA methylation at key CpGs within the relevant DMR.

13.8 IMPRINTING CENTER MUTATIONS Imprinting center mutations are genetic mutations at imprinting control regions that result in epigenetic disruption of expression of the genes under their control (in cis). They are often associated with disruption of methylation at DMRs and, as with other mutations at imprinted loci, they show parent-of-origin-specific pathogenicity. Imprinting center mutations identified to date have largely been microdeletions spanning several kilobases and in some cases megabases [34,47e51]. The 2.9-kb microinsertion identified at the 11p15 H19 DMR represents a further class of imprinting center mutation and some balanced chromosome rearrangements with breakpoints at imprinted loci may be further examples. The mechanism of pathogenicity of imprinting center mutations is often obscure. 264

13.9 MUTATIONS IN IMPRINTED GENES Mutations in a number of imprinted genes have been reported. They are typically only of consequence when inherited on the active allele, that is they show parent-of-origin-dependent pathogenicity [52].

13.10 COPY NUMBER ABNORMALITIES ENCOMPASSING IMPRINTED GENES Large copy number defects encompassing imprinted genes have been reported at a number of loci, either as a result of interstitial disruptions or unbalanced chromosome translocations. As with mutations in imprinted genes, they have parent-of-origin-specific effects: they would only be expected to alter the expression of genes which are active on the disrupted allele.

13.11 MUTATIONS IN IMPRINTING ESTABLISHMENT OR MAINTENANCE MACHINERY Recently, biallelic mutations in ZFP57, a gene important in the establishment of DNA methylation at maternally methylated DMRs, have been found to cause hypomethylation at multiple imprinted loci [56]. This represents an example of a distinct mechanism of imprinting disruption: mutation of a component of the machinery of the establishment or maintenance of imprinting. Other examples include biallelic mutations in the genes NALP7 and C6ORF221, which cause recurrent hydatidiform mole [53,54]. Interestingly, mutations in the related gene NALP2 have been reported in one family with BeckwitheWiedemann syndrome [55].

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

13.11.1 Phenotypes Associated with Constitutional Abnormalities at Imprinted Loci Constitutional abnormalities at imprinted loci underlie a number of congenital syndromes in man (Table 13.3). The study of these disorders and the molecular abnormalities that underlie them resulted in the identification of many of the known imprinted loci and has been central to much of our understanding of normal and abnormal imprinting. In a number of cases these constitutional molecular abnormalities, despite being present soma-wide, are mosaic.

13.12 CHROMOSOME 6Q24 Disruption of the imprinted locus at 6q24 results in transient neonatal diabetes mellitus [57]. In addition to diabetes mellitus from the neonatal period that can last until 18 months of age, other features of the condition include intrauterine growth retardation, macroglossia, and umbilical hernia. Abnormalities at 6q24 account for approximately 90% of cases of transient neonatal diabetes mellitus and result in increased expression of the paternally expressed genes PLAGL1 (Pleomorphic adenoma gene-like 1) and the HYMAI (Hydatidiform mole-associated and imprinted) transcript. Reported abnormalities include paternal UPD, epimutation at the DMRs at PLAGL1 and HYMAI (hypomethylation of the maternal allele) and paternal duplications encompassing both genes [57e59].

13.13 CHROMOSOME 7 SilvereRussell syndrome is a growth-restriction disorder associated with pre- and postnatal growth restriction, relative macrocephaly, growth asymmetry, fifth finger clinodactyly, and a characteristic facial appearance. Maternal uniparental disomy for chromosome 7 is found in approximately 10% of cases. Uniparental disomy usually affects the whole of chromosome 7 but maternal segmental abnormalities have also been reported, providing insights into the likely critical region [60,61]. Extensive work has identified a number of imprinted genes on chromosome 7 (Table 13.2) [62,63]. As discussed below, abnormalities at the 11p15 growth regulatory region account for a further 25e40% of cases of SilvereRussell syndrome.

