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Abstract
Epigenetic medicine is still in its infancy. To date, only a handful of diseases have documented epigenetic correlates upstream of gene regulation including cancer, developmental syndromes and late-onset diseases. The finding that epigenetic markers are dynamic and heterogeneous at tissue and cellular levels, combined with recent identification of a new form of functionally distinct DNA methylation has opened a wider window for investigators to pry into the epigenetic world. It is anticipated that many diseases will be elucidated through this epigenetic inquiry. In this review, we discuss the normal course of DNA methylation during development, taking alcohol as a demonstrator of the epigenetic impact of environmental factors in disease etiology, particularly the growth retardation and neurodevelopmental deficits of fetal alcohol spectrum disorders.
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Affiliation(s)
- Marisol Resendiz
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuanyuan Chen
- Department of Anatomy & Cell Biology, MS508, Indiana University School Medicine, Indianapolis, IN 46202, USA
| | - Nail C Öztürk
- Department of Anatomy & Cell Biology, MS508, Indiana University School Medicine, Indianapolis, IN 46202, USA
- Department of Anatomy, Mersin University School of Medicine, Turkey
| | - Feng C Zhou
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Anatomy & Cell Biology, MS508, Indiana University School Medicine, Indianapolis, IN 46202, USA
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Ehrlich M, Lacey M. DNA methylation and differentiation: silencing, upregulation and modulation of gene expression. Epigenomics 2013; 5:553-68. [PMID: 24059801 PMCID: PMC3864898 DOI: 10.2217/epi.13.43] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Differentiation-related DNA methylation is receiving increasing attention, partly owing to new, whole-genome analyses. These revealed that cell type-specific differential methylation in gene bodies is more frequent than in promoters. We review new insights into the functionality of DNA methylation during differentiation, with emphasis on the methylomes of myoblasts, myotubes and skeletal muscle versus non-muscle samples. Biostatistical analyses of data from reduced representation bisulfite sequencing are discussed. Lastly, a model is presented for how promoter and intragenic DNA hypermethylation affect gene expression, including increasing the efficiency of polycomb silencing at some promoters, downmodulating other promoters rather than silencing them, counteracting enhancers with heterologous specificity, altering chromatin conformation by inhibiting the binding of CTCF, modulating mRNA transcript levels by inhibiting overlapping promoters of noncoding RNA genes or by regulating the use of alternative mRNA promoters, modulating transcription termination, regulating alternative splicing and acting as barriers to the spread of activating chromatin.
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Affiliation(s)
- Melanie Ehrlich
- Hayward Human Genetics Program, Tulane Cancer Center, and Center for Bioinformatics & Genomics, Tulane Health Sciences Center, New Orleans, LA 70112, USA.
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53
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Guibert S, Weber M. Functions of DNA Methylation and Hydroxymethylation in Mammalian Development. Curr Top Dev Biol 2013; 104:47-83. [DOI: 10.1016/b978-0-12-416027-9.00002-4] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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54
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Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons. Proc Natl Acad Sci U S A 2012; 109:15841-6. [PMID: 23019368 DOI: 10.1073/pnas.1208214109] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA cytosine methylation is a central epigenetic marker that is usually mutagenic and may increase the level of sequence divergence. However, methylated genes have been reported to evolve more slowly than unmethylated genes. Hence, there is a controversy on whether DNA methylation is correlated with increased or decreased protein evolutionary rates. We hypothesize that this controversy has resulted from the differential correlations between DNA methylation and the evolutionary rates of coding exons in different genic positions. To test this hypothesis, we compare human-mouse and human-macaque exonic evolutionary rates against experimentally determined single-base resolution DNA methylation data derived from multiple human cell types. We show that DNA methylation is significantly related to within-gene variations in evolutionary rates. First, DNA methylation level is more strongly correlated with C-to-T mutations at CpG dinucleotides in the first coding exons than in the internal and last exons, although it is positively correlated with the synonymous substitution rate in all exon positions. Second, for the first exons, DNA methylation level is negatively correlated with exonic expression level, but positively correlated with both nonsynonymous substitution rate and the sample specificity of DNA methylation level. For the internal and last exons, however, we observe the opposite correlations. Our results imply that DNA methylation level is differentially correlated with the biological (and evolutionary) features of coding exons in different genic positions. The first exons appear more prone to the mutagenic effects, whereas the other exons are more influenced by the regulatory effects of DNA methylation.
