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Cancer Science Institute of Singapore, National University of Singapore, Singapore 2 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Correspondence to Chee Seng Ku, Cancer Science Institute of Singapore, National University of Singapore, Singapore; g0700040@nus.edu.sg Received 5 June 2011 Revised 24 June 2011 Accepted 25 June 2011 Published Online First 8 August 2011
ABSTRACT The advances in next generation sequencing (NGS) technologies have had a signicant impact on epigenomic research. The arrival of NGS technologies has enabled a more powerful sequencing based methoddthat is, ChIP-Seqdto interrogate whole genome histone modications, improving on the conventional microarray based method (ChIP-chip). Similarly, the rst human DNA methylome was mapped using NGS technologies. More importantly, studies of DNA methylation and histone modication using NGS technologies have yielded new discoveries and improved our knowledge of human biology and diseases. The concept that cytosine methylation was restricted to CpG dinucleotides has only been recently challenged by new data generated from sequencing the DNA methylome. Approximately 25% of all cytosine methylation identied in stem cells was in a non-CG context. The non-CG methylation was more enriched in gene bodies and depleted in protein binding sites and enhancers. The recent developments of third generation sequencing technologies have shown promising results of directly sequencing methylated nucleotides and having the ability to differentiate between 5-methylcytosine and 5-hydroxymethylcytosine. The importance of 5-hydroxymethylcytosine remains largely unknown, but it has been found in various tissues. 5-hydroxymethylcytosine was particularly enriched at promoters and in intragenic regions (gene bodies) but was largely absent from non-gene regions in DNA from human brain frontal lobe tissue. The presence of 5-hydroxymethylcytosine in gene bodies was more positively correlated with gene expression levels. The importance of studying 5-methylcytosine and 5-hydroxymethylcytosine separately for their biological roles will become clearer when more efcient methods to distinguish them are available.
INTRODUCTION
Epigenetics refers to the mechanisms that regulate the cell type or tissue specic transcription or gene expression levels without altering the DNA sequences, through biochemical modications such as the addition of a methyl group to cytosines, and post-translational modications of histone proteins. These epigenetic mechanisms play a critical role in the normal stages of cellular developmental and processes such as embryogenesis, cell differentiation (cell lineage specication), inactivation of the X chromosome and genomic imprinting through modulation of transcriptional regulation in a tissue specic manner. Abnormalities in these
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epigenetic mechanisms have been linked to a wide range of diseases.1e6 The importance of exploring the epigenetics of human complex diseases and traits is now being increasingly recognised. Despite the success of genome-wide association studies (GWAS) in identifying thousands of new genetic variants or loci for complex diseases and traits, most of these identied genetic variants confer modest effect sizes with an OR <1.5. Therefore, these genetic variants collectively account for only a small fraction of the heritability of complex phenotypes.7e9 Epigenetic mechanisms are a potential source of the missing heritability. Theoretically, only the germline heritable epigenetic events (inherited through meiosis) may contribute towards the missing heritability as opposed to the non-germline heritable components (inherited through mitosis or somatic epigenetic events). However, it is challenging to determine which epigenetic events are germline heritable. Comparing the epigenetic proles between the disease epigenome, such as the cancer epigenome, with the epigenome from constitutional DNA from the same individual as a reference, is required for distinguishing between germline and somatic epigenetic events. These approaches were also applied previously in cancer genome sequencing studies for a proper assessment of somatic mutations.10 11 In addition, twin studies are also a powerful study design to investigate epigenetic heritability.12e14 Molecular mechanisms of heritability