Literature DB >> 22641018

Functions of DNA methylation: islands, start sites, gene bodies and beyond.

Peter A Jones1.   

Abstract

DNA methylation is frequently described as a 'silencing' epigenetic mark, and indeed this function of 5-methylcytosine was originally proposed in the 1970s. Now, thanks to improved genome-scale mapping of methylation, we can evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences. The emerging picture is that the function of DNA methylation seems to vary with context, and the relationship between DNA methylation and transcription is more nuanced than we realized at first. Improving our understanding of the functions of DNA methylation is necessary for interpreting changes in this mark that are observed in diseases such as cancer.

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Year:  2012        PMID： 22641018     DOI： 10.1038/nrg3230

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  99 in total

1.  Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.

Authors:  Daniel Cortázar; Christophe Kunz; Jim Selfridge; Teresa Lettieri; Yusuke Saito; Eilidh MacDougall; Annika Wirz; David Schuermann; Angelika L Jacobs; Fredy Siegrist; Roland Steinacher; Josef Jiricny; Adrian Bird; Primo Schär
Journal:  Nature       Date:  2011-01-30       Impact factor: 49.962

2.  DNA-binding factors shape the mouse methylome at distal regulatory regions.

Authors:  Michael B Stadler; Rabih Murr; Lukas Burger; Robert Ivanek; Florian Lienert; Anne Schöler; Erik van Nimwegen; Christiane Wirbelauer; Edward J Oakeley; Dimos Gaidatzis; Vijay K Tiwari; Dirk Schübeler
Journal:  Nature       Date:  2011-12-14       Impact factor: 49.962

3.  Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line.

Authors:  Einav Nili Gal-Yam; Gerda Egger; Leo Iniguez; Heather Holster; Steingrímur Einarsson; Xinmin Zhang; Joy C Lin; Gangning Liang; Peter A Jones; Amos Tanay
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-27       Impact factor: 11.205

4.  Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors.

Authors:  C Stirzaker; D S Millar; C L Paul; P M Warnecke; J Harrison; P C Vincent; M Frommer; S J Clark
Journal:  Cancer Res       Date:  1997-06-01       Impact factor: 12.701

5.  Global and gene-specific epigenetic patterns in human bladder cancer genomes are relatively stable in vivo and in vitro over time.

Authors:  I D Markl; J Cheng; G Liang; D Shibata; P W Laird; P A Jones
Journal:  Cancer Res       Date:  2001-08-01       Impact factor: 12.701

6.  Genomic sequencing reveals a positive correlation between the kinetics of strand-specific DNA demethylation of the overlapping estradiol/glucocorticoid-receptor binding sites and the rate of avian vitellogenin mRNA synthesis.

Authors:  H P Saluz; J Jiricny; J P Jost
Journal:  Proc Natl Acad Sci U S A       Date:  1986-10       Impact factor: 11.205

7.  Cytosine methylation does not affect binding of transcription factor Sp1.

Authors:  M A Harrington; P A Jones; M Imagawa; M Karin
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205

8.  Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells.

Authors:  C Nguyen; G Liang; T T Nguyen; D Tsao-Wei; S Groshen; M Lübbert; J H Zhou; W F Benedict; P A Jones
Journal:  J Natl Cancer Inst       Date:  2001-10-03       Impact factor: 13.506

9.  DNMT3A mutations in acute myeloid leukemia.

Authors:  Timothy J Ley; Li Ding; Matthew J Walter; Michael D McLellan; Tamara Lamprecht; David E Larson; Cyriac Kandoth; Jacqueline E Payton; Jack Baty; John Welch; Christopher C Harris; Cheryl F Lichti; R Reid Townsend; Robert S Fulton; David J Dooling; Daniel C Koboldt; Heather Schmidt; Qunyuan Zhang; John R Osborne; Ling Lin; Michelle O'Laughlin; Joshua F McMichael; Kim D Delehaunty; Sean D McGrath; Lucinda A Fulton; Vincent J Magrini; Tammi L Vickery; Jasreet Hundal; Lisa L Cook; Joshua J Conyers; Gary W Swift; Jerry P Reed; Patricia A Alldredge; Todd Wylie; Jason Walker; Joelle Kalicki; Mark A Watson; Sharon Heath; William D Shannon; Nobish Varghese; Rakesh Nagarajan; Peter Westervelt; Michael H Tomasson; Daniel C Link; Timothy A Graubert; John F DiPersio; Elaine R Mardis; Richard K Wilson
Journal:  N Engl J Med       Date:  2010-11-10       Impact factor: 91.245