13.14 CHROMOSOME 11P15 As set out earlier in this chapter, the 11p15 growth-regulatory region, is arranged in two adjacent but independent imprinted domains (Figure 13.2). Two opposing groups of abnormalities in the region result in overgrowth (most characteristically BeckwitheWiedemann syndrome) and growth restriction (most characteristically SilvereRussell syndrome) [64,65]. Overgrowth is caused by abnormalities that result in increased expression of paternally expressed growth promoters such as IGF2 or decreased expression of maternally expressed growth suppressors such as CDKN1C. Growth-promoting abnormalities at 11p15 are found in approximately 80% of cases of BeckwitheWiedemann syndrome and include: paternal uniparental disomy 11p15; epimutations at imprinted domain 1 (hypermethylation of the maternal H19 DMR) or imprinted domain 2 (hypomethylation of the maternal KvDMR1); imprinting center mutations at imprinted domain 1 that result in H19 hypermethylation (microdeletion or microinsertion within the H19 imprinting control region); paternal duplications; maternal deletion of KCNQ1OT1 and KvDMR1; and maternal mutations in CDKN1C [64]. Conversely, abnormalities that result in a net decrease in expression of growth promoters such as IGF2 result in growth restriction. Growth-suppressing abnormalities at 11p15 are found in 25e40% of cases of SilvereRussell syndrome and include epimutations at imprinted domain 1 (hypomethylation of the paternal H19 DMR) and maternal duplications of the region [65].

265

Epigenetics in Human Disease

TABLE 13.3 Phenotypes Associated with Constitutional Abnormalities at Imprinted Loci Locus/Phenotype

Class of Abnormality Abnormality

6q24 Transient neonatal diabetes mellitus

UPD

Paternal UPD 6q24

Epimutation

Hypomethylation maternal PLAGL1 and HYMAI DMRs Duplication paternal 6q24

Duplication imprinted genes Chromosome 7 Growth retardation/SilvereRussell UPD syndrome

Maternal UPD 7, usually affecting the whole chromosome

11p15 Overgrowth/Beckwithe Wiedemann syndrome

UPD

Paternal UPD 11p15

Epimutation

Hypermethylation maternal H19 DMR Hypomethylation maternal KvDMR1 (referred to as KvDMR1 loss of methylation) Microdeletion/microinsertion maternal H19 DMR causing H19 hypermethylation Mutation maternal CDKN1C

Epimutation

Imprinting centre mutation

266

Mutation imprinted genes Deletion imprinted genes Duplication imprinted genes Growth retardation/SilvereRussell Epimutation syndrome Duplication imprinted genes

Deletion encompassing maternal KCNQ1OT1 and KvDMR1 Duplication paternal 11p15 Hypomethylation paternal H19 DMR Duplication maternal 11p15

14q32.2 Maternal UPD 14-like phenotype UPD Deletion imprinted genes Paternal UPD 14-like phenotype UPD Epimutation Deletion imprinted genes

Maternal UPD 14q32.2 Deletion encompassing paternal DLK1 Paternal UPD 14q32.2 Hypermethylation maternal IG-DMR and MEG3-DMR Deletion encompassing maternal MEG3

15q11-q13 PradereWilli syndrome

UPD Epimutation Imprinting center mutation Deletion imprinted genes

Maternal UPD 15q11-q13 Hypermethylation paternal SNRPN DMR Microdeletion paternal SNRPN region causing hypermethylation Deletion paternal 15q11.2 encompassing snoRNAs in SNRPN region

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

TABLE 13.3

Phenotypes Associated with Constitutional Abnormalities at Imprinted Locidcontinued

Locus/Phenotype Angelman syndrome

Class of Abnormality Abnormality UPD Epimutation Imprinting centre mutation Mutation imprinted gene Deletion imprinted genes

Paternal UPD 15q11-13 Hypomethylation maternal SNRPN DMR Microdeletion/inversion upstream of maternal SNRPN causing hypomethylation Mutation maternal UBE3A Deletion maternal 15q11.2 encompassing UBE3A

