Quantifying RNA Editing in Deep Transcriptome Datasets.
Alu editing index
RNA editing
RNAseq
deep sequencing
transcriptome
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2020
2020
Historique:
received:
03
12
2019
accepted:
18
02
2020
entrez:
27
3
2020
pubmed:
27
3
2020
medline:
27
3
2020
Statut:
epublish
Résumé
Massive transcriptome sequencing through the RNAseq technology has enabled quantitative transcriptome-wide investigation of co-/post-transcriptional mechanisms such as alternative splicing and RNA editing. The latter is abundant in human transcriptomes in which million adenosines are deaminated into inosines by the ADAR enzymes. RNA editing modulates the innate immune response and its deregulation has been associated with different human diseases including autoimmune and inflammatory pathologies, neurodegenerative and psychiatric disorders, and tumors. Accurate profiling of RNA editing using deep transcriptome data is still a challenge, and the results depend strongly on processing and alignment steps taken. Accurate calling of the inosinome repertoire, however, is required to reliably quantify RNA editing and, in turn, investigate its biological and functional role across multiple samples. Using real RNAseq data, we demonstrate the impact of different bioinformatics steps on RNA editing detection and describe the main metrics to quantify its level of activity.
Identifiants
pubmed: 32211029
doi: 10.3389/fgene.2020.00194
pmc: PMC7069340
doi:
Types de publication
Journal Article
Langues
eng
Pagination
194Informations de copyright
Copyright © 2020 Lo Giudice, Silvestris, Roth, Eisenberg, Pesole, Gallo and Picardi.
Références
BMC Bioinformatics. 2017 Jan 3;18(1):7
pubmed: 28049429
Sci Rep. 2017 Mar 07;7:43421
pubmed: 28266523
FEBS Lett. 2012 Jul 30;586(16):2313-7
pubmed: 22750143
Sci Rep. 2015 Oct 09;5:14941
pubmed: 26449202
Nat Neurosci. 2019 Jan;22(1):25-36
pubmed: 30559470
Brief Bioinform. 2019 Mar 22;20(2):436-447
pubmed: 29040360
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14687-92
pubmed: 11717408
Cancer Res. 2014 Feb 1;74(3):840-51
pubmed: 24302582
Genome Res. 2007 Nov;17(11):1586-95
pubmed: 17908822
Oncotarget. 2016 Nov 1;7(44):71087-71098
pubmed: 27661005
Nucleic Acids Res. 2014 Jan;42(Database issue):D109-13
pubmed: 24163250
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nat Genet. 2008 Dec;40(12):1413-5
pubmed: 18978789
Biomed Res Int. 2015;2015:538019
pubmed: 25866791
Nat Rev Mol Cell Biol. 2014 May;15(5):313-26
pubmed: 24713629
RNA. 2016 Feb;22(2):290-302
pubmed: 26655226
Chromosoma. 2016 Mar;125(1):51-63
pubmed: 26148686
Nat Protoc. 2020 Mar;15(3):1098-1131
pubmed: 31996844
J Biol Chem. 2008 Mar 14;283(11):7251-60
pubmed: 18178553
Biol Rev Camb Philos Soc. 2012 Feb;87(1):95-110
pubmed: 21682836
Nat Med. 2016 Oct;22(10):1140-1150
pubmed: 27595325
Cancer Cell. 2015 Oct 12;28(4):515-528
pubmed: 26439496
Nat Biotechnol. 2004 Aug;22(8):1001-5
pubmed: 15258596
Cell Rep. 2014 Nov 20;9(4):1482-94
pubmed: 25456137
Nucleic Acids Res. 2013 Jan;41(Database issue):D258-61
pubmed: 23074185
Genome Biol. 2019 Feb 13;20(1):33
pubmed: 30760294
Sci Rep. 2016 Mar 16;6:23226
pubmed: 26980570
RNA. 2016 Feb;22(2):169-74
pubmed: 26787305
Genome Res. 2012 Sep;22(9):1775-89
pubmed: 22955988
Biochem Biophys Res Commun. 2003 Oct 17;310(2):612-8
pubmed: 14521955
Bioinformatics. 2012 Jan 1;28(1):112-8
pubmed: 22039212
Genome Biol. 2016 Jan 30;17:17
pubmed: 26832153
Cancer Cell. 2018 May 14;33(5):817-828.e7
pubmed: 29706454
RNA. 2018 Jun;24(6):828-840
pubmed: 29592874
Nat Methods. 2019 Nov;16(11):1131-1138
pubmed: 31636457
RNA. 2006 Oct;12(10):1802-9
pubmed: 16940548
Cancer Res Treat. 2017 Oct;49(4):1077-1087
pubmed: 28161934
Nucleic Acids Res. 2018 Jan 4;46(D1):D303-D307
pubmed: 29106616
Cell Rep. 2018 Apr 3;23(1):50-57
pubmed: 29617672
Nat Commun. 2014 Aug 27;5:4726
pubmed: 25158696
Nat Rev Genet. 2018 Aug;19(8):473-490
pubmed: 29692414
Int J Oncol. 2017 Feb;50(2):622-630
pubmed: 28035363
EMBO J. 2018 Oct 1;37(19):
pubmed: 30087110
Cancer Res. 2019 Jun 1;79(11):3001-3006
pubmed: 31015229
Neuron. 2012 May 10;74(3):432-9
pubmed: 22578495
Nat Rev Mol Cell Biol. 2016 Feb;17(2):83-96
pubmed: 26648264
RNA. 2008 Jun;14(6):1110-8
pubmed: 18430892
Nature. 2017 Oct 11;550(7675):249-254
pubmed: 29022589
Cell Rep. 2015 Oct 13;13(2):267-76
pubmed: 26440895
J Autoimmun. 2020 Jan;106:102329
pubmed: 31493964
Genome Res. 2014 Mar;24(3):365-76
pubmed: 24347612
Bioinformatics. 2013 Jul 15;29(14):1813-4
pubmed: 23742983
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Methods Mol Biol. 2015;1269:189-205
pubmed: 25577380
Nat Rev Genet. 2017 May;18(5):275-291
pubmed: 28216634
Nat Genet. 2013 Oct;45(10):1113-20
pubmed: 24071849
Science. 2015 May 8;348(6235):660-5
pubmed: 25954002
Nat Med. 2013 Feb;19(2):130-1
pubmed: 23389604
Annu Rev Genet. 2000;34:499-531
pubmed: 11092837
Nat Neurosci. 2019 Sep;22(9):1402-1412
pubmed: 31455887
Genome Biol. 2014 Jan 07;15(1):R5
pubmed: 24393560
Nat Med. 2013 Feb;19(2):209-16
pubmed: 23291631
Cell. 2017 Jun 15;169(7):1187-1200
pubmed: 28622506
Nucleic Acids Res. 2014 Jun;42(11):6876-84
pubmed: 24829451
Nucleic Acids Res. 2017 Jan 4;45(D1):D750-D757
pubmed: 27587585
Front Neuroanat. 2010 Mar 10;4:12
pubmed: 20300467