Literature DB >> 23800863

Hypomethylation marks enhancers within transposable elements.

Zohar Mukamel, Amos Tanay.   

Abstract

Transposable elements (TEs) make up 50% of the human genome and are usually considered a mutational burden. A new study uses signatures of DNA hypomethylation to identify tissue-specific enhancers within TEs, providing fresh evidence that mobile DNA has a non-negligible role in genome regulation and evolution.

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Year:  2013        PMID： 23800863     DOI： 10.1038/ng.2680

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


  11 in total

1.  The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons.

Authors:  Galit Lev-Maor; Rotem Sorek; Noam Shomron; Gil Ast
Journal:  Science       Date:  2003-05-23       Impact factor: 47.728

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.  A distal enhancer and an ultraconserved exon are derived from a novel retroposon.

Authors:  Gill Bejerano; Craig B Lowe; Nadav Ahituv; Bryan King; Adam Siepel; Sofie R Salama; Edward M Rubin; W James Kent; David Haussler
Journal:  Nature       Date:  2006-04-16       Impact factor: 49.962

4.  Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection.

Authors:  Netta Mendelson Cohen; Ephraim Kenigsberg; Amos Tanay
Journal:  Cell       Date:  2011-05-27       Impact factor: 41.582

Review 5.  What fraction of the human genome is functional?

Authors:  Chris P Ponting; Ross C Hardison
Journal:  Genome Res       Date:  2011-08-29       Impact factor: 9.043

6.  Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers.

Authors:  Aurélien A Sérandour; Stéphane Avner; Frédérik Oger; Maud Bizot; Frédéric Percevault; Céline Lucchetti-Miganeh; Gaëlle Palierne; Céline Gheeraert; Frédérique Barloy-Hubler; Christine Le Péron; Thierry Madigou; Emmanuelle Durand; Philippe Froguel; Bart Staels; Philippe Lefebvre; Raphaël Métivier; Jérôme Eeckhoute; Gilles Salbert
Journal:  Nucleic Acids Res       Date:  2012-06-22       Impact factor: 16.971

7.  A high-resolution map of human evolutionary constraint using 29 mammals.

Authors:  Kerstin Lindblad-Toh; Manuel Garber; Or Zuk; Michael F Lin; Brian J Parker; Stefan Washietl; Pouya Kheradpour; Jason Ernst; Gregory Jordan; Evan Mauceli; Lucas D Ward; Craig B Lowe; Alisha K Holloway; Michele Clamp; Sante Gnerre; Jessica Alföldi; Kathryn Beal; Jean Chang; Hiram Clawson; James Cuff; Federica Di Palma; Stephen Fitzgerald; Paul Flicek; Mitchell Guttman; Melissa J Hubisz; David B Jaffe; Irwin Jungreis; W James Kent; Dennis Kostka; Marcia Lara; Andre L Martins; Tim Massingham; Ida Moltke; Brian J Raney; Matthew D Rasmussen; Jim Robinson; Alexander Stark; Albert J Vilella; Jiayu Wen; Xiaohui Xie; Michael C Zody; Jen Baldwin; Toby Bloom; Chee Whye Chin; Dave Heiman; Robert Nicol; Chad Nusbaum; Sarah Young; Jane Wilkinson; Kim C Worley; Christie L Kovar; Donna M Muzny; Richard A Gibbs; Andrew Cree; Huyen H Dihn; Gerald Fowler; Shalili Jhangiani; Vandita Joshi; Sandra Lee; Lora R Lewis; Lynne V Nazareth; Geoffrey Okwuonu; Jireh Santibanez; Wesley C Warren; Elaine R Mardis; George M Weinstock; Richard K Wilson; Kim Delehaunty; David Dooling; Catrina Fronik; Lucinda Fulton; Bob Fulton; Tina Graves; Patrick Minx; Erica Sodergren; Ewan Birney; Elliott H Margulies; Javier Herrero; Eric D Green; David Haussler; Adam Siepel; Nick Goldman; Katherine S Pollard; Jakob S Pedersen; Eric S Lander; Manolis Kellis
Journal:  Nature       Date:  2011-10-12       Impact factor: 49.962