20q13.32 Pseudohypoparathyroidism type 1a Pseudohypoparathyroidsim type 1b

Mutation imprinted gene Epimutation

Imprinting center mutation

Imprinting center mutation

Multiple loci Hypomethylation multiple imprinted loci

Epimutation/unknown

Mutation imprinting machinery

Mutation maternal GNAS Hypomethylation maternal GNAS Exon A/B DMR þ/e GNASXL and NESPAS DMRs Deletion maternal STX16 exon 4e6 causing hypomethylation GNAS exon A/B DMR Deletion maternal NESP55 DMR causing hypomethylation GNAS exon A/B, GNASXL and NESPAS DMRs Hypomethylation maternally methylated DMRs including: PLAGL1, GRB10, KvDMR1 and NESPAS Biallelic mutations ZFP57 causing hypomethylation at multiple maternally methylated DMRs including PLAGL1, GRB10, KCNQ1OT1 and NESPAS

UPD, uniparental disomy; DMR, differentially methylated region.

13.15 CHROMOSOME 14Q32.2 Two opposing groups of abnormalities occur at 14q32.2 causing reciprocal abnormalities at imprinted genes in the region and resulting in two distinct phenotypes. The first, referred to as the paternal UPD 14-like phenotype, is associated with developmental delay, a bell-shaped thorax, abdominal wall defects, and distinctive facial appearance. Causative abnormalities result in decreased expression of the maternally expressed genes such as MEG3 (Maternally expressed gene 3) and RTL1as (Retrotransposon-like gene 1 antisense) and/or increased expression of paternally expressed genes such as DLK1 (Delta, drosophila, homolog-like 1) and RTL1 (Retrotransposon-like gene 1). Reported abnormalities include paternal UPD 14 and maternal 14q32.2 deletions encompassing the MEG3 DMR and/or the IG-DMR [50,51]. The second phenotype, referred to as the maternal UPD 14-like phenotype, is associated with pre- and postnatal growth restriction, developmental delay, and early puberty. Causative abnormalities result in increased expression of the maternally expressed genes such as MEG3

267

Epigenetics in Human Disease

and RTL1as and/or decreased expression of paternally expressed genes such as DLK1 and RTL1. Reported abnormalities include maternal UPD 14; epimutations at the IG-DMR and MEG3DMR (hypomethylation at the maternal allele); and paternal 14q32.2 deletions encompassingDLK1 [50].

13.16 CHROMOSOME 15Q11-Q13 Similar to the 11p15 and 14q32.2 imprinted loci, two opposing groups of abnormalities occur at 15q11.2 and cause distinct phenotypes. PradereWilli syndrome is characterized by moderate developmental delay, neonatal hypotonia, hyperphagia, and hypogonadism. It is caused by a variety of abnormalities at 15q11.2 that reduce expression of paternally expressed genes including SNRPN (Small nucleolar ribonucleoprotein polypeptide N), the SNURF (SNRPN upstream reading frame) and/or the nearby small nucleolar RNAs (snoRNAs). Reported abnormalities include maternal uniparental disomy 15q11.2; epimutations at the SNRPN DMR (hypermethylation of the paternal allele); imprinting center mutations that result in SNRPN DMR hypermethylation (microdeletions affecting a critical region that includes SNRPN exon 1); and paternal deletions that include the snoRNAs adjacent to SNRPN [66e68]. This last abnormality is the most frequent cause of the condition and often encompasses the whole of 15q11.2.

268

Angelman syndrome is characterized by developmental delay with absent or nearly absent speech, an ataxic gait, seizures, and microcephaly. Causative abnormalities reduce expression of the maternally expressed UBE3A (Ubiquitin-protein ligase E3A) and include paternal uniparental disomy 15q11.2; epimutation at the SNRPN DMR (hypomethylation of the maternal allele); imprinting center mutations that result in SNRPN DMR hypomethylation (microdeletions or chromosomal inversion affecting a critical region upstream of SNRPN); maternal deletions at 15q11.2 encompassing UBE3A; and maternal mutations in UBE3A [48,68,69].

