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Literature DB >> 34354263

Transposable elements shape the evolution of mammalian development.

Abstract

Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.

Entities: Species

Year: 2021 PMID： 34354263 DOI： 10.1038/s41576-021-00385-1

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

257 in total

1. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

2. Initial sequencing and comparative analysis of the mouse genome.

Authors: Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal: Nature Date: 2002-12-05 Impact factor: 49.962

3. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.

Authors: Vincent J Lynch; Robert D Leclerc; Gemma May; Günter P Wagner
Journal: Nat Genet Date: 2011-09-25 Impact factor: 38.330

Review 4. Mobile DNA in Health and Disease.

Authors: Haig H Kazazian; John V Moran
Journal: N Engl J Med Date: 2017-07-27 Impact factor: 91.245

5. Regulatory evolution of innate immunity through co-option of endogenous retroviruses.

Authors: Edward B Chuong; Nels C Elde; Cédric Feschotte
Journal: Science Date: 2016-03-04 Impact factor: 47.728

Review 6. Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.

Authors: Hannah K Long; Sara L Prescott; Joanna Wysocka
Journal: Cell Date: 2016-11-17 Impact factor: 41.582

7. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy.

Authors: Vincent J Lynch; Mauris C Nnamani; Aurélie Kapusta; Kathryn Brayer; Silvia L Plaza; Erik C Mazur; Deena Emera; Shehzad Z Sheikh; Frank Grützner; Stefan Bauersachs; Alexander Graf; Steven L Young; Jason D Lieb; Francesco J DeMayo; Cédric Feschotte; Günter P Wagner
Journal: Cell Rep Date: 2015-01-29 Impact factor: 9.423

8. Transposable elements are the primary source of novelty in primate gene regulation.

Authors: Marco Trizzino; YoSon Park; Marcia Holsbach-Beltrame; Katherine Aracena; Katelyn Mika; Minal Caliskan; George H Perry; Vincent J Lynch; Christopher D Brown
Journal: Genome Res Date: 2017-08-30 Impact factor: 9.043

9. Endogenous retroviruses function as species-specific enhancer elements in the placenta.

Authors: Edward B Chuong; M A Karim Rumi; Michael J Soares; Julie C Baker
Journal: Nat Genet Date: 2013-02-10 Impact factor: 38.330

Review 10. Ten things you should know about transposable elements.

Authors: Guillaume Bourque; Kathleen H Burns; Mary Gehring; Vera Gorbunova; Andrei Seluanov; Molly Hammell; Michaël Imbeault; Zsuzsanna Izsvák; Henry L Levin; Todd S Macfarlan; Dixie L Mager; Cédric Feschotte
Journal: Genome Biol Date: 2018-11-19 Impact factor: 13.583

17 in total

Review 1. Mammalian genome innovation through transposon domestication.

Authors: Andrew J Modzelewski; Johnny Gan Chong; Ting Wang; Lin He
Journal: Nat Cell Biol Date: 2022-08-25 Impact factor: 28.213

2. Involvement of the HERV-derived cell-fusion inhibitor, suppressyn, in the fusion defects characteristic of the trisomy 21 placenta.

Authors: Jun Sugimoto; Danny J Schust; Tomomi Yamazaki; Yoshiki Kudo
Journal: Sci Rep Date: 2022-06-22 Impact factor: 4.996

3. Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression.

Authors: Tianzhe Zhang; Ran Zheng; Mao Li; Chenchao Yan; Xianchun Lan; Bei Tong; Pei Lu; Wei Jiang
Journal: Nucleic Acids Res Date: 2022-05-20 Impact factor: 19.160

Review 4. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans.

Authors: Yilan Wang; Boxun Zhao; Jaejoon Choi; Eunjung Alice Lee
Journal: Mob DNA Date: 2021-10-18

Review 5. Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants.

Authors: Benoît Chénais
Journal: Int J Mol Sci Date: 2022-02-25 Impact factor: 5.923