may not be limited to DNA sequence differences.12 The nding that monozygotic twins have very similar epigenetic proles has indicated a high epigenetic heritability.15 In addition, twin studies in epigenetics would be able to: (1) address the extent of and variation in epigenetic heritability across the genome; and (2) investigate whether non-germline heritable (or somatic) epigenetic events contribute to complex phenotypes in monozygotic twins discordant for the phenotypes. Epigenetic studies of disease discordant monozygotic twins offer several advantages in detecting disease related epigenetic differences over a study design involving unrelated disease cases and controls.16e21 The arrival of next generation sequencing (NGS) technologies in 2005 led to a paradigm shift in the approaches to investigating functional genomics in the human genome.22e24 Functional genomics aims to interrogate the functional elements and regulatory mechanisms in the genome including DNA methylation and histone modications. Before 2005, the genome-wide epigenetic (epigenomic) studies were dependent mainly on DNA
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microarray methods, such as the ChIP-chip method (chromatin immunoprecipitation based on microarray hybridisation of the immunoprecipitated DNA fragments), to study histone modications and DNA methylation microarrays. However NGS technologies were swiftly integrated into epigenomic studies and several new and innovative sequencing based methods have been developed together with bioinformatic and analytical tools.25 26 For example, sequencing based approaches such as ChIP-Seq (chromatin immunoprecipitation based on sequencing of the immunoprecipitated DNA fragments) have replaced microarray experiments in the study of histone modications, and the sequencing of the human whole genome DNA methylation (the DNA methylome) after bisulte conversion has also become feasible and replaced the microarrays targeting preselected CpG sites.27e30 Over the past several years, NGS technologies have contributed signicantly to advances in epigenomics and provided new alternatives to study the human epigenome at a much greater resolution.31e35 The aim of this paper is to review the recent advances in epigenomics using NGS technologies and the impact on our understanding of human biology and diseases. We focus mainly on DNA methylation and histone modication, which are relatively well studied epigenetic mechanisms. We also discuss the extent to which germline heritable epigenetic mechanisms explain the missing heritability, and the challenges faced by studies attempting to examine this largely unexplored epigenetic component in complex diseases and traits. Finally, we also highlight the new opportunities offered by third generation sequencing (TGS) technologies in studying epigenomics. are wrapped around by 146 bp of DNA. The N-terminal tails of histone polypeptides can be modied by more than 100 different post-translational modications including methylation, acetylation, phosphorylation, and ubiquitination (collectively known as histone modications). Similarly to DNA methylation, the histone modications can regulate transcription through modication of the chromatin structure or through chromatin condensation. Although their role, function, and relationship to transcriptional regulation for most of these histone modications remains poorly understood, considerable progress has been achieved in recent years through studies applying the ChIP-chip and ChIP-Seq approaches. For example, methylation of histone H3 lysine 4 (H3K4) and H3 lysine 36 is associated with transcription activation. In contrast, methylation of H3 lysine 9 (H3K9), H3 lysine 27 (H3K27), and H4 lysine 20 (H4K20) is correlated with repression of transcription.31e34 Figure 1 illustrates the epigenetic mechanisms. An important prerequisite for further understanding of the role and function of epigenetics in normal biology and the development of disease is the ability to investigate comprehensively the pattern and distribution of epigenetic markers in the whole genome from multiple tissue types, which requires newer and more powerful methods. In the following sections, we briey discuss the traditional methods used to interrogate epigenetic mechanisms in order to appreciate the improvements made by sequencing based approaches enabled by NGS and TGS technologies.