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DNA hypermethylation of alternatively spliced and repeat sequences in humans. Mol Genet Genomics 2012; 287:631-42. [PMID: 22740315 PMCID: PMC3407362 DOI: 10.1007/s00438-012-0703-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/11/2012] [Indexed: 01/24/2023]
Abstract
DNA methylation is presently accepted as a tentative regulatory parameter in splicing. Recently, we reported significant methylation differences among various exonic splicing-enhancing elements and alternative splicing events, based on CpG methylation data from the Human Epigenome Project for chromosomes 6, 20 and 22. Presently, using a different computational approach and the same database, we report: (a) significant increase of hypermethylation in intronic and exonic sequences close to acceptor sites, relative to overall introns and exons, respectively (1,973 CpGs examined); (b) frequent CpGs, mostly hypomethylated, in donors and infrequent CpGs mostly hypermethylated, in acceptors; and (c) hypermethylation in cassette exons which are occasionally spliced and have weaker average splicing potential, relative to constitutive exons (p < 0.0001). CpGs are hypomethylated in non-coding exons (only 16 % hypermethylation). Single-exon genes, similarly to first exons, frequently contain hypomethylated CpGs, while in internal and last exons CpGs are more frequently hypermethylated. Methylation is also more frequent in strange introns and splice sites processed by the minor spliceosome, e.g., ATAC, (p < 0.0001 in all cases), but not in sites of incomplete processing, e.g., retained introns or bleeding exons, (p = 0.706 and p = 0.313, respectively). Most Alus, which are known to contribute to transcript presentation, are heavily methylated, in contrast with other Alus, e.g., AluJo and mammalian interspersed repetitive elements which have been previously associated with alternative expression. These results elucidate the role of intragenic methylation in association with alternative splicing and facilitate the evaluation of genomic variations/polymorphisms and the development of tools for the prediction of alternative splicing events.
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56
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Schober ME, Ke X, Xing B, Block BP, Requena DF, McKnight R, Lane RH. Traumatic brain injury increased IGF-1B mRNA and altered IGF-1 exon 5 and promoter region epigenetic characteristics in the rat pup hippocampus. J Neurotrauma 2012; 29:2075-85. [PMID: 22413999 DOI: 10.1089/neu.2011.2276] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Traumatic brain injury (TBI) is a major cause of acquired cognitive disability in childhood. Such disability may be blunted by enhancing the brain's endogenous neuroprotective response. An important endogenous neuroprotective response is the insulin-like growth factor-1 (IGF-1) mRNA variant, IGF-1B. IGF-1B mRNA, characterized by exon 5 inclusion, encodes the IGF-1 and Eb peptides. IGF-1A mRNA excludes exon 5 and encodes the IGF-1 and Ea peptides. A region in the human IGF-1B homologue acts as an exon-splicing enhancer (ESE) to increase IGF-1B mRNA. It is not known if TBI is associated with increased brain IGF-1B mRNA. Epigenetic modifications may underlie altered gene expression in the brain after TBI. We hypothesized that TBI would increase hippocampal IGF-1B mRNA in 17-day-old rats, associated with DNA methylation and/or histone modifications at the promoter site 1 (P1) or exon 5/ESE region. Hippocampi from rat pups after controlled cortical impact (CCI) were used to measure IGF-1B mRNA, DNA methylation, and histone modifications at the P1, P2, and exon5/ESE regions. In CCI hippocampi, IGF-1B mRNA peaked at post-injury day (PID) 2 (1700±320% sham), but normalized by PID 14. IGF-1A peaked at PID 3 (280±52% sham), and remained elevated at PID 14. Increased IGF-1B mRNA was associated with increased methylation at P1, and increased histone modifications associated with gene activation at P2 and exon5/ESE, together with differential methylation in the exon 5/ESE regions. We report for the first time that hippocampal IGF-1B mRNA increased after developmental TBI. We speculate that epigenetic modifications at the P2 and exon 5/ESE regions are important in the regulation of IGF-1B mRNA expression. The exon 5/ESE region may present a means for future therapies to target IGF-1B transcription after TBI.
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Affiliation(s)
- Michelle E Schober
- Division of Critical Care, Department of Pediatrics, University of Utah School of Medicine Salt Lake City, Utah 84158, USA.
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Epigenetics in social insects: a new direction for understanding the evolution of castes. GENETICS RESEARCH INTERNATIONAL 2012; 2012:609810. [PMID: 22567395 PMCID: PMC3335566 DOI: 10.1155/2012/609810] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 12/21/2011] [Indexed: 11/23/2022]
Abstract
Epigenetic modifications to DNA, such as DNA methylation, can expand a genome's
regulatory flexibility, and thus may contribute to the evolution of phenotypic plasticity. Recent work has demonstrated the importance of DNA methylation in alternative queen
and worker “castes” in social insects, particularly honeybees. Social insects are an excellent system for addressing questions about epigenetics and evolution because: (1)
they have dramatic caste polyphenisms that appear to be tied to differential methylation,
(2) DNA methylation is widespread in various groups of social insects, and (3) there are
intriguing connections between the social environment and DNA methylation in many
species, from insects to mammals. In this article, we review research on honeybees, and,
when available, other social insects, on DNA methylation and queen and worker caste
differences. We outline a conceptual framework for the effects of methylation on caste
determination in honeybees that may help guide studies of epigenetic regulation in other
polyphenic taxa. Finally, we suggest future paths of study for social insect epigenetic
research, including the importance of comparative studies of DNA methylation on a
broader range of species, and highlight some key unanswered mechanistic questions
about how DNA methylation affects gene regulation.
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Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, Reddy SU, Chandak GR, Raghunath M, Sivasubbu S, Chakraborty K, Scaria V, Sengupta S. High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One 2012; 7:e31621. [PMID: 22355382 PMCID: PMC3280313 DOI: 10.1371/journal.pone.0031621] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/10/2012] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability.
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Affiliation(s)
- Satish Sati
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | | | - Ashok Patowary
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vaibhav Jain
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Sourav Ghosh
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Shadab Ahmad
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Meghna Singh
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - S. Umakar Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | | | | | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail: (VS); (S. Sengupta)
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail: (VS); (S. Sengupta)
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