Complex regulation of ADAR-mediated RNA-editing across tissues

BMC Genomics
Melanie A HuntleyRobert Gentleman

Abstract

RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have catastrophic effects, particularly in the central nervous system. Thus, understanding how the process of RNA-editing is regulated has important implications for human health. However, at present, very little is known about the regulation of editing across tissues, and individuals. Here we present an analysis of RNA-editing patterns from 9 different tissues harvested from a single mouse. For comparison, we also analyzed data for 5 of these tissues harvested from 15 additional animals. We find that tissue specificity of editing largely reflects differential expression of substrate transcripts across tissues. We identified a surprising enrichment of editing in intronic regions of brain transcripts, that could account for previously reported higher levels of editing in brain. There exists a small but remarkable amount of editing which is tissue-specific, despite comparable expression levels of the edit site across multiple tissues. Expression levels of editing enzymes and their isoforms can explain some, but not all of this variation. Together, these data suggest a complex regulation of the...Continue Reading

References

Nov 28, 2000·Annual Review of Genetics·J M Gott, R B Emeson
Jun 5, 2002·Annual Review of Biochemistry·Brenda L Bass
Aug 7, 2002·The Journal of Biological Chemistry·Dominic C J JaikaranAndrew M MacMillan
Mar 6, 2003·The Journal of Biological Chemistry·Dan-Sung C ChoKazuko Nishikura
Jul 4, 2003·The EMBO Journal·Angela GalloMary A O'Connell
Jul 10, 2003·Current Opinion in Neurobiology·Peter H Seeburg, Jochen Hartner
Aug 9, 2003·Science·Barry HoopengardnerRobert Reenan
Aug 14, 2003·American Journal of Human Genetics·Yoshinori MiyamuraYasushi Tomita
Aug 13, 2005·Progress in Nucleic Acid Research and Molecular Biology·Louis Valente, Kazuko Nishikura
Apr 19, 2006·The Journal of Biological Chemistry·Kaari A ChilibeckAndrew M MacMillan
Aug 8, 2006·Progress in Nucleic Acid Research and Molecular Biology·Ann M TothCharles E Samuel
Nov 23, 2006·RNA Biology·Stefan MaasKazuko Nishikura
Mar 21, 2007·RNA·Johan OhlsonMarie Ohman
Oct 3, 2007·Genome Research·Nurit PazGideon Rechavi
Apr 12, 2008·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Nicholas P WhitneyJialin C Zheng
Jun 14, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Elizabeth Y RulaRonald B Emeson
May 28, 2009·IUBMB Life·Yongfeng JinQi Li
Jul 23, 2009·RNA·Sivan OsenbergEli Eisenberg
Feb 12, 2010·Bioinformatics·Thomas D Wu, Serban Nacu
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Dec 25, 2010·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·Cyril X GeorgeCharles E Samuel
Oct 21, 2011·Nature·David BrawandHenrik Kaessmann
Apr 25, 2012·Genome Biology·Petr DanecekDavid J Adams
Oct 18, 2012·Nucleic Acids Research·Anmol M KiranPavel V Baranov
Jan 1, 2013·Genome Biology·Yiannis A SavvaRobert A Reenan
Feb 19, 2013·Nature Neuroscience·Allissa A DillmanMark R Cookson
Oct 29, 2013·Nucleic Acids Research·Gokul Ramaswami, Jin Billy Li
Apr 12, 2014·PLoS Genetics·Jia-Yu ChenChuan-Yun Li
Sep 27, 2014·Genome Research·Ulrich BraunschweigBenjamin J Blencowe
Mar 3, 2015·Nature Methods·Qing Zhang, Xinshu Xiao
May 15, 2015·Nature·Christopher R SibleyJernej Ule

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Citations

Jan 18, 2017·Epigenetics & Chromatin·Sara El KennaniJérôme Govin
Jul 28, 2019·Biology of Reproduction·Pavla BrachovaLane K Christenson
Apr 21, 2020·Hypertension·Xiaoxue YangXinping Yang
Sep 25, 2019·Journal of Translational Medicine·Theodoulakis Christofi, Apostolos Zaravinos
Mar 15, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Tuangtong VongpipatanaYukio Kawahara
Jul 1, 2017·Molecular Biology of the Cell·Benjamin C StarkJohn A Cooper
Mar 27, 2019·Journal of Animal Science and Biotechnology·Yuebo ZhangLixian Wang
Mar 29, 2019·Journal of Animal Science and Biotechnology·Yuanyuan ZhangXuemei Deng
Aug 10, 2019·Communications Biology·Akira TanaveTsuyoshi Koide
Sep 19, 2020·Journal of Animal Science and Biotechnology·Rong ZhouKui Li
May 3, 2018·Frontiers in Neuroscience·Dessislava MladenovaJohn S Mattick
May 21, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Helen PiontkivskaMarta L Wayne
Jun 25, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yalan YangZhonglin Tang
Mar 14, 2020·Cellular and Molecular Life Sciences : CMLS·Manon RuffinLoic Guillot
Jan 20, 2019·Proceedings of the National Academy of Sciences of the United States of America·Anne L SapiroGalit Shohat-Ophir
Jan 8, 2021·Nucleic Acids Research·Qian YangYi Liu
Dec 20, 2020·Non-coding RNA·Holly R PinkneySarah D Diermeier
Jan 12, 2020·Communications Biology·Akira TanaveTsuyoshi Koide
Sep 28, 2021·Nucleic Acids Research·Dezhong LvYongsheng Li

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Datasets Mentioned

BETA
ERP000614

Methods Mentioned

BETA
deamination
RNA-seq

Software Mentioned

VariantTools
Bioconductor
GSNAP
HTSeqGenie

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