Methods developed to study DNA methylation include the use of methylation sensitive restriction enzymes, afnity enrichment using antibodies specic to 5-methylcytosine (5mC), and bisulte conversion. However, a number of limitations are associated with each of these methodsdfor example, enzyme digestion methods are restricted to restriction enzyme recognition sites and as a result only a very small subset of all methylation sites can be interrogated. In comparison, methods that rely on afnity enrichment using antibodies are biased towards enrichment of sites containing relatively high levels of cytosine methylation, namely, CpG islands. These methods were coupled with microarray based methods to enable genome-wide analysis of DNA methylation and histone modications based on the ChIP-chip method.27 31 39 40 A limitation of microarray based methods is that they do not allow a truly comprehensive interrogation of DNA methylation and histone modications throughout the whole genome, as synthesising the probes for microarrays requires prior knowledge of the regions to be targeted. Thus only those genomic regions that are probed by the microarrays will be interrogated. For example, this is evident from the conventional ChIP-chip studies where the immunoprecipitated DNA fragments that are associated with a specic histone modication could not be detected unless there are probes covering the genomic regions. In contrast, sequencing based approaches such as ChIP-Seq, in theory, are able to capture all the DNA fragments that are isolated by immunoprecipitation if the sequencing depth or coverage is sufcient.24 28 29 Similarly, the current DNA methylation microarrays are only able to interrogate a small fraction of the entire DNA methylome. High density microarrays such as the Innium Human Methylation 450 BeadChip allow researchers to investigate >450 000 CpG sites out of the approximately 28 million CpG sites in the human genome (<0.02%).41 42 There is also ascertainment bias in selecting these
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>450 000 CpG sites to be interrogated. This type of microarray is widely accepted as a genome-wide tool for DNA methylation yet it is still restricted to preselected CpG sites. This incomplete interrogation of DNA methylation patterns in the human genome will reduce the power of discoveries. For example, methylation in the non-CG context, revealed through sequencing of the entire DNA methylome, would be overlooked when using microarrays.38 Table 1 summarises the pros and cons of the common approaches to mapping DNA methylation and histone modications and gure 2 illustrates the ChIP-chip and ChIP-seq methods. Readers should refer to these references for a more comprehensive review of different methodologies in studying DNA methylation and histone modications.27e29 clearly shows that the throughput of NGS technologies has enabled a much larger scale of DNA methylation studies to be performed. However, sequencing of DNA methylation still uses the conventional approach of bisulte conversion to differentiate methylated from unmethylated cytosines of which there are several disadvantages (please see New opportunities from TGS technologies). Third generation sequencing technologies, such as SMRT sequencing, offer new opportunities to sequence directly the methylated cytosines without bisulte conversion.46 47
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Table 1
Method Bisulte treatment
Cons
< Incomplete conversion < Degradation of DNA < Not easily adapted to array hybridisation
Most suitable application High resolution study of DNA methylation at small or large scale
difference into a genetic difference, easily detectable by sequencing < Single base pair resolution Methylation sensitive restriction enzymes digestion Afnity enrichment by 5-methylcytosine antibodies
< Highly sensitive, simple
techniques
< Limited by methylation d sensitive restriction
Targeted, site specic study of DNA methylation Rapid, large scale, low resolution study of DNA methylation
of DNA methylation in complex genomes < Rapid and efcient genome-wide assessment of DNA methylation
< Productive for genome-wide mapping of
ChIP-chip
be probed < High signal-to-noise ratios < Limited dynamic range < Cross-hybridisation between similar sequences
< Difculty in the ambiguous aligning of short
ChIP-seq
is based on counting the sequence reads < Wider dynamic range < Bar coding allows sample multiplexing for NGS
The information in this table is summarised from three excellent review papers by Laird, Hurd and Nelson, and Hirst and Marra.27e29 NGS, next generation sequencing.
specically in embryonic stem cells as well as induced pluripotent stem cells to maintain pluripotency. This also suggests that changes in epigenetic mechanisms are taking place during the cell differentiation stages. The non-CG methylation was restored in induced pluripotent stem cells from differentiated cells.38 Dynamic changes in the human methylome during Figure 2 Genome-wide mapping of histone modications and other DNAeprotein interactions has relied on (A) chromatin immunoprecipitation (ChIP) coupled with microarrays (ie, ChIP-chip) and (B) next generation sequencing (NGS) technologies (ie, ChIP-Seq) which have provided more precise and comprehensive landscapes of histone modications in the entire genome. Reprinted by permission from Macmillan Publishers Ltd: Nat Rev Genet (9:179-91), copyright (2008).
