Epigenetics: updated for 6th Epigenetics Edition 1 Rosanna Weksberg 1,2 , Darci T Butcher 1 , Daria Grafodatskaya 1 , Sanaa Choufani 1 , Benjamin Tycko 3 1 Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, On 2 Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, On 3 Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY Synopsis Despite the tremendous advances in human genetics enabled by the original public and private human genome projects and brought to fruition with high throughput genotyping and “Nextgen” DNA sequencing, many aspects of human biology still cannot be adequately explained by genetics alone. Normal human development requires the specification of a multitude of cell types/organs that depend on transcriptional regulation programmed by epigenetic mechanisms. Epigenetics refers to modifications to DNA and its associated proteins that define the distinct gene expression profiles for individual cell types at specific developmental stages. Disruption of such control mechanisms is associated with a variety of diseases with behavioral, endocrine or neurologic manifestations, and quite strikingly with disorders of tissue growth, including cancer. While the involvement of epigenetic alterations in many of these diseases have been known to specialists for some time, the importance of epigenetics in general clinical medicine has only just begun to emerge. Current research is focused on characterizing cis- and trans-acting influences of the genetic background on epigenetic marks, delineating cell type/tissue specific epigenetic marks in human health and disease, studying the interaction between epigenetic marks and the environment especially with respect to fetal programming and risks for common adult onset disorders, and modulating adverse epigenetic states by drug-based and nutritional therapies. The role of epigenetic marks in translating the primary genomic sequence has now moved to the forefront of human genetics, with clear implications for our understanding of human development and disease. A number of initiatives have now been implemented to define human epigenetic patterns at high resolution with complete genomic coverage. These data should provide keys to unravel genetic and DRAFT
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Epigenetics: updated for 6th
Epigenetics
Edition
1
Rosanna Weksberg1,2, Darci T Butcher1, Daria Grafodatskaya1, Sanaa Choufani1, Benjamin
Tycko3 1 Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, On 2 Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, On 3 Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY
Synopsis
Despite the tremendous advances in human genetics enabled by the original public and
private human genome projects and brought to fruition with high throughput genotyping and
“Nextgen” DNA sequencing, many aspects of human biology still cannot be adequately
explained by genetics alone. Normal human development requires the specification of a
multitude of cell types/organs that depend on transcriptional regulation programmed by
epigenetic mechanisms. Epigenetics refers to modifications to DNA and its associated proteins
that define the distinct gene expression profiles for individual cell types at specific
developmental stages. Disruption of such control mechanisms is associated with a variety of
diseases with behavioral, endocrine or neurologic manifestations, and quite strikingly with
disorders of tissue growth, including cancer. While the involvement of epigenetic alterations in
many of these diseases have been known to specialists for some time, the importance of
epigenetics in general clinical medicine has only just begun to emerge. Current research is
focused on characterizing cis- and trans-acting influences of the genetic background on
epigenetic marks, delineating cell type/tissue specific epigenetic marks in human health and
disease, studying the interaction between epigenetic marks and the environment especially with
respect to fetal programming and risks for common adult onset disorders, and modulating
adverse epigenetic states by drug-based and nutritional therapies. The role of epigenetic marks in
translating the primary genomic sequence has now moved to the forefront of human genetics,
with clear implications for our understanding of human development and disease. A number of
initiatives have now been implemented to define human epigenetic patterns at high resolution
with complete genomic coverage. These data should provide keys to unravel genetic and
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Epigenetics: updated for 6th Edition
environmental factors that impinge on epigenomes to affect normal processes such as
development and aging and lead to human diseases when these processes go awry.
Keywords
Epigenetic, DNA methylation, histone modification, imprinting, gene expression, human disease,
cancer, X-inactivation chromatin
Websites
Otago Imprinted Genes: http://igc.otago.ac.nz
UCSC Genome Browser: http://genome.ucsc.edu/
Introduction
Despite the tremendous advances in human genetics enabled by the original public and private
human genome projects and brought to fruition with high throughput genotyping and “Nextgen”
DNA sequencing, many aspects of human biology still cannot be adequately explained by
genetics alone. Normal human development requires the specification of a multitude of cell
types/organs that depend on transcriptional regulation programmed by epigenetic mechanisms.
Epigenetics refers to modifications to DNA and its associated proteins that define the distinct
gene expression profiles for individual cell types at specific developmental stages. Disruption of
such control mechanisms is associated with a variety of diseases with behavioral, endocrine or
neurologic manifestations, and quite strikingly with disorders of tissue growth, including cancer.
While the involvement of epigenetic alterations in many of these diseases have been known to
specialists for some time, the importance of epigenetics in general clinical medicine has only just
begun to emerge. Current research is focused on characterizing cis- and trans-acting influences
of the genetic background on epigenetic marks, delineating cell type/tissue specific epigenetic
marks in human health and disease, studying the interaction between epigenetic marks and the
environment especially with respect to fetal programming and risks for common adult onset
disorders, and modulating adverse epigenetic states by drug-based and nutritional therapies.
X patients exhibit changes in DNA methylation of rDNA, sub-telomeric repeats and Y-
chromosome specific satellites (149). By CHIP-sequencing, it was established that in erythroid
cells ATRX binds to CpG rich tandem repeat sequences clustered at sub-telomeric regions,
thereby affecting the expression of associated genes including α-globin, which accounts for
theα-thalassemia phenotype of ATR-X syndrome (152).
CHARGE association (CHD7): Nonsense or missense mutations and deletionsresulting in
haploinsufficiency of the Chromodomain Helicase DNA-binding protein CHD7 causes the
majority of cases of CHARGE association (153, 154).Clinical diagnosis for CHARGE is based
on non-random associations of the following congenital abnormalities: Coloboma of the eye,
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Heart defects, Atresia of the nasal choanae, Retarded growth and development, Genital
abnormalities, Ear abnormalities/deafness/vestibular disorder(153, 155). Studies in model
organisms, Drosophila and mouse, have found phenotypes that overlap those found in humans
(156, 157).In Drosophila reduced expression of kismet/CHD7 results in deficits in axonal
pruning, guidance and extension as well as defects in memory and motor function. Kismet has
also been shown to regulate the repressive histone H3 methylation mark of lysine 27 (158) and
the loss of kismet/CHD7 expression results in increased repressive chromatin marks, thereby
repressing expression of other genes than it would normally regulate. Similarly, in human cell
lines, CHD7 has been shown to bind to chromatin regions that are active as demonstrated by
histone H3 lysine 4 (H3K4) methylation and DNAse1 hypersensitivity of these binding sites
(158).