8.  Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

Authors:  Aurélie Kapusta; Zev Kronenberg; Vincent J Lynch; Xiaoyu Zhuo; LeeAnn Ramsay; Guillaume Bourque; Mark Yandell; Cédric Feschotte
Journal:  PLoS Genet       Date:  2013-04-25       Impact factor: 5.917

9.  DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.

Authors:  Mingchao Xie; Chibo Hong; Bo Zhang; Rebecca F Lowdon; Xiaoyun Xing; Daofeng Li; Xin Zhou; Hyung Joo Lee; Cecile L Maire; Keith L Ligon; Philippe Gascard; Mahvash Sigaroudinia; Thea D Tlsty; Theresa Kadlecek; Arthur Weiss; Henriette O'Geen; Peggy J Farnham; Pamela A F Madden; Andrew J Mungall; Angela Tam; Baljit Kamoh; Stephanie Cho; Richard Moore; Martin Hirst; Marco A Marra; Joseph F Costello; Ting Wang
Journal:  Nat Genet       Date:  2013-05-26       Impact factor: 38.330

10.  DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes.

Authors:  Dvir Aran; Sivan Sabato; Asaf Hellman
Journal:  Genome Biol       Date:  2013-03-12       Impact factor: 13.583
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  8 in total

Review 1.  The role of transposable elements in health and diseases of the central nervous system.

Authors:  Matthew T Reilly; Geoffrey J Faulkner; Joshua Dubnau; Igor Ponomarev; Fred H Gage
Journal:  J Neurosci       Date:  2013-11-06       Impact factor: 6.167

Review 2.  The 'omics' of adrenocortical tumours for personalized medicine.

Authors:  Guillaume Assié; Anne Jouinot; Jérôme Bertherat
Journal:  Nat Rev Endocrinol       Date:  2014-02-04       Impact factor: 43.330

3.  Tc1-like transposable elements in plant genomes.

Authors:  Yuan Liu; Guojun Yang
Journal:  Mob DNA       Date:  2014-06-03

Review 4.  Human transgenerational responses to early-life experience: potential impact on development, health and biomedical research.

Authors:  Marcus Pembrey; Richard Saffery; Lars Olov Bygren
Journal:  J Med Genet       Date:  2014-07-25       Impact factor: 6.318

5.  Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children.

Authors:  Tobias Bauer; Saskia Trump; Naveed Ishaque; Loreen Thürmann; Lei Gu; Mario Bauer; Matthias Bieg; Zuguang Gu; Dieter Weichenhan; Jan-Philipp Mallm; Stefan Röder; Gunda Herberth; Eiko Takada; Oliver Mücke; Marcus Winter; Kristin M Junge; Konrad Grützmann; Ulrike Rolle-Kampczyk; Qi Wang; Christian Lawerenz; Michael Borte; Tobias Polte; Matthias Schlesner; Michaela Schanne; Stefan Wiemann; Christina Geörg; Hendrik G Stunnenberg; Christoph Plass; Karsten Rippe; Junichiro Mizuguchi; Carl Herrmann; Roland Eils; Irina Lehmann
Journal:  Mol Syst Biol       Date:  2016-03-24       Impact factor: 11.429

Review 6.  Transposable Elements in Human Cancer: Causes and Consequences of Deregulation.

Authors:  Sumadi Lukman Anwar; Wahyu Wulaningsih; Ulrich Lehmann
Journal:  Int J Mol Sci       Date:  2017-05-04       Impact factor: 5.923

Review 7.  HSV-1 and Endogenous Retroviruses as Risk Factors in Demyelination.

Authors:  Raquel Bello-Morales; Sabina Andreu; Inés Ripa; José Antonio López-Guerrero
Journal:  Int J Mol Sci       Date:  2021-05-27       Impact factor: 5.923

8.  Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes.

Authors:  Yongcheng Dong; Ziyan Huang; Qifan Kuang; Zhining Wen; Zhibin Liu; Yizhou Li; Yi Yang; Menglong Li
Journal:  BMC Genomics       Date:  2017-08-29       Impact factor: 3.969
  8 in total

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