differentiation were also demonstrated by another study through whole genome bisulte sequencing, where the developmental stage was reected in both the level of global methylation and extent of non-CpG methylation. The total level of global methylation and the degree of non-CpG methylation is inversely correlated to the level of differentiation.49
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approaches.52 A recent study has shown that most tissue specic gene regulation mediated by DNA methylation occurs at alternative promoters located in gene bodies instead of 59 promoters. More specically, the majority of methylated CpG islands were shown to be in intragenic and intergenic regions. In contrast, <3% of CpG islands in 59 promoters were methylated. This was found through generating a map of DNA methylation from the human brain encompassing 24.7 million of the 28 million CpG sites. Similarly, these distribution patterns across the genome would not have been unravelled if the studies were restricted to interrogating a proportion of CpG sites. The study showed that intragenic DNA methylation plays a role in regulating transcription from alternative promoters, and this is consistent with transcriptomic studies which have shown that many genes have alternative promoters within gene bodies.52 The NGS and sequencing based methods have contributed to the advances in the epigenomics of stem cell research and the knowledge of stem cell molecular biology. For example, it was found that induced pluripotent stem cells showed signicant reprogramming variability, including aberrant reprogramming of DNA methylation through whole genome proling of DNA methylation at a single base resolution in ve human induced pluripotent stem cell lines together with embryonic stem cells, somatic cells, and differentiated induced pluripotent stem cells.53 Data also revealed that the epigenomic landscapes in embryonic stem cells and lineage committed cells are vastly different through comparisons of the chromatin modication proles and DNA methylomes in the stem cells and primary broblasts. This has provided new insights into the epigenetic mechanisms modulating the properties of pluripotency and cell fate commitment.54 However, the bioethical issues surrounding the use of human embryonic stem cells in research have to be given serious consideration. Adult stem cells and induced pluripotent stem cells generated from somatic cells provide an alternative source and should be considered for use in stem cell research.55 56 In addition to the conventional DNA methylation studies (ie, 5mC), research on 5hmC is also gaining its impetus. 5hmC is generated by TET proteins through oxidation of 5mC and is present at low levels in diverse cell types in mammals (gure 3).57 58 Currently, information on the genome-wide distribution of 5hmC is limited. However, two novel and specic approaches to prole the whole genome localisation of 5hmC have been developed recently. These two methods were developed to enable the precipitation of 5hmC in genomic DNA. The rst approach, termed GLIB (glucosylation, periodate oxidation, biotinylation), uses a combination of enzymatic and chemical steps to isolate DNA fragments containing a few down to a single 5hmC and entails the addition of a glucose molecule to each 5hmC. The second approach involves the conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulte, followed by immunoprecipitation of CMS-containing DNA with a specic antiserum to CMS. Both methods are specic to DNA containing 5hmC.59 Applying these methods to 5hmC-containing DNA from mouse embryonic stem cells showed strong enrichment within exons and near transcriptional start sites. The enrichment of 5hmC at the transcriptional start sites suggested a role for 5hmC in transcriptional regulation. Additionally, 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Genes with 5hmC at their start sites were disproportionately likely to contain bivalent H3K27 and H3K4 trimethylation at their promoters.
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Figure 3 Cytosine methylation (5-methylcytosine) is catalysed by DNA methyltransferase (DNMT) enzymes. These enzymes (DNMT3A and DNMT3B) catalyse the de novo covalent addition of a methyl group to cytosine in newly synthesised DNA as well as maintenance of 5methylcytosine (DNMT1) during mitosis. 5-hydroxymethylcytosine is generated by TET (Tet) proteins through oxidation of 5-methylcytosine. Reprinted from Clin Chim Acta, 412, Dahl C, Grnbk K, Guldberg P, Advances in DNA methylation: 5-hydroxymethylcytosine revisited, 831e6, Copyright (2011), with permission from Elsevier.
