Literature DB >> 20176473

Genomic gems: SINE RNAs regulate mRNA production.

Steven L Ponicsan1, Jennifer F Kugel, James A Goodrich.   

Abstract

Mammalian short interspersed elements (SINEs) are abundant retrotransposons that have long been considered junk DNA; however, RNAs transcribed from mouse B2 and human Alu SINEs have recently been found to control mRNA production at multiple levels. Upon cell stress B2 and Alu RNAs bind RNA polymerase II (Pol II) and repress transcription of some protein-encoding genes. Bi-directional transcription of a B2 SINE establishes a boundary that places the growth hormone locus in a permissive chromatin state during mouse development. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity through exonization via alternative splicing. Given the diverse means by which SINE encoded RNAs impact production of mRNAs, this genomic junk is proving to contain hidden gems. 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID： 20176473      PMCID： PMC2859989          DOI： 10.1016/j.gde.2010.01.004

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


  63 in total

1.  Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo.

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Journal:  Gene       Date:  1999-11-01       Impact factor: 3.688

2.  Initial sequencing and analysis of the human genome.

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Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

Review 3.  Transcriptional coactivator complexes.

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Journal:  Annu Rev Biochem       Date:  2001       Impact factor: 23.643

4.  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

5.  Alu-containing exons are alternatively spliced.

Authors:  Rotem Sorek; Gil Ast; Dan Graur
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

6.  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

7.  Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.

Authors:  Jason M Johnson; John Castle; Philip Garrett-Engele; Zhengyan Kan; Patrick M Loerch; Christopher D Armour; Ralph Santos; Eric E Schadt; Roland Stoughton; Daniel D Shoemaker
Journal:  Science       Date:  2003-12-19       Impact factor: 47.728

8.  A slow RNA polymerase II affects alternative splicing in vivo.

Authors:  Manuel de la Mata; Claudio R Alonso; Sebastián Kadener; Juan P Fededa; Matías Blaustein; Federico Pelisch; Paula Cramer; David Bentley; Alberto R Kornblihtt
Journal:  Mol Cell       Date:  2003-08       Impact factor: 17.970

9.  Transposable B2 SINE elements can provide mobile RNA polymerase II promoters.

Authors:  O Ferrigno; T Virolle; Z Djabari; J P Ortonne; R J White; D Aberdam
Journal:  Nat Genet       Date:  2001-05       Impact factor: 38.330

10.  AluGene: a database of Alu elements incorporated within protein-coding genes.

Authors:  Tal Dagan; Rotem Sorek; Eilon Sharon; Gil Ast; Dan Graur
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971
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  63 in total

1.  Loss of Function of an RNA Polymerase III Subunit Leads to Impaired Maize Kernel Development.

Authors:  Hailiang Zhao; Yao Qin; Ziyi Xiao; Qi Li; Ning Yang; Zhenyuan Pan; Dianming Gong; Qin Sun; Fang Yang; Zuxin Zhang; Yongrui Wu; Cao Xu; Fazhan Qiu
Journal:  Plant Physiol       Date:  2020-06-26       Impact factor: 8.340

2.  Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins.

Authors:  Glen M Borchert; Nathaniel W Holton; Jonathan D Williams; William L Hernan; Ian P Bishop; Joel A Dembosky; James E Elste; Nathaniel S Gregoire; Jee-Ah Kim; Wesley W Koehler; Joe C Lengerich; Arianna A Medema; Marilyn A Nguyen; Geoffrey D Ower; Michelle A Rarick; Brooke N Strong; Nicholas J Tardi; Nathan M Tasker; Darren J Wozniak; Craig Gatto; Erik D Larson
Journal:  Mob Genet Elements       Date:  2011-05

3.  Transposable element insertions have strongly affected human evolution.

Authors:  Roy J Britten
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-01       Impact factor: 11.205

Review 4.  Something silent this way forms: the functional organization of the repressive nuclear compartment.

Authors:  Joan C Ritland Politz; David Scalzo; Mark Groudine
Journal:  Annu Rev Cell Dev Biol       Date:  2013-07-05       Impact factor: 13.827

Review 5.  Epigenetics components of aging in the central nervous system.

Authors:  Yue-Qiang Zhao; I King Jordan; Victoria V Lunyak
Journal:  Neurotherapeutics       Date:  2013-10       Impact factor: 7.620

6.  Five months of voluntary wheel running downregulates skeletal muscle LINE-1 gene expression in rats.

Authors:  Matthew A Romero; Petey W Mumford; Paul A Roberson; Shelby C Osburn; Hailey A Parry; Andreas N Kavazis; L Bruce Gladden; Tonia S Schwartz; Brent A Baker; Ryan G Toedebusch; Thomas E Childs; Frank W Booth; Michael D Roberts
Journal:  Am J Physiol Cell Physiol       Date:  2019-10-16       Impact factor: 4.249

Review 7.  Origin and evolution of SINEs in eukaryotic genomes.

Authors:  D A Kramerov; N S Vassetzky
Journal:  Heredity (Edinb)       Date:  2011-06-15       Impact factor: 3.821

Review 8.  Dark matters in AMD genetics: epigenetics and stochasticity.

Authors:  Leonard M Hjelmeland
Journal:  Invest Ophthalmol Vis Sci       Date:  2011-03-01       Impact factor: 4.799

9.  General transcription factors and subunits of RNA polymerase III: Paralogs for promoter- and cell type-specific transcription in multicellular eukaryotes.

Authors:  Martin Teichmann; Giorgio Dieci; Chiara Pascali; Galina Boldina
Journal:  Transcription       Date:  2010-07-30

10.  Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

Authors:  Claudia Carrieri; Laura Cimatti; Marta Biagioli; Anne Beugnet; Silvia Zucchelli; Stefania Fedele; Elisa Pesce; Isidre Ferrer; Licio Collavin; Claudio Santoro; Alistair R R Forrest; Piero Carninci; Stefano Biffo; Elia Stupka; Stefano Gustincich
Journal:  Nature       Date:  2012-10-14       Impact factor: 49.962
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