Literature DB >> 26855260

How retrotransposons shape genome regulation.

Paolo Mita1, Jef D Boeke2.   

Abstract

Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 26855260      PMCID: PMC4914423          DOI: 10.1016/j.gde.2016.01.001

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  111 in total

1.  Frequent human genomic DNA transduction driven by LINE-1 retrotransposition.

Authors:  O K Pickeral; W Makałowski; M S Boguski; J D Boeke
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

2.  Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.

Authors:  Jichang Wang; Gangcai Xie; Manvendra Singh; Avazeh T Ghanbarian; Tamás Raskó; Attila Szvetnik; Huiqiang Cai; Daniel Besser; Alessandro Prigione; Nina V Fuchs; Gerald G Schumann; Wei Chen; Matthew C Lorincz; Zoltán Ivics; Laurence D Hurst; Zsuzsanna Izsvák
Journal:  Nature       Date:  2014-10-15       Impact factor: 49.962

3.  So much "junk" DNA in our genome.

Authors:  S Ohno
Journal:  Brookhaven Symp Biol       Date:  1972

4.  Gene regulation for higher cells: a theory.

Authors:  R J Britten; E H Davidson
Journal:  Science       Date:  1969-07-25       Impact factor: 47.728

Review 5.  Human transposon tectonics.

Authors:  Kathleen H Burns; Jef D Boeke
Journal:  Cell       Date:  2012-05-11       Impact factor: 41.582

6.  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

7.  The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster.

Authors:  Yuh Chwen G Lee
Journal:  PLoS Genet       Date:  2015-06-04       Impact factor: 5.917

8.  Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription.

Authors:  Ahsan Huda; Pierre R Bushel
Journal:  Transcr Open Access       Date:  2013-06-19

9.  An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Authors:  Frank M J Jacobs; David Greenberg; Ngan Nguyen; Maximilian Haeussler; Adam D Ewing; Sol Katzman; Benedict Paten; Sofie R Salama; David Haussler
Journal:  Nature       Date:  2014-09-28       Impact factor: 49.962

10.  Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma.

Authors:  Nemanja Rodić; Jared P Steranka; Alvin Makohon-Moore; Allison Moyer; Peilin Shen; Reema Sharma; Zachary A Kohutek; Cheng Ran Huang; Daniel Ahn; Paolo Mita; Martin S Taylor; Norman J Barker; Ralph H Hruban; Christine A Iacobuzio-Donahue; Jef D Boeke; Kathleen H Burns
Journal:  Nat Med       Date:  2015-08-10       Impact factor: 53.440

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  62 in total

1.  Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare).

Authors:  Emilie Debladis; Tzuu-Fen Lee; Yan-Jiun Huang; Jui-Hsien Lu; Sandra M Mathioni; Marie-Christine Carpentier; Christel Llauro; Davy Pierron; Delphine Mieulet; Emmanuel Guiderdoni; Pao-Yang Chen; Blake C Meyers; Olivier Panaud; Eric Lasserre
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-02-10       Impact factor: 6.237

Review 2.  Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication.

Authors:  Danni Jin; Karin Musier-Forsyth
Journal:  J Biol Chem       Date:  2019-01-30       Impact factor: 5.157

3.  Multiple Transcriptional and Post-transcriptional Pathways Collaborate to Control Sense and Antisense RNAs of Tf2 Retroelements in Fission Yeast.

Authors:  Pierre-Luc Mallet; Marc Larochelle; François Bachand
Journal:  Genetics       Date:  2016-12-22       Impact factor: 4.562

Review 4.  tRNAs as primers and inhibitors of retrotransposons.

Authors:  German Martinez
Journal:  Mob Genet Elements       Date:  2017-11-01

5.  Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster.

Authors:  Vincenzo Guida; Filippo M Cernilogar; Angela Filograna; Roberto De Gregorio; Hirotsugu Ishizu; Mikiko C Siomi; Gunnar Schotta; Gian Carlo Bellenchi; Davide Andrenacci
Journal:  Genetics       Date:  2016-08-24       Impact factor: 4.562

Review 6.  Endogenous Retroelements and the Host Innate Immune Sensors.

Authors:  X Mu; S Ahmad; S Hur
Journal:  Adv Immunol       Date:  2016-08-23       Impact factor: 3.543

7.  Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies.

Authors:  Raphaelle Laureau; Annie Dyatel; Gizem Dursuk; Samantha Brown; Hannah Adeoye; Jia-Xing Yue; Matteo De Chiara; Anthony Harris; Elçin Ünal; Gianni Liti; Ian R Adams; Luke E Berchowitz
Journal:  Dev Cell       Date:  2020-12-04       Impact factor: 12.270

8.  Long Terminal Repeat Retrotransposon Afut4 Promotes Azole Resistance of Aspergillus fumigatus by Enhancing the Expression of sac1 Gene.

Authors:  Mandong Hu; Zongwei Li; Dingchen Li; Jingya Zhao; Yong Chen; Zelei Wang; Fangyan Chen; Li Han
Journal:  Antimicrob Agents Chemother       Date:  2021-09-13       Impact factor: 5.191

Review 9.  The role of retrotransposable elements in ageing and age-associated diseases.

Authors:  Vera Gorbunova; Andrei Seluanov; Paolo Mita; Wilson McKerrow; David Fenyö; Jef D Boeke; Sara B Linker; Fred H Gage; Jill A Kreiling; Anna P Petrashen; Trenton A Woodham; Jackson R Taylor; Stephen L Helfand; John M Sedivy
Journal:  Nature       Date:  2021-08-04       Impact factor: 49.962

Review 10.  Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution.

Authors:  William B Miller; Francisco J Enguita; Ana Lúcia Leitão
Journal:  Cells       Date:  2021-05-07       Impact factor: 6.600

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