It is expected that some differences in the composition and pattern of cytosine methylation are likely to be found between the genomes of cells from different developmental stages; however, these differences remain poorly understood. Most of the targeted sequencing approaches or microarrays have focused on CG methylation, from which subsequent discoveries could not have been made without sequencing the entire DNA methylome. These discoveries will also provide new directions to study the prevalence and pattern of non-CG methylation in different adult stem cells that are found in various tissue types and differentiated cell types. These studies will also elucidate whether non-CG methylation is exclusively conned to embryonic stem cells, or if it also occurs in adult stem cells. The knowledge of the roles of non-CG methylation in maintaining the pluripotency and inducing the differentiation of adult stem cells will have important implications for regenerative medicine. Although Lister et al (2009) completed sequencing the DNA methylome of stem cells and differentiated broblasts, their study used bisulte sequencing and was thus unable to distinguish between 5mC and 5-hydroxymethylcytosine (5hmC). Therefore it is unclear whether and to what extent there were differences in the composition of 5mC and 5hmC between the genomes of stem cells and broblasts. Furthermore, methylation beyond the CG and non-CG contexts such as 5-methyladenine or methylation in other nucleotides can also not be studied. These are the major limitations of the current methods using bisulte conversion and NGS to study DNA methylation. The ability to investigate 5hmC and methylation of other nucleotides will be important and is anticipated to provide further biological insights into human biology and diseases.50 The absence of non-CG methylation in differentiated cells was also corroborated by sequencing the entire DNA methylome of peripheral blood mononuclear cells. The investigators found that <0.2% of non-CG sites were methylated, suggesting that non-CG methylation is minor in human peripheral blood mononuclear cells.48 In addition, this study also investigated allele specic methylation (ie, paternal and maternal alleles can exhibit different methylation patterns) between the two haploid methylomes by integrating the methylome data with the whole genome sequencing data that were generated previously.51 This led to identication of 599 haploid differentially methylated regions covering 287 genes and demonstrated that allele specic methylation is highly correlated with allele specic expression.48 The assumption that DNA methylation regulates gene expression mainly through its effects at 59 promoters has also been challenged by recent studies applying NGS based
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Likewise, a majority (w60%) of genes reported to contain bivalent H3K27 and H3K4 trimethylation have 5hmC at their start sites. Collectively, these ndings indicate that 5hmC, similar to 5mC, has a probable role in transcriptional regulation but support a model in which 5mC and 5hmC have different roles in transcription.59 New insights into 5hmC were also gained from other studies. 5hmC is mostly associated with euchromatin, and whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated with increased transcriptional levels. Most, if not all, 5hmC in the genome depends on preexisting 5mC and the balance between these two modications is different between genomic regions.60 Other studies have provided data to support further the important roles of TET proteins. The binding of TET1 throughout the genome of embryonic stem cells, with the majority of binding sites located at transcription start sites of CpG-rich promoters and within genes, was recently shown by Williams et al (2011). The hydroxymethylcytosine modication is found in gene bodies and, in contrast to methylcytosine, is also enriched at CpG-rich transcription start sites.61 Wu et al also showed in mouse embryonic stem cells that Tet1 is preferentially bound to CpGrich sequences at promoters of both transcriptionally active and Polycomb-repressed genes.62 expression and DNA and histone methylation patterns of progenitor and luminal lineage enriched cells through applications of NGS.64 However, a major limitation associated with the study was that the DNA methylation data were limited to a fraction of the genome, as only the methylation status of the recognition site of the BssHII enzyme was evaluated (an inherent limitation of using restriction enzymes for DNA methylation). The other limitation was that the cell fractions used in the study were not homogenously pure. However, these limitations could be overcome through whole genome sequencing of bisulte treated genomic DNA isolated from single cells (please see New opportunities from TGS technologies for analysis of DNA methylation patterns in single cells). Mapping and analysis of chromatin state dynamics in nine human cell types has been performed by a recent study using ChIP-Seq coupled with NGS.65 More specically, nine chromatin marks across nine cell types were mapped to systematically characterise regulatory elements, their cell type specicities, and their functional interactions. Chromatin states showed distinct associations with transcriptional start sites, transcripts, evolutionarily conserved non-coding regions, DNase hypersensitive sites, binding sites for the regulators