X-linked mental retardation (KDM5C): Mutations in the X-linked gene KDM5C, encoding a
histone demethylase, cause a spectrum of phenotypes, ranging from syndromic to non-syndromic
intellectual disability (ID). The clinical features in males with KDM5C mutations include mild
to severe intellectual disability, epilepsy, short stature, hyperreflexia, aggressive behaviors and
microcephaly (159-164). KDM5C escapes X-inactivation, and has a functional Y-linked
homologue, KDM5D, so female heterozygous mutation carriers are usually unaffected but
sometimes demonstrate mild ID or learning difficulties (72). KDM5C have several conserved
functional domains, including the Bright/ARID domain responsible for DNA binding; the
catalytic JmjC domain; and two PHD domains, responsible for histone binding (165, 166).
KDM5C can bind to the repressive histone mark H3K9me3 and removes the active epigenetic
mark H3K4me3/2, thus establishing a repressive chromatin state (167, 168). KDM5C point
mutations found in patients can suppress demethylase activity and/or H3K9me3 binding in vitro,
depending on the location of the mutation (168). Chromatin immunoprecipitation (CHIP) in cell
lines showed that JARID1C co-localizes with REST, a transcriptional repressor in the neuron-
restrictive silencing elements, in the promoters of a subset of REST target genes, including
BDNF and SCN2A, suggesting that the loss of JARID1C activity impairs REST-mediated
neuronal gene regulation (169).
Kleefstra syndrome (EHMT1): Haploinsufficiency of the EHMT1 gene due heterozygous
deletions or mutations causes the 9q subtelomeric deletion syndrome, also known as Kleefstra
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syndrome. These individuals demonstrate moderate to severe ID, childhood hypotonia and facial
dysmorphology (170). EHMT1 encodes a histone methyltransferase catalyzing mono and di
H3K9 methylation through its catalytic SET and PreSET domains (171, 172). H3K9me2 is a
euchromatic silencing mark (173). It has been shown in mouse that Ehmt1 forms a heteromeric
complex with another H3K9 methyltransferase, G9a, and knockouts of either of these genes lead
to very similar phenotypes in mice, including embryonic lethality and loss of H3K9 methylation
(171, 172). In conditional knockouts in the forebrain of Ehmt1, G9a or both, behavioral
abnormalities, including defects in learning, motivation, and environmental adaptation were
observed (174). Furthermore, Ehmt1/G9a deficiency in the forebrain led to de-repression of
non-neuronal genes, suggesting that the role of the Ehmt1/G9a complex is to protect neurons
from transcriptional noise. Distortion of this transcriptional homeostasis has been proposed to
lead to the ID phenotype (174).
Sotos syndrome (NSD1): Haploinsufficiency due to mutations or deletions of the NSD1 gene,
encoding a histone methyltransferase, causes Sotos syndrome, an overgrowth condition
associated with macrocephaly, facial dysmorphology, advanced bone age and learning
difficulties or mild ID(175).Some mutations of this gene are associated with another overgrowth
condition, Weaver syndrome(176). NSD1 has a catalytic lysine methyltransferase SET domain
and four zinc-binding PHD domains and functions primarily to mono and di-methylate H3K36
(177). The role of H3K36 methylation is not completely understood; in model organisms it has
been found within gene bodies of expressed genes and is associated with suppression of
intragenic transcriptional initiation (178). ChIP-CHIP experiments using promoter microarrays
have shown that NSD1 binds to promoters of genes playing a role in various processes, such as
cell growth/cancer, keratin biology, and bone morphogenesis (179). In addition it was found that
four of the NSD1 PHD domains bind histone H3 methylated at K4 and K9, and that the large
majority of point mutations found in Sotos syndrome disrupt this binding (180).
Kabuki syndrome (MLL2): Recently whole exome sequencing has uncovered heterozygous
mutations in theMLL2 gene as the cause of Kabuki syndrome, characterized by mild to moderate
ID, multiple congenital anomalies, short stature and typical facial features(181). MLL2 belongs
to the SET1 family of histone H3K4 methyltransferases. It has a catalytic SET domain, five
PHD domains, and an HMG-I binding motif (182). MLL2 is a part of a multi-protein complex
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that catalyzes mono, di- and trimethylation of H3K4 (183). H3K4 trimethylation is associated
with active transcription(178) and the reduction of MLL2 in human HeLa cells results in
downregulation of a number of genes involved in cell adhesion, cytoskeleton organization,
transcriptional regulation and development (183). Interestingly in mice Mll2 has been shown to
be crucial for the epigenetic reprogramming that takes place before fertilization in oocytes by
trimethylation H3K4, with deficiency of Mll2 resulting in anovulation (184).
Rubinstein-Taybi syndrome (CREBBP/EP300): Haploinsufficency of chromosome 16p13.3 due
to microdeletion or mutation in either the CREB-binding protein (CREBBP) or EIA-binding
protein (p300) results in Rubinstein-Taybi syndrome (RSTS), characterized by multiple
congenital anomalies, including postnatal growth deficiency, microcephaly, specific facial
characteristics, broad thumbs and big toes and ID (185). Both of these homologous proteins
contain a histone acetyltransferase domain (HAT) and have been demonstrated to have
overlapping functions, but there are some differences in expression patterns and necessity for
specific processes and signaling molecule responsiveness (186-190). Using mouse models the
HAT activity has been demonstrated to be important for long-term potentiation, learning and
memory (191, 192), which are in part regulated by histone acetylation dependent transcription
(193, 194).
ICF syndrome (DNMT3Band ZBTB24): Immunodeficiency, centromere instability, and facial
anomalies (ICF) syndrome is a very rare disorder caused by mutations in DNMT3B in the
majority of cases, and of the epigenetic regulator gene ZBTB24 in a minority of cases (195, 196).