10.  Dynamic CpG island methylation landscape in oocytes and preimplantation embryos.

Authors:  Sébastien A Smallwood; Shin-Ichi Tomizawa; Felix Krueger; Nico Ruf; Natasha Carli; Anne Segonds-Pichon; Shun Sato; Kenichiro Hata; Simon R Andrews; Gavin Kelsey
Journal:  Nat Genet       Date:  2011-06-26       Impact factor: 38.330
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  2000 in total

Review 1.  Epigenetic plasticity and the hallmarks of cancer.

Authors:  William A Flavahan; Elizabeth Gaskell; Bradley E Bernstein
Journal:  Science       Date:  2017-07-21       Impact factor: 47.728

2.  Methylation of the dopamine transporter gene in blood is associated with striatal dopamine transporter availability in ADHD: A preliminary study.

Authors:  Corinde E Wiers; Falk W Lohoff; Jisoo Lee; Christine Muench; Clara Freeman; Amna Zehra; Stefano Marenco; Barbara K Lipska; Pavan K Auluck; Ningping Feng; Hui Sun; David Goldman; James M Swanson; Gene-Jack Wang; Nora D Volkow
Journal:  Eur J Neurosci       Date:  2018-08       Impact factor: 3.386

3.  Linking inter-individual variability to endocrine disruptors: insights for epigenetic inheritance.

Authors:  Sarah E Latchney; Ashley M Fields; Martha Susiarjo
Journal:  Mamm Genome       Date:  2017-12-07       Impact factor: 2.957

Review 4.  How to stomach an epigenetic insult: the gastric cancer epigenome.

Authors:  Nisha Padmanabhan; Toshikazu Ushijima; Patrick Tan
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2017-05-17       Impact factor: 46.802

Review 5.  Genetic and epigenetic control of metabolic health.

Authors:  Robert Wolfgang Schwenk; Heike Vogel; Annette Schürmann
Journal:  Mol Metab       Date:  2013-09-25       Impact factor: 7.422

6.  Clinical epigenetics and multidrug-resistant bacterial infections: host remodelling in critical illness.

Authors:  Ettore Crimi; Giuditta Benincasa; Silvia Cirri; Rebecca Mutesi; Mario Faenza; Claudio Napoli
Journal:  Epigenetics       Date:  2020-04-14       Impact factor: 4.528

7.  Increased 5-methylcytosine and decreased 5-hydroxymethylcytosine levels are associated with reduced striatal A2AR levels in Huntington's disease.

Authors:  Izaskun Villar-Menéndez; Marta Blanch; Shiraz Tyebji; Thais Pereira-Veiga; José Luis Albasanz; Mairena Martín; Isidre Ferrer; Esther Pérez-Navarro; Marta Barrachina
Journal:  Neuromolecular Med       Date:  2013-02-06       Impact factor: 3.843

Review 8.  Epigenetic regulation of ASC/TMS1 expression: potential role in apoptosis and inflammasome function.

Authors:  Antero Salminen; Anu Kauppinen; Mikko Hiltunen; Kai Kaarniranta
Journal:  Cell Mol Life Sci       Date:  2013-11-28       Impact factor: 9.261

Review 9.  Epigenetics and development of food allergy (FA) in early childhood.

Authors:  Xiumei Hong; Xiaobin Wang
Journal:  Curr Allergy Asthma Rep       Date:  2014-09       Impact factor: 4.806

10.  DNA methylation in promoter regions of genes involved in the reproductive and metabolic function of children born to women with PCOS.

Authors:  Bárbara Echiburú; Fermín Milagro; Nicolás Crisosto; Francisco Pérez-Bravo; Cristian Flores; Ana Arpón; Francisca Salas-Pérez; Sergio E Recabarren; Teresa Sir-Petermann; Manuel Maliqueo
Journal:  Epigenetics       Date:  2020-04-20       Impact factor: 4.528
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