c-Myc (MYC) and NF-kB, and inactive genomic regions associated with the nuclear lamina. Chromatin states drastically reduced the large combinatorial space of chromatin datasets to a manageable set of biologically interpretable annotations, thus providing an efcient and robust way to track coordinated changes across cell types. This allowed the systematic identication and comparison of more than 100 000 promoter and enhancer elements. This study is of signicance because chromatin proling has emerged as a powerful means of genome annotation and detection of regulatory activity as it provides a systematic means of detecting cis-regulatory elements. Therefore, chromatin proling is especially well suited to the characterisation of non-coding portions of the genome, which remain largely uncharacterised. The results also have implications for the interpretation of GWASs. Disease variants were frequently found to coincide with enhancer elements specic to a relevant cell type. For example, 33 enhancers were found in the 9p21 region where multiple single nucleotide polymorphisms (SNPs) within the region were associated with coronary artery disease and type 2 diabetes. More specically, the coronary artery disease risk alleles of SNPs rs10811656 and rs10757278 are located in one of the enhancers and disrupt a binding site for STAT1.66 In addition, the 8q24 cancer risk allele (rs6983267) increases prostate enhancer activity in vivo relative to the nonrisk allele also demonstrated.67 Intersecting with non-coding SNPs from GWAS datasets has suggested potential mechanistic explanations for disease variantsdthat is, how disease variants lead to the observed disease phenotypes, either through their presence within cell type specic enhancer states or by their effect on binding motifs for predicted regulators.65
Histone modications
In addition, the rst genome-wide mapping of histone modications using NGS technologies has identied a number of activation marks such as mono-methylations of H3K27, H3K9, H4K20, H3K79, and H2BK5, and histone marks that are linked to transcriptional repression such as trimethylations of H3K27, H3K9, and H3K79. This has provided new insights into the function of histone modications in transcriptional regulation.63 Cellular differentiation involves the gradual loss of pluripotency and acquisition of cell type specic features. This process is precisely controlled by cell type specic epigenetic programmes. Understanding these processes requires genomewide analysis of epigenetic and gene expression proles. New discoveries have been made through applications of NGS technologies for proling histone and DNA methylation, as well as gene expression patterns of normal human mammary progenitor enriched and luminal lineage committed cells.64 Integrative analysis of the gene expression, DNA methylation, and histone H3 K4 and K27 trimethylation proles of progenitor enriched and more differentiated luminal epithelial cell populations from multiple individuals were performed to understand better the regulation of human mammary epithelial cell type specication. Signicant differences in histone H3 lysine27 tri-methylation (H3K27me3) enrichment and DNA methylation of genes expressed in a cell type specic manner were observed, suggesting their regulation by epigenetic mechanisms and a dynamic interplay between the two processes that together dene developmental potential. The analysis further identied key regulators of mammary epithelial and luminal lineage commitment. The epigenetically regulated genes identied will accelerate the dissection of human mammary epithelial lineage commitment and luminal differentiation. Additionally, the list of genes epigenetically regulated in a cell type specic manner provides a rich resource for the further analysis of human breast development and the role of epigenetic mechanisms in breast tumorigenesis.64 This study has generated the rst comprehensive epigenomic prole of human mammary epithelial cells by analysing gene
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epigenetic proles from their parents and acquire different somatic epigenetic markers throughout their lifetime. The role of epigenetic changes in the mechanism of complex phenotype loci remains largely unexplored. However, in the context of GWAS there is growing evidence supporting the importance of epigenetics in complex phenotypes. For example, the nding of SNPs associated with diseases located within 500 kb of known imprinted genes has provided some evidence to support the importance of epigenetics in complex diseases. A total of ve SNPs associated with breast cancer, basal cell carcinoma, and type 2 diabetes were found to have parental origin specic associations. These SNPs were located in two genomic regions, 11p15 and 7q32, each harbouring a cluster of imprinted genes.68 An SNP association in the imprinted region of chromosome 14q32.2 was also found for type 1 diabetes.69 However, the importance of parental origin of sequence variants in association with complex diseases has been largely understudied in GWAS because unrelated samples were investigated. Pedigree or family information would be needed to investigate the parent-of-origin effects. In addition, studies investigating monozygotic twins who were discordant for autoimmune disease (specically systemic lupus erythematosus) identied widespread changes in the DNA methylation status of a signicant number