Patients with ICF have low levels of immunoglobulins and reduced B- and T-lymphocyte counts
(197). Most patients have DNA hypomethylation and chromatin under-condensation localized to
juxtocentromeric (adjacent to the centromere) regions of chromosomes 1, 9 and 16, probably
accounting for the diagnostic secondary chromosomal fusions observed in metaphase analyses
from affected lymphocytes(198-201). Aberrant hypomethylation also occurs in alpha satellite
DNA, constitutive heterochromatin, Alu sequences and some imprinted genes (200-203).
Disease due to Abnormal Reading of Epigenetic Marks
Rett syndrome (MECP2): Heterozygous mutations of the X-linked gene MECP2 cause Rett
syndrome in girls. Rett syndrome is characterized by developmental arrest between 5 and 18
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months of age, followed by regression of acquired skills, loss of speech, stereotypical
movements, microcephaly, seizures, and severe intellectual disability(204). The function of
MECP2 has been very extensively studied but the mechanism by which its deficiency results in
the phenotypes of Rett syndrome remains incompletely understood. Initially, MeCP2 was
identified as a protein capable of binding methylated DNA(205). It was found to have abundant
binding sites distributed throughout the genome and was demonstrated to function in repression
of transcription (206-208). The best established mechanism by which MECP2 downregulates
gene expression is through recruitment of histone deacetylases (HDACs) which transform
chromatin into a repressive state by removing acetyl groups from histones H3 and H4 (206, 208,
209). However, there is growing evidence that the role of MECP2 in transcription regulation is
more complex; for example in mice it was shown to bind to the transcriptional activator CREB
to activate transcription of a large number of genes in the hypothalamus (210). MECP2
deficiency can lead to Rett syndrome through dysregulation of specific genes, such as BDNF,
which has been shown to have a MECP2 binding site. Furthermore, reduction of Bdnf in mice
mimics some features of the Mecp2-null mice phenotype (211) and Bdnf overexpression in
Mecp2 knockout mice can partially rescue the phenotype by improving their locomotor
function, extending lifespan (212) and rescuing synaptic dysfunction (213). These data suggest
that BDNF is indeed an important and clinically relevant Mecp2 transcriptional target. Recent
findings suggest that MECP2 is almost as abundant as histone H1 in mouse neurons but not in
glia (214), so MECP2 function in neurons might affect genome-wide chromatin remodelling
rather than only regulating the expression of specific genes. In addition targeted deletion of
Mecp2 in mice results in increased expression of repetitive elements in neurons (214), prompting
investigators to suggest that this affects overall transcriptional noise in neurons, and the ability of
neurons to respond adequately to environmental signals (215).
Lastly it is relevant consider that known functional interactions between the proteins
involved in chromatin disorders suggest that their targets can in part overlap leading to shared or
overlapping phenotypes such as ID. For example MECP2 and ATRX are components of the
same chromatin remodeling complex (216, 217). EHMT2, a partner of EHMT1, has been shown
to be a component of the same protein complex as KDM5C (169). Identification of dysregulated
genes and epigenetic marks in these chromatin disorders is the subject of ongoing research.
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Methods for Studying Epigenetic Marks
Mapping DNA Methylation
Many techniques have been developed to study DNA methylation. One of the first methods to
score DNA methylation at a specific locus was Southern blotting of genomic DNA digested with
methylation-sensitive restriction enzymes (218). Certain restriction enzymes (e.g., HpaII, SmaI,
NotI) that containCpG as part of their recognition sequences do not cut that site when the C is
methylated. Therefore, failure to cleave by a methyl-sensitive restriction enzyme is evidence of
DNA methylation at that site. Restriction enzymes can also be used in combination with
microarray platforms to evaluate genome-wide DNA methylation patterns, including promoter
methylation and allele-specific methylation (219, 220).
The gold standard which allows for the comprehensive analysis of CpG sites is sodium
bisulfite chemical conversion of DNA. Sodium bisulfite deaminates non-methylated dCs to dU
residues; during subsequent PCR amplification, the latter are converted to A/T base pairs.
However, if the C is methylated, the DNA sequence does not change (221). A number of
methods have been developed to determine the levels of DNA methylation across multiple CpG
sites. PCR primers can be designed to amplify specific genomic regions. Methylation-specific
PCR provides a semi-quantitative measurement of DNA methylation levels. An alternative
approach involves amplification of bisulfite PCR products followed by cloning and sequencing.
This more thorough approach permits DNA methylation levels of a larger number of individual
CpG sites to be quantified, and the precise patterns of methylation to be displayed. One of the
newer technologies, Pyrosequencing, determines an absolute value for DNA methylation at
individual CpG sites across a region. By combining sodium bisulfite conversion and microarrays
or massively parallel Nextgen sequencing genome-wide DNA methylation patterns can be
determined for a large number of CpG sites (104, 222).
Mapping Histone Modifications and Chromatin Structure
To determine the interaction of histone proteins with DNA, specifically histones that carry
various modifications, chromatin immunoprecipitation (ChIP) is employed. This methodology
detects the covalent modifications of histones bound to either active or inactive genes.
Generally, cells or tissues are briefly fixed with formaldehyde to cross-link the proteins to the
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DNA. The fixed chromatin is fragmented, usually by sonication, to enable targeted analysis.
The chromatin is next subjected to immunoprecipitation (IP) with an antibody specific for a
given protein or, more often, a unique covalent modification of a certain residue (e.g. acetylation
or methylation of lysine 9 of histone H3). After IP and removal of the cross-links, one can then
amplify specific regions of interest by quantitative or semi-quantitative PCR. A PCR product
indicates that the protein with that particular modification was associated with the DNA of the
targeted genome region. Alternatively, ChIP can be combined with microarray technology or
Nextgen sequencing to define genome-wide histone modifications locations in various tissues
and disease states. A large scale project, the NIH Roadmap Epigenetics Mapping Consortium,
has begun to map DNA methylation and a large number of histone modifications in a number of
tissues, including normal, cancers and pluripotent cells, and the data from this project are being
made publically available(223).Also important in the study of chromatin is the three dimensional
long-range interaction of regions of DNA and their associated proteins. To determine the three
dimensional interaction of chromatin segments at long distances from each other, a method
called Chromatin Confirmation Capture (3C) has been developed (224). Newer modifications of
the 3C method have been derived to facilitate genome wide interaction mapping using next
generation sequencing (225).
