Literature DB >> 20689072

Epigenome mapping in normal and disease States.

Alika K Maunakea1, Iouri Chepelev, Keji Zhao.   

Abstract

Epigenomes are comprised, in part, of all genome-wide chromatin modifications, including DNA methylation and histone modifications. Unlike the genome, epigenomes are dynamic during development and differentiation to establish and maintain cell type-specific gene expression states that underlie cellular identity and function. Chromatin modifications are particularly labile, providing a mechanism for organisms to respond and adapt to environmental cues. Results from studies in animal models clearly demonstrate that epigenomic variability leads to phenotypic variability, including susceptibility to disease that is not recognized at the DNA sequence level. Thus, capturing epigenomic information is invaluable for comprehensively understanding development, differentiation, and disease. Herein, we provide a brief overview of epigenetic processes, how they are relevant to human health, and review studies using technologies that enable epigenome mapping. We conclude by describing feasible applications of epigenome mapping, focusing on epigenome-wide association studies (eGWAS), which have the potential to revolutionize current studies of human diseases and will likely promote the discovery of novel diagnostic, preventative, and treatment strategies.

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Year:  2010        PMID: 20689072      PMCID: PMC2917837          DOI: 10.1161/CIRCRESAHA.110.222463

Source DB:  PubMed          Journal:  Circ Res        ISSN: 0009-7330            Impact factor:   17.367


  172 in total

1.  Chromosomal instability and tumors promoted by DNA hypomethylation.

Authors:  Amir Eden; François Gaudet; Alpana Waghmare; Rudolf Jaenisch
Journal:  Science       Date:  2003-04-18       Impact factor: 47.728

Review 2.  The history of cancer epigenetics.

Authors:  Andrew P Feinberg; Benjamin Tycko
Journal:  Nat Rev Cancer       Date:  2004-02       Impact factor: 60.716

Review 3.  The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications.

Authors:  Bradley E Bernstein; Emily L Humphrey; Chih Long Liu; Stuart L Schreiber
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

Review 4.  Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.

Authors:  Leonie Ringrose; Renato Paro
Journal:  Annu Rev Genet       Date:  2004       Impact factor: 16.830

5.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors:  Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal:  Nat Genet       Date:  2007-02-04       Impact factor: 38.330

6.  Bisulfite-catalyzed transamination of cytosine and cytidine.

Authors:  R Shapiro; J M Weisgras
Journal:  Biochem Biophys Res Commun       Date:  1970-08-24       Impact factor: 3.575

7.  Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells.

Authors:  Gang Wei; Lai Wei; Jinfang Zhu; Chongzhi Zang; Jane Hu-Li; Zhengju Yao; Kairong Cui; Yuka Kanno; Tae-Young Roh; Wendy T Watford; Dustin E Schones; Weiqun Peng; Hong-Wei Sun; William E Paul; John J O'Shea; Keji Zhao
Journal:  Immunity       Date:  2009-01-16       Impact factor: 31.745

Review 8.  Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two.

Authors:  Katie E Prothero; Jill M Stahl; Laura Carrel
Journal:  Chromosome Res       Date:  2009       Impact factor: 5.239

9.  Monozygotic twins exhibit numerous epigenetic differences: clues to twin discordance?

Authors:  Arturas Petronis; Irving I Gottesman; Peixiang Kan; James L Kennedy; Vincenzo S Basile; Andrew D Paterson; Violeta Popendikyte
Journal:  Schizophr Bull       Date:  2003       Impact factor: 9.306

10.  Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome.

Authors:  Dana C Dolinoy; Jennifer R Weidman; Robert A Waterland; Randy L Jirtle
Journal:  Environ Health Perspect       Date:  2006-04       Impact factor: 9.031

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  77 in total

1.  Histone methyltransferase Dot1L plays a role in postembryonic development in Xenopus tropicalis.

Authors:  Luan Wen; Liezhen Fu; Xiaogang Guo; Yonglong Chen; Yun-Bo Shi
Journal:  FASEB J       Date:  2014-11-03       Impact factor: 5.191

Review 2.  In utero oxidative stress epigenetically programs antioxidant defense capacity and adulthood diseases.

Authors:  Rita S Strakovsky; Yuan-Xiang Pan
Journal:  Antioxid Redox Signal       Date:  2012-01-11       Impact factor: 8.401

3.  Liganded thyroid hormone receptor induces nucleosome removal and histone modifications to activate transcription during larval intestinal cell death and adult stem cell development.

Authors:  Kazuo Matsuura; Kenta Fujimoto; Liezhen Fu; Yun-Bo Shi
Journal:  Endocrinology       Date:  2011-12-06       Impact factor: 4.736

4.  The myth of genetic enhancement.

Authors:  Philip M Rosoff
Journal:  Theor Med Bioeth       Date:  2012-06

5.  The decade of the epigenomes?

Authors:  Joost H A Martens; Hendrik G Stunnenberg; Colin Logie
Journal:  Genes Cancer       Date:  2011-06

Review 6.  Endothelial epigenetics in biomechanical stress: disturbed flow-mediated epigenomic plasticity in vivo and in vitro.

Authors:  Yi-Zhou Jiang; Elisabetta Manduchi; Juan M Jiménez; Peter F Davies
Journal:  Arterioscler Thromb Vasc Biol       Date:  2015-04-02       Impact factor: 8.311

7.  A wavelet-based method to exploit epigenomic language in the regulatory region.

Authors:  Nha Nguyen; An Vo; Kyoung-Jae Won
Journal:  Bioinformatics       Date:  2013-10-04       Impact factor: 6.937

8.  BLUEPRINT: mapping human blood cell epigenomes.

Authors:  Joost H A Martens; Hendrik G Stunnenberg
Journal:  Haematologica       Date:  2013-10       Impact factor: 9.941

Review 9.  Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.

Authors:  Carlos A Aguilar; Harold G Craighead
Journal:  Nat Nanotechnol       Date:  2013-10       Impact factor: 39.213

10.  Gene × environment interaction by a longitudinal epigenome-wide association study (LEWAS) overcomes limitations of genome-wide association study (GWAS).

Authors:  Debomoy K Lahiri; Bryan Maloney
Journal:  Epigenomics       Date:  2012-12       Impact factor: 4.778

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