A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals.

Genome Biology and Evolution
Niko PopitschMiguel Gallach

Abstract

In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

References

Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Aug 15, 2002·Trends in Genetics : TIG·Laurence D Hurst
Dec 31, 2005·Nucleic Acids Research·A S HinrichsW J Kent
Jan 19, 2006·Nature Reviews. Genetics·J V ChamaryLaurence D Hurst
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Dec 18, 2007·Molecular Biology and Evolution·Nadia D SinghAndrew G Clark
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 27, 2009·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Willemijn M GommansStefan Maas
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Nov 1, 2011·PloS One·Linnéa Smeds, Axel Künstner
Jan 10, 2012·Science·Sandra Garrett, Joshua J C Rosenthal
Sep 12, 2012·Genetics·Hiroshi AkashiTomoko Ohta
Oct 17, 2012·PLoS Genetics·Josep M ComeronSamuel Bailin
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Nov 3, 2012·BMC Research Notes·Ismael A VergaraNansheng Chen
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Nov 17, 2012·Nature Reviews. Genetics·Carrie F Olson-ManningThomas Mitchell-Olds
Jul 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·Liang Chen
Jul 5, 2013·Nature·Javier Prado-MartinezTomas Marques-Bonet
Aug 27, 2013·Bioinformatics·Fritz J SedlazeckArndt von Haeseler
Oct 1, 2013·Nature Structural & Molecular Biology·Georges St LaurentRobert A Reenan
Oct 29, 2013·Nucleic Acids Research·Gokul Ramaswami, Jin Billy Li
Nov 5, 2013·Cell Reports·Isabel X WangVivian G Cheung
Nov 12, 2013·Molecular Biology and Evolution·Matthew C RobinsonNadia D Singh
Feb 26, 2014·Proceedings of the National Academy of Sciences of the United States of America·Guixia Xu, Jianzhi Zhang
Nov 14, 2014·Molecular Biology and Evolution·Guixia Xu, Jianzhi Zhang
Oct 21, 2015·Proceedings of the National Academy of Sciences of the United States of America·Wen HuangTrudy F C Mackay
Mar 11, 2017·PLoS Genetics·Yuange DuanJian Lu

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Citations

May 23, 2021·Molecular Biology and Evolution·Yoav ShoshanEli Eisenberg

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Methods Mentioned

BETA
RNA-Seq
DNA-Seq

Software Mentioned

STAR aligner
SAMtools
ConDeTri
BDGP
ballet
editome
NextGenMap
liftover
rehh

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