Cancer Epigenetics
As amply demonstrated by the disorders discussed above, epigenetic aberrations can result in a
diverse array of non-neoplastic human diseases. The contribution of epigenetic alterations to a
number of different cancers has been studied even longer and equally intensively and is too
broad to cover comprehensively; instead we restrict our discussion here to general principles,
with selected illustrations. Changes in DNA methylation were the first epigenetic alteration
identified in cancer (226), and subsequent work over 3 decades has shown that both hyper- and
hypo-methylation are important and pervasive pathogenic mechanisms both in early and late
stages of human neoplasia (227). Not surprisingly histone modifications and miRNA expression
are also altered in cancer (228). It has become increasingly apparent recently that proteins
regulating epigenetic marks, including histone methyltransferases and demethylases, DNA
methyltransferases, and chromatin remodeling SWI-SNF complexes are also dysregulated, not
just by over- or under-expression but also by recurrent cancer-associated somatic mutations.
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DNA methylation and histone methylation profiles, as well as miRNA signatures, are being used
as epigenetic biomarkers to diagnose and predict recurrence risk for a number of tumour types,
and it is hoped that such profiles will also become useful for individualizing anti-cancer therapies
(229).
DNA Hypermethylation in Cancer
CpG hypermethylation in gene promoters is the best characterized epigenetic abnormality in
human malignancies. A common paradigm in cancer epigenetics is hypermethylation of the
CpG-rich promoter regions of tumor suppressor genes, resulting in epigenetic silencing of these
genes (14). Indeed, for some of the most important tumor suppressors, such as the CDKN2A
gene encoding the p16 cell cycle inhibitor, promoter hypermethylation can be the most common
mechanism underlying their functional loss during tumor formation, with the corresponding
genetic pathways for loss of function (deletion/mutation) being utilized less commonly (230).
Hypermethylated promoter DNA is associated with virtually every type of human tumor, with
each type of tumor having its own signature of methylated genes, such as the methylation of
GSTP1 in prostate cancer, the von Hippel-Landau syndrome gene VHL in renal cancer, the
mismatch repair gene MLH1 in colon and endometrial cancers, and sometimes BRCA1 in breast
cancer (231-236). In some of these examples, the same tumor suppressor gene is mutated or
methylated as alternative pathways in the same tumor type: loss-of-function mutations in MLH1
and VHL are found in the germlines of patients with hereditary colon and renal cancer,
respectively, and these same genes are hypermethylated and silenced in sporadic tumors of the
same histologic type (231, 237).
While gain of DNA methylation is often discussed as a late event in tumor progression,
CpG hypermethylation in specific sequences often occurs early in cancer formation, sometimes
preceding tumorigenesis. Examples of early epigenetic aberrations can also be cited in other
adult malignancies: in cigarette smokers, CDKN2A promoter methylation occurs in dysplastic
bronchial epithelial cells prior to the formation of overt lung cancers(238), promoter
hypermethylation of tumor suppressor genes is already detectable in the premalignant lesion
Barrett’s esophagus (239, 240). One of the best substantiated examples of a very early
epigenetic lesion predisposing to subsequent tumor formation is gain of methylation of the H19
DMR on the maternal allele, which leads to loss of imprinting of IGF2 expression and can often
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be detected in non-neoplastic kidney cells both in BWS-associated and sporadic cases of the
pediatric kidney cancer Wilms tumor (227).
DNA hypermethylation has attracted much attention as a biomarker for cancer detection
and classification. To be clinically applicable, an ideal tumor biomarker must be specific for
cancer, and readily detectable in clinical specimens obtained through minimally invasive
procedures. DNA hypermethylation seems to fulfill these requirements and has been considered
to be a promising biomarker. Examining the methylation of a subset of genes (GSTP1, APC,
RASSF1, and MDR1) distinguished primary prostate cancer from benign prostate tissues with
sensitivities and specificities of greater than 90% (241, 242). DNA methylation alterations can
be detected and used as biomarkers in feces for colorectal cancer, urine for bladder cancer
screening and sputum to predict the occurrence of lung cancer (243-245). However, for reasons
that are complex but partly financial, these types of tests largely remain at the research stage and
have not yet been widely adopted in clinical practice.
DNA Hypomethylation in Cancer
Global DNA hypomethylation in cancer cells was in fact identified prior to promoter
hypermethylation (246), with studies indicating that genome-wide 5-methyl-C is reduced an
average of 10% in a number of different tumor types (226, 247). Thus the net decrease in the
genomic methyl-C content in cancer cells often exceeds the localized increases in DNA
methylation (248). There is some evidence that hypomethylation of DNA can result in genomic
instability leading to mutations, deletions, amplifications, inversions and translocations (249).
Poor prognosis in colon cancer is associated with hypomethylation of repetitive elements (250).
Hypomethylation can also lead to the reactivation of silenced genes and miRNAs leading to a
cascade of aberrant expression (251, 252). While most abnormalities in DNA methylation in
human cancers cannot yet be explained by a clear genetic mechanism, there are at least several
recurrent cancer-associated somatic mutations, in the IDH1/2, TET2 and DNMT3A genes, that
have been proposed as candidates for explaining altered DNA methylation in certain tumor types
such as acute myeloid leukemias (AML) and myelodysplastic syndrome (MDS) (253).
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Abnormalities of Histone Modifications in Cancer
Epigenetic alterations in cancer are not restricted to DNA methylation. Genome-wide mapping
of histone marks has demonstrated global reductions in acetylated H4 lysine 16 (H4K16ac) and
H4 lysine 20 trimethylation (H4K20me3), both resulting in or correlating with repression of gene
expression (254). Histone deacetylases (HDACs) have been found to be over-expressed in a
number of cancer types, and in some cancers that can be dysregulation of histone
acetyltransferases (HATs) due to translocations resulting in deleterious gene fusion products
(255-257). Aberrant histone methylation of H3K9 and H3K27 also results in gene silencing in
many cancers (258, 259). EZH2, a histone methyltransferase of H3K27, is frequently over-
expressed in breast and prostate tumours, in addition to other tumours (260-262). As is true for
aberrant DNA methylation, most abnormalities in histone modifications in cancer are not yet
explained by a single genetic lesion. However, with high coverage sequencing technologies an
increasing number of chromatin modifying enzymes, such as CREB, JARID1C, EZH2 and the
SWI/SNF family proteins hSNF5/INI1 and PBRM1, are now being found mutated in specific
types of human cancers (263-267).