13.17 CHROMOSOME 20Q13.32 Abnormalities at the imprinted 20q13.32 locus that disturb expression of GNAS (Guanine nucleotide binding protein alpha-stimulating activity polypeptide) and its surrounding transcripts result in a group of disorders associated with parathyroid hormone resistance (pseudohypoparathyroidism). Pseudoparathryoidism type 1a is characterized by Albright’s hereditary osteodystrophy and resistance to numerous hormones typically including thyroid-stimulating hormone and gonadotrophins in addition to parathyroid hormone. It is caused by mutations on the maternal GNAS allele [70,71]. Pseudohypoparathroidism type 1b is characterized by resistance to parathyroid hormone and in some cases thyroid-stimulating hormone without features of Albright’s hereditary osteodystrophy. Causative epimutations are frequently found and result in hypomethylation of the maternal GNAS Exon A/B DMR and in some cases the GNASXL and NESPAS DMRs [71]. In addition, two distinct types of imprinting center mutations have been reported: deletions of the maternal STX16 (Syntaxin 16) exons 4e6 that result in hypomethylation at the GNAS Exon A/B DMR; and deletions of the maternal NESP55 DMR that cause hypomethylation at the maternal GNAS Exon A/B, GNASXL, and NESPAS DMRs.

13.18 HYPOMETHYLATION AT MULTIPLE IMPRINTED LOCI A number of individuals have recently been reported with hypomethylation at multiple maternally methylated loci including PLAGL1, GRB10, KvDMR1, and NESPAS. This pattern has been identified in individuals originally diagnosed with transient neonatal diabetes mellitus and BeckwitheWiedemann syndrome [72,73]. However, the spectrum of phenotypes with which hypomethylation at multiple imprinted loci manifests and the determinants of the

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

phenotypic features remain to be identified. Some cases presenting with features of transient neonatal diabetes mellitus are caused by biallelic mutations in ZFP57 [56]. The underlying cause in others is unknown.

13.19 CONCLUSION A variety of molecular mechanisms can disrupt imprinted loci and cause a number of human syndromes. Their study has proved valuable in our understanding of these disorders themselves. It has also led to important advances in our understanding of the mechanisms by which imprinting is established and maintained and by which it can be abrogated. Despite the considerable advances that have been made in these areas over the last few decades, much remains to be understood.

References [1] Bird A. Perceptions of epigenetics. Nature 2007;447:396e8. [2] Ledford H. Language: Disputed definitions. Nature 2008;455:1023e8. [3] Waddington CH. The Strategy of the Genes. London: Allen & Unwin; 1957. [4] Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008;9:465e76. [5] Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992;69:915e26. [6] Walsh CP, Chaillet JR, Bestor TH. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 1998;20:116e7. [7] Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999;99:247e57. [8] Chen T, Li E. Structure and function of eukaryotic DNA methyltransferases. Curr Top Dev Biol 2004;60:55e89. [9] Karpf AR, Matsui S. Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells. Cancer Res 2005;65:8635e9. [10] Dodge JE, Okano M, Dick F, Tsujimoto N, Chen T, Wang S, et al. Inactivation of Dnmt3b in mouse embryonic fibroblasts results in DNA hypomethylation, chromosomal instability, and spontaneous immortalization. J Biol Chem 2005;280:17986e91. [11] Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 2009;10:295e304. [12] Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007;39:457e66. [13] Metivier R, Gallais R, Tiffoche C, Le PC, Jurkowska RZ, Carmouche RP, et al. Cyclical DNA methylation of a transcriptionally active promoter. Nature 2008;452:45e50. [14] Gruenbaum Y, Cedar H, Razin A. Substrate and sequence specificity of a eukaryotic DNA methylase. Nature 1982;295:620e2. [15] Schaefer CB, Ooi SK, Bestor TH, Bourc’his D. Epigenetic decisions in mammalian germ cells. Science 2007;316:398e9. [16] Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001;293:1089e93. [17] Shi Y. Histone lysine demethylases: emerging roles in development, physiology and disease. Nat Rev Genet 2007;8:829e33. [18] Haberland M, Montgomery RL, a ndOlson EN. The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet 2009;10:32e42. [19] Probst AV, Dunleavy E, Almouzni G. Epigenetic inheritance during the cell cycle. Nat Rev Mol Cell Biol 2009;10:192e206. [20] Wang J, Mager J, Chen Y, Schneider E, Cross JC, Nagy A, et al. Imprinted X inactivation maintained by a mouse Polycomb group gene. Nat Genet 2001;28:371e5. [21] Schwartz YB, Pirrotta V. Polycomb complexes and epigenetic states. Curr Opin Cell Biol 2008;20:266e73. [22] Francis NJ, Follmer NE, Simon MD, Aghia G, Butler JD. Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell 2009;137:110e22.

