Literature DB >> 21173775

Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing.

Bjorn-Erik Wulff1, Masayuki Sakurai, Kazuko Nishikura.   

Abstract

Catalysed by members of the adenosine deaminase acting on RNA (ADAR) family of enzymes, adenosine-to-inosine (A-to-I) editing converts adenosines in RNA molecules to inosines, which are functionally equivalent to guanosines. Recently, global approaches to studying this widely conserved phenomenon have emerged. The use of bioinformatics, high-throughput sequencing and other approaches has increased the number of known editing sites by several orders of magnitude, and we now have a greater understanding of the control and the biological significance of editing. This Progress article reviews some of these recent global studies and their results.

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Year:  2010        PMID: 21173775      PMCID: PMC3075016          DOI: 10.1038/nrg2915

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


  38 in total

1.  DARNED: a DAtabase of RNa EDiting in humans.

Authors:  Anmol Kiran; Pavel V Baranov
Journal:  Bioinformatics       Date:  2010-06-14       Impact factor: 6.937

2.  Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates.

Authors:  Nurit Paz-Yaacov; Erez Y Levanon; Eviatar Nevo; Yaron Kinar; Alon Harmelin; Jasmine Jacob-Hirsch; Ninette Amariglio; Eli Eisenberg; Gideon Rechavi
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-21       Impact factor: 11.205

Review 3.  Functions and regulation of RNA editing by ADAR deaminases.

Authors:  Kazuko Nishikura
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

4.  Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.

Authors:  H Rosaria Chiang; Lori W Schoenfeld; J Graham Ruby; Vincent C Auyeung; Noah Spies; Daehyun Baek; Wendy K Johnston; Carsten Russ; Shujun Luo; Joshua E Babiarz; Robert Blelloch; Gary P Schroth; Chad Nusbaum; David P Bartel
Journal:  Genes Dev       Date:  2010-04-22       Impact factor: 11.361

5.  A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.

Authors:  Alexander Wait Zaranek; Erez Y Levanon; Tomer Zecharia; Tom Clegg; George M Church
Journal:  PLoS Genet       Date:  2010-05-20       Impact factor: 5.917

6.  Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing.

Authors:  Sivan Osenberg; Nurit Paz Yaacov; Michal Safran; Sharon Moshkovitz; Ronit Shtrichman; Ofra Sherf; Jasmine Jacob-Hirsch; Gilmor Keshet; Ninette Amariglio; Joseph Itskovitz-Eldor; Gideon Rechavi
Journal:  PLoS One       Date:  2010-06-21       Impact factor: 3.240

7.  Small RNA expression and strain specificity in the rat.

Authors:  Sam E V Linsen; Elzo de Wit; Ewart de Bruijn; Edwin Cuppen
Journal:  BMC Genomics       Date:  2010-04-19       Impact factor: 3.969

8.  A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.

Authors:  Mats Ensterö; Orjan Akerborg; Daniel Lundin; Bei Wang; Terrence S Furey; Marie Ohman; Jens Lagergren
Journal:  BMC Bioinformatics       Date:  2010-01-04       Impact factor: 3.169

9.  Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA.

Authors:  Mats Ensterö; Chammiran Daniel; Helene Wahlstedt; François Major; Marie Ohman
Journal:  Nucleic Acids Res       Date:  2009-09-08       Impact factor: 16.971

10.  Adenosine deamination in human transcripts generates novel microRNA binding sites.

Authors:  Glen M Borchert; Brian L Gilmore; Ryan M Spengler; Yi Xing; William Lanier; Debashish Bhattacharya; Beverly L Davidson
Journal:  Hum Mol Genet       Date:  2009-09-23       Impact factor: 6.150

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  43 in total

1.  Fragile balance: RNA editing tunes the synapse.

Authors:  Gary J Bassell
Journal:  Nat Neurosci       Date:  2011-11-23       Impact factor: 24.884

2.  A closer look at RNA editing.

Authors:  Lior Pachter
Journal:  Nat Biotechnol       Date:  2012-03-07       Impact factor: 54.908

3.  Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.

Authors:  Jae Hoon Bahn; Jae-Hyung Lee; Gang Li; Christopher Greer; Guangdun Peng; Xinshu Xiao
Journal:  Genome Res       Date:  2011-09-29       Impact factor: 9.043

4.  Cooperative roles of fish protein kinase containing Z-DNA binding domains and double-stranded RNA-dependent protein kinase in interferon-mediated antiviral response.

Authors:  Ting-Kai Liu; Yi-Bing Zhang; Ying Liu; Fan Sun; Jian-Fang Gui
Journal:  J Virol       Date:  2011-09-21       Impact factor: 5.103

5.  Antagonistic and stimulative roles of ADAR1 in RNA silencing.

Authors:  Kazuko Nishikura; Masayuki Sakurai; Kantaro Ariyoshi; Hiromitsu Ota
Journal:  RNA Biol       Date:  2013-07-30       Impact factor: 4.652

6.  Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila.

Authors:  Georges St Laurent; Michael R Tackett; Sergey Nechkin; Dmitry Shtokalo; Denis Antonets; Yiannis A Savva; Rachel Maloney; Philipp Kapranov; Charles E Lawrence; Robert A Reenan
Journal:  Nat Struct Mol Biol       Date:  2013-09-29       Impact factor: 15.369

7.  microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs.

Authors:  Jodi E Eipper-Mains; Drew D Kiraly; Dasaradhi Palakodeti; Richard E Mains; Betty A Eipper; Brenton R Graveley
Journal:  RNA       Date:  2011-06-27       Impact factor: 4.942

8.  Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals.

Authors:  Young Seok Ju; Jong-Il Kim; Sheehyun Kim; Dongwan Hong; Hansoo Park; Jong-Yeon Shin; Seungbok Lee; Won-Chul Lee; Sujung Kim; Saet-Byeol Yu; Sung-Soo Park; Seung-Hyun Seo; Ji-Young Yun; Hyun-Jin Kim; Dong-Sung Lee; Maryam Yavartanoo; Hyunseok Peter Kang; Omer Gokcumen; Diddahally R Govindaraju; Jung Hee Jung; Hyonyong Chong; Kap-Seok Yang; Hyungtae Kim; Charles Lee; Jeong-Sun Seo
Journal:  Nat Genet       Date:  2011-07-03       Impact factor: 38.330

9.  New insights from existing sequence data: generating breakthroughs without a pipette.

Authors:  Alex M Plocik; Brenton R Graveley
Journal:  Mol Cell       Date:  2013-02-21       Impact factor: 17.970

10.  Micro-editing mistake translates into a devastating brain tumor.

Authors:  Dan Dominissini; Ninette Amariglio; Gideon Rechavi
Journal:  J Clin Invest       Date:  2012-10-24       Impact factor: 14.808

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