Aberrant miRNA Expression in Cancer
Comparisons of tumor tissues and corresponding normal tissues have revealed global changes in
miRNA expression during tumorigenesis (268). In chronic lymphocytic leukemia miR-15 and
16, which target the anti-apoptotic gene BCL2, are downregulated (269). Similarly, let-7, which
targets the oncogene RAS is downregulated in lung cancer (269). Upregulation of miR-21, which
targets PTEN has been shown to occur in glioblastoma (270). These alterations in miRNA
expression may occur through a number of mechanisms including chromosomal abnormalities,
transcription factor binding and epigenetic alterations (271). Silencing of miRNA expression has
been shown to occur by aberrant hypermethylation in a number of cancers (272, 273). As is true
for the other epigenetic factors discussed above, the role of miRNA dysregulation in cancer has
been validated genetically by findings of DNA deletions encompassing miRNA genes, e.g. on
chromosome 13 in chronic lymphocytic leukemias (274).
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Therapies Targeting Epigenetic Modifications in Cancer
Two classes of medications, DNA methylation inhibitors and HDAC inhibitors, have been
approved by the US Food and Drug Administration as treatment for cancer (275). The DNA
methylation inhibitors, 5-azacytidine (azacytidine) and 5-aza-2’-deoxycytidine (decitabine), are
nucleoside analogs that get incorporated into the genomes of growing tumor cells and act as
suicide inhibitors of DNA methyltransferase enzymes, leading to progressive loss of DNA
methylation with each S-phase of the cell cycle. These medications have been approved for use
in the treatment of MDS and have shown some promise for treating AML and other
haematological malignancies (276). The histone deacetylase (HDAC) inhibitor vorinostat
(suberoylanilide hydroxamic acid; SAHA) is being used with good results in treating patients
with cutaneous T-cell lymphoma in the U.S. (277). Beyond treatment for cancers, such
medications are being used and developed to treat a wider spectrum of diseases. Resveratrol, a
natural compound in red wine, which inhibits sirtuins (a family of HDACs) is being evaluated as
treatment for type II diabetes and metabolic syndrome (278). Valproic acid (VPA), also an
HDAC inhibitor, is currently used to treat seizures and mood disorders (279, 280), and VPA in
combination with other medications have been shown to inhibit cancers in vitro (281). The wide
array of epigenetic alterations identified in human disease could present valuable targets for
approved medications as well as for novel ones that have yet to be developed.
Environmental Influences on Epigenetic Traits
Trans-generational effects of the environment on our epigenome were recently documented for 2
tragic historical events, the Dutch Hunger-winter (1944) and the Great Chinese Famine (1958-
1961). Studies of children born following these periods are reported to have an increase risk for
schizophrenia (282, 283). Children who were conceived during the Dutch famine had six decade
later changes in DNA methylation in the IGF2 gene which encodes a growth hormone critical for
normal embryonic development (284). These data constitute the first concrete evidence that in
humans the mothers diet early in pregnancy can directly affect the programming of the
epigenome early in utero that shape our development later in life.
The role of diet and environment in the expression of imprinted genes has not been
extensively explored. We are only beginning to understand which environmental signals can
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alter methylation of specific genes or the genome as a whole. There is evidence that
environmental exposure to compounds such as cadmium (285) and arsenic (286), may be a
predisposing factor that leads to epigenetic instability, aging, and cancer.
Both folate and the enzyme methyltetrahydrofolatereductase (MTHFR) are important for
DNA synthesis and methylation. In fact, mice lacking the enzyme Mthfr have been shown to
have decreased global DNA methylation. In humans, MTHFR enzyme activity depends on an
individual’s genotype for the functional polymorphism MTHFR 1298A->C and correlates
positively with the level of global DNA methylation (287). Further, humans on a folate depleted
diet demonstrate decreased global DNA methylation (288). Conversely, in a study of adult males
on hemodialysis, adding an exogenous source of folate led to an increase in both global and
locus-specific DNA methylation, including H19, IGF2, and SYDL1 (289). Lastly, dietary
supplementation with folic acid and B vitamins has been clearly shown to modify tumor
incidence in mouse models (290, 291).
Abnormalities in Epigenetic Programming Linked to Infertility
and Assisted Reproduction
In mice and humans, oocytes retrieved following hormonal induction or embryos studied after in
vitro culture have shown methylation and/or expression anomalies in several imprinted genes
(292-295). Studies of human oocytes harvested after medical hormonal induction showed loss of
methylation at the maternal MEST/PEG1 DMR on chromosome band 7q33 (296) and gain of
methylation at the maternal H19 DMR (IC1) on chromosome band 11p15.5 (295). Increasing
attention has recently been focused on reports of increased rates of epigenetic errors in human
following infertility/ART. In particular, two rare epigenetic disorders, BWS and AS, exhibited
an increased incidence in retrospective studies (odds-ratios 6 -17 and 6 - 12, respectively) in
children born following infertility/ART (297-302). The data are especially compelling in that the
increased incidence is attributable to an increase in specific epigenetic errors at two different
chromosomal locations, with both locations being affected by abnormal imprinting on the
maternal (oocyte-derived) alleles. Furthermore, in ART-conceived AS and BWS patients, loss
of maternal methylation at their respective DMRs (chromosomes 15q11 and 11p15) occurs 8 and
1.9 times more often, respectively, than in individuals born from spontaneous conceptions (124,
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303, 304). Such evidence supports the hypothesis that ART-conceived children have an
increased rate of epigenetic errors over that in the general population.
In humans, it is still unclear whether maternal loss of methylation observed in children
post-ART is the result of the procedure itself or of an underlying infertility with oocyte
abnormalities in the couple seeking ART interventions, or both. However, idiopathic male
infertility is also associated with aberrant methylation at both maternal and paternal alleles,
suggesting that male germ cells represent another potential source for methylation defects in
children conceived via ART (305, 306). Recently, ovarian stimulation (part of
subfertility/infertility treatment) was linked to perturbed genomic imprinting at both maternally
and paternally expressed genes. These data demonstrate that superovulation has dual effects
during oogenesis: disruption of imprint acquisition in growing oocytes, and disruption of a
maternal-effect gene product subsequently required for imprint maintenance during pre-
implantation development (307).
