Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing.
A-to-I RNA editing
ADAR
BioID
BirA
DZF-domain
ILF2
ILF3
STRBP
ZFR
Journal
Cell reports
ISSN: 2211-1247
Titre abrégé: Cell Rep
Pays: United States
ID NLM: 101573691
Informations de publication
Date de publication:
19 05 2020
19 05 2020
Historique:
received:
31
01
2020
revised:
11
04
2020
accepted:
23
04
2020
entrez:
21
5
2020
pubmed:
21
5
2020
medline:
22
5
2021
Statut:
ppublish
Résumé
Adenosine-to-inosine RNA editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes that deaminate adenosine to inosine. Although many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data, we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a broadly influential negative regulator of editing. This work demonstrates the broad roles that RNA binding proteins play in regulating editing levels, and establishes DZF-domain-containing proteins as a group of highly influential RNA editing regulators.
Identifiants
pubmed: 32433965
pii: S2211-1247(20)30609-4
doi: 10.1016/j.celrep.2020.107656
pmc: PMC7306178
mid: NIHMS1596751
pii:
doi:
Substances chimiques
RNA-Binding Proteins
0
ADAR protein, human
EC 3.5.4.37
ADARB1 protein, human
EC 3.5.4.4
Adenosine Deaminase
EC 3.5.4.4
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
107656Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM124215
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH115080
Pays : United States
Organisme : NCRR NIH HHS
ID : P41 RR011823
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM102484
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007790
Pays : United States
Informations de copyright
Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests The authors declare no competing interests.
Références
Nat Genet. 2012 Nov;44(11):1243-8
pubmed: 23001123
Nat Med. 2016 Oct;22(10):1140-1150
pubmed: 27595325
J Cell Sci. 2017 Feb 15;130(4):745-753
pubmed: 28082424
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
Nat Neurosci. 2019 Jan;22(1):25-36
pubmed: 30559470
Cell Mol Life Sci. 2015 Nov;72(22):4383-97
pubmed: 26047657
Nucleic Acids Res. 2018 Aug 21;46(14):7323-7338
pubmed: 29733375
Nucleic Acids Res. 2012 Oct;40(18):9356-68
pubmed: 22833610
Annu Rev Biochem. 2010;79:321-49
pubmed: 20192758
Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2318-2327
pubmed: 30659150
Nucleic Acids Res. 2014 Jan;42(Database issue):D109-13
pubmed: 24163250
Bioinformatics. 2016 Jan 15;32(2):289-91
pubmed: 26424858
Mol Cell. 2019 Mar 7;73(5):866-868
pubmed: 30849393
Mol Cell. 2016 Aug 18;63(4):696-710
pubmed: 27453046
Mol Cell Biol. 2008 Jul;28(14):4629-41
pubmed: 18458058
Genome Res. 2009 Jun;19(6):978-86
pubmed: 19420382
Nat Commun. 2018 Dec 21;9(1):5450
pubmed: 30575730
PLoS One. 2012;7(8):e42882
pubmed: 22900061
Nat Biotechnol. 2004 Aug;22(8):1001-5
pubmed: 15258596
Cell Rep. 2014 Nov 20;9(4):1482-94
pubmed: 25456137
PLoS Biol. 2004 Dec;2(12):e391
pubmed: 15534692
Nat Commun. 2018 May 31;9(1):2154
pubmed: 29855470
Mol Cell. 2017 Jul 20;67(2):214-227.e7
pubmed: 28625552
Immunity. 2015 Nov 17;43(5):933-44
pubmed: 26588779
Nat Rev Genet. 2018 Aug;19(8):473-490
pubmed: 29692414
Genome Res. 2004 Dec;14(12):2379-87
pubmed: 15545495
Nat Methods. 2014 Jan;11(1):51-4
pubmed: 24270603
Cell. 2013 Apr 25;153(3):575-89
pubmed: 23622242
Nature. 2019 Jan;565(7737):43-48
pubmed: 30559380
J Mol Biol. 2000 Dec 15;304(5):821-33
pubmed: 11124029
EMBO J. 2011 Aug 16;30(20):4211-22
pubmed: 21847096
Nucleic Acids Res. 2013 Feb 1;41(4):2581-93
pubmed: 23275536
Nucleic Acids Res. 2018 Aug 21;46(14):7379-7395
pubmed: 29992293
J Clin Invest. 2012 Aug;122(8):2793-806
pubmed: 22751105
Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):E2453-61
pubmed: 24927568
Nat Rev Mol Cell Biol. 2016 Feb;17(2):83-96
pubmed: 26648264
Nature. 2017 Apr 6;544(7648):115-119
pubmed: 28355180
Mol Cell Biol. 2005 Aug;25(16):6956-63
pubmed: 16055709
Nature. 2017 Oct 11;550(7675):249-254
pubmed: 29022589
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
RNA Biol. 2017 Nov 2;14(11):1485-1491
pubmed: 28640667
Mol Cell. 2016 Mar 17;61(6):903-13
pubmed: 26990993
Nature. 1997 May 15;387(6630):303-8
pubmed: 9153397
Gene. 1999 Mar 4;228(1-2):197-211
pubmed: 10072773
Nat Methods. 2013 Jul;10(7):623-9
pubmed: 23685885
Genome Med. 2013 Nov 29;5(11):105
pubmed: 24289319
Nature. 1999 May 6;399(6731):75-80
pubmed: 10331393
J Cell Biol. 2012 Mar 19;196(6):801-10
pubmed: 22412018
Genome Biol. 2017 Oct 30;18(1):205
pubmed: 29084589
Commun Biol. 2019 Jan 14;2:19
pubmed: 30652130
Cell Rep. 2020 May 19;31(7):107654
pubmed: 32433963
Sci Rep. 2016 Sep 26;6:34043
pubmed: 27665741
Science. 2015 Sep 4;349(6252):1115-20
pubmed: 26275108
Nat Med. 2019 Jan;25(1):95-102
pubmed: 30559422
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genome Res. 2016 Jun;26(6):852-62
pubmed: 27197207
Nucleic Acids Res. 2014 Jun;42(11):6876-84
pubmed: 24829451
Mol Biol Cell. 2014 Jan;25(1):169-83
pubmed: 24173718
EBioMedicine. 2017 Jul;21:65-78
pubmed: 28673861
RNA Biol. 2013 Feb;10(2):192-204
pubmed: 23353575