269

Epigenetics in Human Disease

[23] Herzing LB, Romer JT, Horn JM, Ashworth A. Xist has properties of the X-chromosome inactivation centre. Nature 1997;386:272e5. [24] Sleutels F, Zwart R, Barlow DP. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002;415:810e3. [25] Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007;447:425e32. [26] Moore T, Haig D. Genomic imprinting in mammalian development: a parental tug-of-war. Trends Genet 1991;7:45e9. [27] Haig D. Genomic imprinting and kinship: how good is the evidence? Annu Rev Genet 2004;38:553e85. [28] Murrell A, Heeson S, Reik W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet 2004;36:889e93. [29] Davis TL, Yang GJ, McCarrey JR, Bartolomei MS. The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet 2000;9:2885e94. [30] Lucifero D, Mertineit C, Clarke HJ, Bestor TH, Trasler JM. Methylation dynamics of imprinted genes in mouse germ cells. Genomics 2002;79:530e8. [31] Scott RH, Douglas J, Baskcomb L, Huxter N, Barker K, Hanks S, et al. Constitutional 11p15 abnormalities, including heritable imprinting center mutations, cause nonsyndromic Wilms tumor. Nat Genet 2008a;40:1329e34. [32] Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000;405:482e5. [33] Cui H, Niemitz EL, Ravenel JD, Onyango P, Brandenburg SA, Lobanenkov VV, et al. Loss of imprinting of insulin-like growth factor-II in Wilms’ tumor commonly involves altered methylation but not mutations of CTCF or its binding site. Cancer Res 2001;61:4947e50. [34] Sparago A, Cerrato F, Vernucci M, Ferrero GB, Silengo MC, Riccio A. Microdeletions in the human H19 DMR result in loss of IGF2 imprinting and BeckwitheWiedemann syndrome. Nat Genet 2004;36:958e60. [35] Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 2000;405:486e9. [36] Pant V, Kurukuti S, Pugacheva E, Shamsuddin S, Mariano P, Renkawitz R, et al. Mutation of a single CTCF target site within the H19 imprinting control region leads to loss of Igf2 imprinting and complex patterns of de novo methylation upon maternal inheritance. Mol Cell Biol 2004;24:3497e504.