In Utero Epigenetic Programming of Adult Traits and Disease
The Developmental Origins of Health and Disease (DOHAD) hypothesis, pioneered by David
Barker (308), has predicted among other things that maternal stress during pregnancy (dietary
inadequacy, toxic exposures, and perhaps psychological stress) might lead to persistent
epigenetic changes in the fetus, which could play a role in modulating the subsequent onset of
adult cardiovascular, metabolic and psychiatric diseases. In mice, maternal behavior in the
neonatal period may correlate with epigenetic programming of adult behavior. Recent studies
have indicated that mothers showing strong nurturing behavior toward their pups, by frequently
licking and grooming their offspring, produce alterations in the patterns of DNA methylation, for
example in the promoter of the glucocorticoid receptor gene, in the hippocampus of their pups
(309). This area of research has now become quite active and it will be important to follow
progress in this area over the next several years.
GeneticEpigenetic Interactions
With the exponentially increasing volume of human genetic data from SNP and DNA copy
number analyses on microarrays, genome-wide association studies (GWAS), and “post-GWAS”
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studies such as whole exome and whole genome sequencing, it becomes crucial to consider
interactions between the genome and the epigenome. In principle, these interactions can be of
two types: interactions in cis, in which the local DNA sequence and haplotype can affect the
pattern of epigenetic marks on a given allele, and interactions in trans, in which the overall
genome, including mutations, DNA gains and losses, and whole chromosomal aneuploidies, can
affect epigenetic patterns at various sites distrubed across all the chromosomes. A small but
increasing number of studies are starting to address these central questions about genome-
epigenome interactions. By analyzing multiple tissue samples from multiple human individuals
using high throughput genetic and epigenetic profiling methods these studies are starting to
uncover recurrent and highly predictable genome-epigenome interactions.
In 2008 Kerkel et al. used the MSNP method, pre-digestion of genomic DNA by
methylation-sensitive restriction enzyme(s) followed by probe synthesis and hybridization to
SNP arrays, to examine allele-specific DNA methylation (ASM) in several human tissues (220).
Their study was designed to detect new examples of imprinted genes, but instead they found
numerous examples of previously unsuspected ASM at loci outside of imprinted regions. Most
of these examples of non-imprinted ASM showed a strong correlation of CpG methylation
patterns with local SNP genotypes, indicating cis-regulation of this epigenetic phenomenon.
That paper was quickly followed by other reports examining various types of human cells and
tissues for ASM or similar phenomena of methylation quantitative trait loci (mQTLs) and allele-
specific transcription factor binding (ASTF). All of these papers confirmed that for the majority
of genes and intergenic regions showing strong ASM, mQTLs or ASTF the allelic asymmetry is
dictated not by parent-of-origin but rather by local SNPs, i.e. by the haplotype in which the
epigenetic pattern is embedded (310). Thus while ASM due to parental imprinting is a potent
mechanism for regulating functional gene dosage, it affects fewer genes than this more newly
recognized phenomenon of haplotype-dependent ASM. In parallel with this work, many
laboratories have used microarrays and Nextgen sequencing to map the related phenomena of
haplotype-dependent allele-specific RNA expression (ASE) and eQTLs, which turn out to affect
up to 10 percent of human genes.
Importantly for clinical genetics these widespread phenomena of haplotype-dependent
ASM, ASTF and ASE, in contrast to imprinting, do not violate any Mendelian principles: while
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the allele-specific epigenetic patterns are not actually passed through the germline, in each
generation these patterns are re-established and maintained in the fetal and adult tissues under the
strong cis-acting influence of the local DNA sequence. So for counseling purposes each locus
with haplotype-dependent epigenetic asymmetry can be thought of as inherited with the DNA
sequence as a Mendelian trait.
Recent data have indicated that there can also be trans-acting effects of chromosomal
aneuploidies on epigenetic patterns in human tissues. In particular, the chromosomal aneuploidy
that causes Down syndrome (trisomy 21) has been shown to produce gene-specific and highly
recurrent changes in DNA methylation in blood leukocytes including T-lymphocytes (311).
Additional studies are in progress to test for this phenomenon in brain cells with trisomy 21, and
in other situations such as cancer cells with recurrent simple chromosomal aneuploidies.
The Future: Epigenomics
As we have highlighted throughout this chapter, the role of epigenetic marks in translating the
primary genomic sequence has now moved to the forefront of human genetics, with clear
implications for our understanding of human development and disease. A number of initiatives
have now been implemented to define human epigenetic patterns at high resolution with
complete genomic coverage. The technology is now available to investigate multiple tissue-
specific epigenomes in humans, and the NIH Roadmap Epigenomics Mapping Consortium
(www.roadmapepigenomics.org) was launched to produce a public resource of human
epigenomic data to catalyze basic biology and disease oriented research (223). Another parallel
initiative is the NIH Epigenomics of Health and Disease Roadmap Program, which funds
investigator-initiated research. While a good part of what we know so far about epigenetics in
disease has come from cancer research, it is telling that most of the initial research grants from
this program have been targeted to other complex diseases ranging from Alzheimer’s to adult
heart disease and diabetes to autism. These initiatives interface with the International Human
Epigenomics Consortium, which was established to accelerate and coordinate epigenomics
research worldwide (312). These data should provide keys to unravel genetic and environmental
factors that impinge on epigenomes to affect normal processes such as development and aging
and lead to human diseases when these processes go awry.
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Figure Legends
Figure 1. Epigenetic Organization of Chromatin: Layering of DNA methylation, histone modification to control gene expression. DNA of a gene promoter can be unmethylated (white circles) and in most cases the gene is expressed or the promoter can be methylated (blue circles) and in most cases the gene is not expressed. DNA is not independent of its associated histone proteins. Histone modifications are established and maintained independently or dependently on the DNA methylation state of a region. These protein modifications can active (open orange circles) or repress (filled orange circles) gene transcription. Although not shown in this figure, but mentioned in the text, additional epigenetic processes, including microRNA and long non-coding RNAs, also contribute to gene regulation. The DNA/histone protein nucleosome core is further compacted to form higher order chromatin structures that also contribute to gene regulation.
