Literature DB >> 20591835

Retrotransposition and genomic imprinting.

Michael Cowley1, Rebecca J Oakey.   

Abstract

Studies of large imprinted clusters, such as the Gnas locus, have revealed much about the significance of DNA methylation, transcription and other factors in the establishment and maintenance of imprinted gene expression. However, the complexity of such loci can make manipulating them and interpreting the results challenging. We review here a distinct class of imprinted genes, which have arisen by retrotransposition, and which have the potential to be used as models for the dissection of the fundamental features and mechanisms required for imprinting. They are also of interest in their own right, generating diversity in the transcriptome and providing raw material upon which selection can act.

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Year:  2010        PMID: 20591835      PMCID: PMC3814061          DOI: 10.1093/bfgp/elq015

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN: 2041-2649            Impact factor:   4.241


  36 in total

1.  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

2.  Human L1 element target-primed reverse transcription in vitro.

Authors:  Gregory J Cost; Qinghua Feng; Alain Jacquier; Jef D Boeke
Journal:  EMBO J       Date:  2002-11-01       Impact factor: 11.598

3.  Retrotransposed genes such as Frat3 in the mouse Chromosome 7C Prader-Willi syndrome region acquire the imprinted status of their insertion site.

Authors:  J H Chai; D P Locke; T Ohta; J M Greally; R D Nicholls
Journal:  Mamm Genome       Date:  2001-11       Impact factor: 2.957

4.  A novel active L1 retrotransposon subfamily in the mouse.

Authors:  J L Goodier; E M Ostertag; K Du; H H Kazazian
Journal:  Genome Res       Date:  2001-10       Impact factor: 9.043

5.  Imprinting of the G(s)alpha gene GNAS1 in the pathogenesis of acromegaly.

Authors:  B E Hayward; A Barlier; M Korbonits; A B Grossman; P Jacquet; A Enjalbert; D T Bonthron
Journal:  J Clin Invest       Date:  2001-03       Impact factor: 14.808

6.  Identification of a methylation imprint mark within the mouse Gnas locus.

Authors:  J Liu; S Yu; D Litman; W Chen; L S Weinstein
Journal:  Mol Cell Biol       Date:  2000-08       Impact factor: 4.272

7.  Regulation of alternative splicing by histone modifications.

Authors:  Reini F Luco; Qun Pan; Kaoru Tominaga; Benjamin J Blencowe; Olivia M Pereira-Smith; Tom Misteli
Journal:  Science       Date:  2010-02-04       Impact factor: 47.728

8.  Paternal imprinting of Galpha(s) in the human thyroid as the basis of TSH resistance in pseudohypoparathyroidism type 1a.

Authors:  Emily L Germain-Lee; Chang Lin Ding; Zhichao Deng; Janet L Crane; Motoyasu Saji; Matthew D Ringel; Michael A Levine
Journal:  Biochem Biophys Res Commun       Date:  2002-08-09       Impact factor: 3.575

9.  Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.

Authors:  Itoshi Nikaido; Chika Saito; Yosuke Mizuno; Makiko Meguro; Hidemasa Bono; Moritoshi Kadomura; Tomohiro Kono; Gerard A Morris; Paul A Lyons; Mitsuo Oshimura; Yoshihide Hayashizaki; Yasushi Okazaki
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

10.  The gsalpha gene: predominant maternal origin of transcription in human thyroid gland and gonads.

Authors:  Giovanna Mantovani; Emilia Ballare; Enza Giammona; Paolo Beck-Peccoz; Anna Spada
Journal:  J Clin Endocrinol Metab       Date:  2002-10       Impact factor: 5.958

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  16 in total

1.  Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment.

Authors:  Katrin Grothaus; Deniz Kanber; Alexandra Gellhaus; Barbara Mikat; Julia Kolarova; Reiner Siebert; Dagmar Wieczorek; Bernhard Horsthemke
Journal:  Epigenetics       Date:  2016-02-18       Impact factor: 4.528

2.  Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting.

Authors:  Michael Cowley; Anna de Burca; Ruth B McCole; Mandeep Chahal; Ghazal Saadat; Rebecca J Oakey; Reiner Schulz
Journal:  PLoS One       Date:  2011-04-20       Impact factor: 3.240

3.  Non-Coding RNAs at the Gnas and Snrpn-Ube3a Imprinted Gene Loci and Their Involvement in Hereditary Disorders.

Authors:  Antonius Plagge
Journal:  Front Genet       Date:  2012-11-26       Impact factor: 4.599

4.  Novel retrotransposed imprinted locus identified at human 6p25.

Authors:  Aiping Zhang; David A Skaar; Yue Li; Dale Huang; Thomas M Price; Susan K Murphy; Randy L Jirtle
Journal:  Nucleic Acids Res       Date:  2011-03-18       Impact factor: 16.971

5.  Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.

Authors:  Brian DeVeale; Derek van der Kooy; Tomas Babak
Journal:  PLoS Genet       Date:  2012-03-29       Impact factor: 5.917

Review 6.  Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family.

Authors:  Gernot Wolf; David Greenberg; Todd S Macfarlan
Journal:  Mob DNA       Date:  2015-10-02

7.  A Mouse Model for Imprinting of the Human Retinoblastoma Gene.

Authors:  Vasiliki Tasiou; Michaela Hiber; Laura Steenpass
Journal:  PLoS One       Date:  2015-08-14       Impact factor: 3.240

8.  Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites.

Authors:  Fiorella C Grandi; James M Rosser; Simon J Newkirk; Jun Yin; Xiaoling Jiang; Zhuo Xing; Leanne Whitmore; Sanum Bashir; Zoltán Ivics; Zsuzsanna Izsvák; Ping Ye; Y Eugene Yu; Wenfeng An
Journal:  Genome Res       Date:  2015-05-20       Impact factor: 9.043

9.  Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus.

Authors:  Michael Cowley; Andrew J Wood; Sabrina Böhm; Reiner Schulz; Rebecca J Oakey
Journal:  Nucleic Acids Res       Date:  2012-07-11       Impact factor: 16.971

Review 10.  Small regulatory RNAs controlled by genomic imprinting and their contribution to human disease.

Authors:  Michael Girardot; Jérôme Cavaillé; Robert Feil
Journal:  Epigenetics       Date:  2012-11-15       Impact factor: 4.528

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