270

[37] Szabo PE, Tang SH, Silva FJ, Tsark WM, Mann JR. Role of CTCF binding sites in the Igf2/H19 imprinting control region. Mol Cell Biol 2004;24:4791e800. [38] Murrell A, Ito Y, Verde G, Huddleston J, Woodfine K, Silengo MC, et al. Distinct methylation changes at the IGF2-H19 locus in congenital growth disorders and cancer. PLoS ONE 2008;3:e1849. [39] Cui H, Onyango P, Brandenburg S, Wu Y, Hsieh CL, Feinberg AP. Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2. Cancer Res 2002;62:6442e6. [40] Sullivan MJ, Taniguchi T, Jhee A, Kerr N, Reeve AE. Relaxation of IGF2 imprinting in Wilms tumours associated with specific changes in IGF2 methylation. Oncogene 1999;18:7527e34. [41] Apostolidou S, bu-Amero S, O’Donoghue K, Frost J, Olafsdottir O, Chavele KM, et al. Elevated placental expression of the imprinted PHLDA2 gene is associated with low birth weight. J Mol Med 2007;85:379e87. [42] Lewis A, Mitsuya K, Umlauf D, Smith P, Dean W, Walter J, et al. Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet 2004;36:1291e5. [43] Redrup L, Branco MR, Perdeaux ER, Krueger C, Lewis A, Santos F, et al. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 2009;136:525e30. [44] Lewis A, Reik W. How imprinting centres work. Cytogenet Genome Res 2006;113:81e9. [45] Shin JY, Fitzpatrick GV, Higgins MJ. Two distinct mechanisms of silencing by the KvDMR1 imprinting control region. EMBO J 2008;27:168e78. [46] Kotzot D. Complex and segmental uniparental disomy updated. J Med Genet 2008;45:545e56. [47] Buiting K, Saitoh S, Gross S, Dittrich B, Schwartz S, Nicholls RD, et al. Inherited microdeletions in the Angelman and PradereWilli syndromes define an imprinting centre on human chromosome 15. Nat Genet 1995;9:395e400. [48] Buiting K, Barnicoat A, Lich C, Pembrey M, Malcolm S, Horsthemke B. Disruption of the bipartite imprinting center in a family with Angelman syndrome. Am J Hum Genet 2001;68:1290e4. [49] Bastepe M, Frohlich LF, Linglart A, Abu-Zahra HS, Tojo K, Ward LM, et al. Deletion of the NESP55 differentially methylated region causes loss of maternal GNAS imprints and pseudohypoparathyroidism type Ib. Nat Genet 2005;37:25e7. [50] Kagami M, Sekita Y, Nishimura G, Irie M, Kato F, Okada M, et al. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. Nat Genet 2008;40:237e42.