Figure 2. A)Histone Modifications of Histone H3 and H4 N-terminal Tails. Post-translational modifications of N-terminal tails (these can also occur in the C-terminal domain but are not shown here) can occur in combination and are read by the appropriate protein to establish local and global decondensed or open and condensed or closed chromatin states. Ac, acetylation (blue squares); Me, methylation (green circles); P, phosphorylation (red triangles).
B) Snapshot from UCSC genome browser representing H3K4 methylation in the promoter of the tumour-suppressor gene CDKN2A. This diagram is an example of epigenetic data available in UCSC genome browser. The description of each genomic feature is shown on the left. Two isoforms of CDKINC genes are shown in black and blue, here we focus on a shorter (black) isoform. Enrichment for active histone H3K4me3 is shown by multiple colours in 9 cell lines. The peak of H3K4me3 coincides with transcription start site of CDKN2A, CpG island (green), as well transcription factor binding sites (TxN factor CHIP) and DNase clusters, which is indicator of open chromatin. All of these marks – H3K4me3, transcription factor binding as well DNase clusters indicate that CDKN2A is active transcribed in these cell lines. Information about other histone marks and DNA methylation levels is available from at the USCS genome browser under multiple tracks from the Regulation section. This image was downloaded from UCSC genome browser http://genome.ucsc.edu/(Kent et al. 2002). The ENCODE Regulation data if from (Rosenbloom et al. 2010).
Figure 3. Ideograms of Human Imprinted Genes. Ideograms were generated using http://www.dna-rainbow.org/ideograms/. Ideogram of each human chromosome known to have an imprinted gene based on the imprinted gene catalogue last updated Jan, 2011 (http://igc.otago.ac.nz) and recent literature. The G-bands, areas with proportional more A-T base pairs, are normally colored black in schematic representations. To compare the schematic ideograms with our rendered chromosomes, we colored the A-T bases black and the G-C bases white. Blue areas in the rendered chromosomes identify bases not known yet. Blue genes are paternally expressed, red genes are maternally expressed. Bold genes are implicated in growth, underlined genes play roles is neurodevelopment. Genes in italics have no reported function in growth or neurodevelopment.
Figure 4. Schematic representation of imprinted gene clusters on human chromosome 11p15.5. Imprinted genes are indicated as filled boxes and non-imprinted genes as empty boxes.
Paternally expressed genes are indicated in blue and maternally expressed genes in red colour. Hollow rectangles show the location on normally unmethylated imprinting center (IC) and filled rectangles indicated the IC is normally methylated. Methylation alterations, such as loss of methylation (yellow hexagon) and gain of methylation (blue hexagon), show the locations of these changes in each of the two syndromes: BWS and RSS spectrum. In the telomeric domain are two imprinted genes, H19 and insulin-like growth factor 2 (IGF2). IGF2 is a paternally expressed fetal growth factor and H19 is a noncoding RNA. IC1 is usually methylated on the paternal chromosome and unmethylated on the maternal chromosome. Normally, the H19 gene is expressed from the maternal allele and IGF2 from the paternal allele. Loss of methylation (LOM) at IC1 leads to bi-allelic expression of H19 and no expression of IGF2, resulting in RSS. Conversely, gain of methylation (GOM) at IC1 leads to bi-allelic expression of IGF2 and no expression of H19 resulting in BWS. The centromeric domain contains several imprinted genes, including KCNQ1, KCNQ1OT1 (long non-coding RNA within the KCNQ1 gene, not shown in this figure), and CDKN1C. IC2 at the promoter for KCNQ1OT1 regulates expression of KCNQ1OT1, which is a paternally expressed noncoding transcript that further regulates in cis the expression of the maternally expressed imprinted genes in the centromeric domain. LOM at IC2 leading to bi-allelic expression of KCNQ1OT1 is found in 50% of BWS patients. This epigenetic alteration leads to reduced expression of the growth-regulating gene, CDKN1C.
Figure 5. Schematic maps of the imprinted domains on chromosome bands 15q11-q13. A) Arrows represent the genes (note that sizes of genes are not to scale). Colors of the arrows represent pattern of expression, blue: paternal, red: maternal, black: biallelic, and dashed arrows show unconfirmed monoallelic patterns of expression. The names of the genes are shown above the respective arrows. IC is an imprinting centre located upstream of SNURF/SNRPN. Blue circles show regions of differential DNA methylation on the maternal chromosome. BP1, BP2 and BP3 are recurrent breakpoints. Green lines indicate regions of typical deletions (class I and II) associated with Angelman Syndrome (maternal deletions) and Prader-Willi (paternal deletions), and maternal duplications associated with ASD. B) Zoom into the SNURF-SNRPN –UBE3A region. Circles are IC critical elements, black circle is the AS smallest overlapping region (AS-SRO), white circle is PWS-SRO. Boxes are genes, colors of boxes represent pattern of expression, blue: paternal, red: maternal. Arrows denote the direction of expression. SNURF-SNRPN is a multiexonic gene, expressed in multiple isoforms, with the first 3 coding exons encoding SNURF, a protein of unknown function, SNRPN encodes SmN , a spliceosomal protein involved involved in mRNA splicing. PWRN1, u1A, u1B are alternative transcription start cites of SNURF-SNRPN. SnoRNAs are encoded within introns of SNURF-SNRPN, with individual genes for SNORD 107,64, 108, 109A and 109B, while SNORD 116 and 115 are multicopy gene clusters. The function of the snoRNAs is not completely understood, they are possibly involved in modulationg alternative splicing/regulation nucleolar size. Some of the splice variants of SNURF-SNRPN span UBE3A (UBE3A-as), which possibly regulates imprinted expression of UBE3A. Green lines are small atypical deletions associated with PWS.
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Summary
40
Despite the tremendous advances in human genetics enabled by the original public and private human genome projects and brought to fruition with high throughput genotyping and “Nextgen” DNA sequencing, many aspects of human biology still cannot be adequately explained by genetics alone. Normal human development requires the specification of a multitude of cell types/organs that depend on transcriptional regulation programmed by epigenetic mechanisms. Epigenetics refers to modifications to DNA and its associated proteins that define the distinct gene expression profiles for individual cell types at specific developmental stages. Disruption of such control mechanisms is associated with a variety of diseases with behavioral, endocrine or neurologic manifestations, and quite strikingly with disorders of tissue growth, including cancer. While the involvement of epigenetic alterations in many of these diseases have been known to specialists for some time, the importance of epigenetics in general clinical medicine has only just begun to emerge. Current research is focused on characterizing cis- and trans-acting influences of the genetic background on epigenetic marks, delineating cell type/tissue specific epigenetic marks in human health and disease, studying the interaction between epigenetic marks and the environment especially with respect to fetal programming and risks for common adult onset disorders, and modulating adverse epigenetic states by drug-based and nutritional therapies.