of genes. Subsequent gene ontology analysis revealed enrichment in categories associated with immune function. Thus, this study also supports the concept that epigenetic changes may be critical in the manifestation of autoimmune disease.20 Data are accumulating to support the roles of epigenetic differences in monozygotic twins discordant for diseases.16e19 By contrast, Baranzini et al (2010) did not nd evidence for epigenetic (as well as genetic and transcriptomic) differences that explained monozygotic twins who were discordant for multiple sclerosis.21 The biological effect of the SNPs associated with epigenetic markers, is mediated through a variant specic epigenetic change. The associations of these SNPs with complex phenotypes can be identied by GWAS.48 70 71 DNA methylation associated with genetic variation in HapMap cell lines was studied and association analyses of methylation levels with more than 3 million SNPs identied 180 CpG-sites in 173 genes that were associated with nearby SNPs (usually within 5 kb).70 Integration of whole genome sequencing data with whole genome DNA methylation48 and histone modication data should facilitate the identication of DNA sequence genetic variations associated with the epigenetic markers, where the contribution of these epigenetic markers to complex phenotypes can be captured indirectly through SNPs by conventional genetic association studies or GWAS. These epigenetic markers may be germline heritable and thus account for heritability. Mapping allele specic DNA methylation or SNPs associated with DNA methylation can help to extract maximum information from GWAS.72e75 If epigenetic markers (or similarly copy number variants (CNVs)) are tagged by SNPs as the surrogate markers in GWAS, then they would not, in theory, account for the missing heritability. However, the effect sizes of SNPs (surrogate markers) found to be associated with complex phenotypes in GWAS could be underestimated, if the true causal variants (epigenetic markers or CNVs) were identied and which could then account for the missing heritability. However, present data are still rudimentary and it is unclear to what extent epigenetic markers can be tagged by the SNPs genotyped in GWAS and to what extent the effect size will be found to be higher when the true causal variant is identied.
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By contrast, germline heritable epigenetic markers that cannot be tracked by DNA sequence variations would be missed by GWAS. It is currently unclear to what extent these heritable epigenetic markers can be detected by DNA sequence variations and through the genotyping of surrogate markers. This implies that these heritable epigenetic markers have to be studied directly. Further studies would be needed to address these uncertainties. In summary, studies of germline heritable epigenetic effects on complex phenotypes are still rudimentary; however, high throughput sequencing technologies will undoubtedly contribute directly to the advances in epigenomic studies of complex phenotypes or indirectly through identication of DNA sequence variations tagging epigenetic markers. These technological developments have overcome the technical hurdles in mapping and characterising epigenetic markers in the whole genome. However, there are issues and challenges in studying somatic epigenetic events in complex phenotypesdfor example, the need for DNA samples to be extracted from the specic tissue related to the disease.
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tissue to prioritise when multiple cell types or tissue are involved in a complex disease, and whether it is feasible in terms of sample collection, cost effectiveness and time to study all tissue types.76e78 Furthermore, it is also unclear whether the disease associated epigenetic changes can be revealed by a simple casee control study design (like conventional genetic association studies) or by other more robust study designs which need to be developed. It is also unclear what sample size is required to achieve adequate statistical power to detect the disease associated epigenetic changes. heterogeneity in epigenetics research.84 More powerful sequencing technologies in the future will accelerate research studies by providing greater resolution at the single cell level,84 single molecule DNA sequencing level,85 and the single nucleotide level. Third generation sequencing technologies are characterised by single molecule DNA sequencing without amplication. As a result, this has simplied the steps in library preparation for sequencing with minimal sample manipulation in experiments. For example, the Helicos sequencing platform was used to sequence chromatin immunoprecipitated DNA directly.86 87 A further advantage is that only a small quantity of immunoprecipitated DNA (approximately 50 pg) is required and in contrast to nanogrammes of DNA required for NGS platforms. The requirement of a small amount of DNA is particular crucial for single cell sequencing and for clinical samples with a limited amount of DNA. As a proof-of-principle study using TGS for ChIP-Seq experiments, a good agreement was obtained for the ChIP-Seq data produced by the Helicos and Illumina sequencing platforms,87 suggesting that TGS yields comparable results and is able to overcome the limitations associated with NGS in ChIP-Seq experiments.
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