CHAPTER 13 Epigenetic Mechanisms of Human Imprinting Disorders

[51] Kagami M, O’Sullivan MJ, Green AJ, Watabe Y, Arisaka O, Masawa N, et al. The IG-DMR and the MEG3-DMR at human chromosome 14q32.2: hierarchical interaction and distinct functional properties as imprinting control centers. PLoS Genet 2010;6:e1000992. [52] Hatada I, Ohashi H, Fukushima Y, Kaneko Y, Inoue M, Komoto Y, et al. An imprinted gene p57KIP2 is mutated in BeckwitheWiedemann syndrome. Nat Genet 1996;14:171e3. [53] Murdoch S, Djuric U, Mazhar B, Seoud M, Khan R, Kuick R, et al. Mutations in NALP7 cause recurrent hydatidiform moles and reproductive wastage in humans. Nat Genet 2006;38:300e2. [54] Parry DA, Logan CV, Hayward BE, Shires M, Landolsi H, Diggle C, et al. Mutations causing familial biparental hydatidiform mole implicate c6orf221 as a possible regulator of genomic imprinting in the human oocyte. Am J Hum Genet 2011;89:451e8. [55] Meyer E, Lim D, Pasha S, Tee LJ, Rahman F, Yates JR, et al. Germline mutation in NLRP2 (NALP2) in a familial imprinting disorder (BeckwitheWiedemann Syndrome). PLoS Genet 2009;5:e1000423. [56] Mackay DJ, Callaway JL, Marks SM, White HE, Acerini CL, Boonen SE, et al. Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nat Genet 2008;40:949e51. [57] Gardner RJ, Mackay DJ, Mungall AJ, Polychronakos C, Siebert R, Shield JP, et al. An imprinted locus associated with transient neonatal diabetes mellitus. Hum Mol Genet 2000;9:589e96. [58] Temple IK, Gardner RJ, Mackay DJ, Barber JC, Robinson DO, Shield JP. Transient neonatal diabetes: widening the understanding of the etiopathogenesis of diabetes. Diabetes 2000;49:1359e66. [59] Temple IK, Shrubb V, Lever M, Bullman H, Mackay DJ. Isolated imprinting mutation of the DLK1/GTL2 locus associated with a clinical presentation of maternal uniparental disomy of chromosome 14. J.Med.Genet 2007;44:637e40. [60] Monk D, Bentley L, Hitchins M, Myler RA, Clayton-Smith J, Ismail S, et al. Chromosome 7p disruptions in SilvereRussell syndrome: delineating an imprinted candidate gene region. Hum Genet 2002;111:376e87. [61] Monk D, Wakeling EL, Proud V, Hitchins M, bu-Amero SN, Stanier P, et al. Duplication of 7p11.2-p13, including GRB10, in SilvereRussell syndrome. Am J Hum Genet 2000;66:36e46. [62] Hitchins MP, Monk D, Bell GM, Ali Z, Preece MA, Stanier P, et al. Maternal repression of the human GRB10 gene in the developing central nervous system; evaluation of the role for GRB10 in SilvereRussell syndrome. Eur J Hum Genet 2001;9:82e90. [63] Bentley L, Nakabayashi K, Monk D, Beechey C, Peters J, Birjandi Z, et al. The imprinted region on human chromosome 7q32 extends to the carboxypeptidase A gene cluster: an imprinted candidate for SilvereRussell syndrome. J Med Genet 2003;40:249e56. [64] Weksberg R, Shuman C, Smith AC. BeckwitheWiedemann syndrome. Am J Med Genet C.Semin.Med Genet 2005;137:12e23. [65] Abu-Amero S, Monk D, Frost J, Preece M, Stanier P, Moore GE. The genetic aetiology of SilvereRussell syndrome. J Med Genet 2008;45:193e9. [66] Ohta T, Gray TA, Rogan PK, Buiting K, Gabriel JM, Saitoh S, et al. Imprinting-mutation mechanisms in PradereWilli syndrome. Am J Hum Genet 1999;64:397e413. [67] Sahoo T, del GD, German JR, Shinawi M, Peters SU, Person RE, et al. PradereWilli phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet 2008;40:719e21. [68] Buiting K, Gross S, Lich C, Gillessen-Kaesbach G, el-Maarri O, Horsthemke B. Epimutations in PradereWilli and Angelman syndromes: a molecular study of 136 patients with an imprinting defect. Am J Hum Genet 2003;72:571e7. [69] Kishino T, Lalande M, Wagstaff J. UBE3A/E6-AP mutations cause Angelman syndrome. Nat Genet 1997;15:70e3. [70] Patten JL, Johns DR, Valle D, Eil C, Gruppuso PA, Steele G, et al. Mutation in the gene encoding the stimulatory G protein of adenylate cyclase in Albright’s hereditary osteodystrophy. N Engl J Med 1990;322:1412e9. [71] Bastepe M, Juppner H. GNAS locus and pseudohypoparathyroidism. Horm Res 2005;63:65e74. [72] Mackay DJ, Hahnemann JM, Boonen SE, Poerksen S, Bunyan DJ, White HE, et al. Epimutation of the TNDM locus and the BeckwitheWiedemann syndrome centromeric locus in individuals with transient neonatal diabetes mellitus. Hum Genet 2006;119:179e84. [73] Bliek J, Verde G, Callaway J, Maas SM, De CA, Sparago A, et al. Hypomethylation at multiple maternally methylated imprinted regions including PLAGL1 and GNAS loci in BeckwitheWiedemann syndrome. Eur J Hum Genet 2009;17:611e9. [74] Imprinted Gene Database. 2008. Available at http://www.geneimprint.com/site/genes-by-species. [75] Catalogue of Imprinted Genes and Parent of Origin Effects. 2009. Available at http://www.otago.ac.nz/IGC.

271