An epigenetic trait is defined as a “stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence”. Epigenetic patterns, essential for controlling gene expression in normal growth and development, are established by a number of mechanisms including DNA methylation at cytosine residues in CpG dinucleotides and covalent modifications of histone proteins, as well as by less well understood mechanisms controlling long-range chromatin architecture within the cell nucleus. Although DNA methylation and histone modifications are regulated by different sets of enzymes, cross-talk between these modifications occurs through interactions of enzymes and other proteins that create and recognize these patterns. The relationship between these two central types of epigenetic modifications is known to be bi-directional, with histone marks being more labile and DNA methylation more stable. Thus DNA methylation can act to “lock in” epigenetic states. However, regulating metastable states of gene expression is so crucial in development and tissue homeostasis that other mechanisms, in addition to histone modifications and DNA methylation, come into play to establish and maintain epigenetic states. Regulatory non-coding RNAs, including small interfering RNA (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) play important roles in gene expression regulation at several levels transcription, mRNA degradation, splicing, transport and translation.
Epigenetic mechanisms are wide variety of normal developmental processes. Alterations in genes and proteins that are responsible for maintaining epigenomic patterns are the cause of a number of human disorders and diseases. Genomic imprinting, the unequal contribution of maternal and paternal allele to the offspring, caused by DNA methylation contributes to a number of human disorders. Imprinted genes typically function in growth regulation and neurodevelopment, and the corresponding disease phenotypes due to genetic or epigenetic aberrations in these genes indeed entail major abnormalities of intrauterine growth or post-natal cognition and behavior. These disorders include Beckwith-Wiedemann, Russell Silver, Prader-
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Willi and Angelman Syndromes. A number of disorders have been described with mutations or deletions in genes that are important for maintaining normal epigenetic regulation. Loss of function of these genes can disrupt normal establishment, maintenance, or reading of epigenetic marks, thereby resulting in altered chromatin structure and gene expression. Many of these disorders are associated with intellectual disability (ID); other features include facial dysmorphology and various congenital anomalies. These include CHARGE Association, Kleefstra, Sotos, Kabuki and Rett syndromes.
Epigenetic aberrations can result in a diverse array of non-neoplastic human diseases. Changes in DNA methylation were the first epigenetic alteration identified in cancer, and subsequent work over 3 decades has shown that both hyper- and hypo-methylation are important and pervasive pathogenic mechanisms both in early and late stages of human neoplasia. Not surprisingly histone modifications and miRNA expression are also altered in cancer. It has become increasingly apparent recently that proteins regulating epigenetic marks, including histone methyltransferases and demethylases, DNA methyltransferases, and chromatin remodeling SWI-SNF complexes are also dysregulated, not just by over- or under-expression but also by recurrent cancer-associated somatic mutations. Two classes of medications, DNA methylation inhibitors and HDAC inhibitors, have been approved by the US Food and Drug Administration as treatment for cancer. The wide array of epigenetic alterations identified in human disease could present valuable targets for approved medications as well as for novel ones that have yet to be developed.
Trans-generational effects of the environment on our epigenome have been documented providing evidence that in humans the mothers diet early in pregnancy can directly affect the programming of the epigenome early in utero that shape our development later in life. In mice and humans, oocytes retrieved following hormonal induction or embryos studied after in vitro culture have shown methylation and/or expression anomalies in several imprinted genes. Increasing attention has recently been focused on reports of increased rates of epigenetic errors in human following infertility/artificial reproductive technologies (ART). In particular, two rare disorders exhibited an increased incidence in retrospective studies in children born following infertility/ART.
The role of epigenetic marks in translating the primary genomic sequence has now moved to the forefront of human genetics, with clear implications for our understanding of human development and disease. A number of initiatives have now been implemented to define human epigenetic patterns at high resolution with complete genomic coverage. The technology is now available to investigate multiple tissue-specific epigenomes in humans, and the NIH Roadmap Epigenomics Mapping Consortium (www.roadmapepigenomics.org) was launched to produce a public resource of human epigenomic data to catalyze basic biology and disease oriented research. Another parallel initiative is the NIH Epigenomics of Health and Disease Roadmap Program, which funds investigator-initiated research. While a good part of what we know so far about epigenetics in disease has come from cancer research, it is telling that most of the initial research grants from this program have been targeted to other complex diseases ranging from Alzheimer’s to adult heart disease and diabetes to autism. These initiatives interface with the International Human Epigenomics Consortium, which was established to accelerate and coordinate epigenomics research worldwide. These data should provide keys to unravel genetic and environmental factors that impinge on epigenomes to affect normal
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processes such as development and aging and lead to human diseases when these processes go awry.
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Figure 1. See text for complete legend.
DNA CpG sites methylatedor unmethylated
Nucleosomes
Histone N‐terminal tail modifications
Condensed “closed” chromatin and uncondensed “open” chromatin
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Figure 2. See text for complete legend
H3
H4
N‐ S G R G K G G K G L G K G G A K R H R K V L D ….K….1 3 5 8 12 16 18 20 91
N‐ A R T K Q T A R K S T G G K A P R K Q L T K A A R K S A P ..K ..Y ..K ..K ..2 3 4 8 9 10 11 14 17 18 23 26 27 28 36 41 56 79
AcetylationMethylationPhosphorylation
A
B
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Chr 1
Chr 2Chr 4
Chr 6Chr 7 Chr 8
Chr 10
Chr 11
Chr 13 Chr 14
Chr 15
Chr 16
Chr 19 Chr 20
Chr 18
‐TP73
‐DIRAS3
LRRTM1‐
NAP1L5‐
‐PLAGL1,HYMAI
‐PRIM2
‐IGF2R
‐GRB10*
* GRB10 is maternally expressed in placenta and paternally expressed in brain