β-Actin mRNA interactome mapping by proximity biotinylation.
FUBP3
RNA-BioID
RNA-binding protein
mRNA localization
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876
Informations de publication
Date de publication:
25 06 2019
25 06 2019
Historique:
pubmed:
14
6
2019
medline:
27
3
2020
entrez:
14
6
2019
Statut:
ppublish
Résumé
The molecular function and fate of mRNAs are controlled by RNA-binding proteins (RBPs). Identification of the interacting proteome of a specific mRNA in vivo remains very challenging, however. Based on the widely used technique of RNA tagging with MS2 aptamers for RNA visualization, we developed a RNA proximity biotinylation (RNA-BioID) technique by tethering biotin ligase (BirA*) via MS2 coat protein at the 3' UTR of endogenous MS2-tagged β-actin mRNA in mouse embryonic fibroblasts. We demonstrate the dynamics of the β-actin mRNA interactome by characterizing its changes on serum-induced localization of the mRNA. Apart from the previously known interactors, we identified more than 60 additional β-actin-associated RBPs by RNA-BioID. Among these, the KH domain-containing protein FUBP3/MARTA2 has been shown to be required for β-actin mRNA localization. We found that FUBP3 binds to the 3' UTR of β-actin mRNA and is essential for β-actin mRNA localization, but does not interact with the characterized β-actin zipcode element. RNA-BioID provides a tool for identifying new mRNA interactors and studying the dynamic view of the interacting proteome of endogenous mRNAs in space and time.
Identifiants
pubmed: 31189591
pii: 1820737116
doi: 10.1073/pnas.1820737116
pmc: PMC6600913
doi:
Substances chimiques
3' Untranslated Regions
0
Actins
0
RNA, Messenger
0
RNA-Binding Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
12863-12872Subventions
Organisme : NINDS NIH HHS
ID : R01 NS083085
Pays : United States
Déclaration de conflit d'intérêts
The authors declare no conflict of interest.
Références
J Neurosci. 1999 Oct 15;19(20):8818-29
pubmed: 10516301
Brain Res Mol Brain Res. 2000 Jun 23;79(1-2):192-201
pubmed: 10925159
Curr Biol. 2001 Jul 10;11(13):1010-6
pubmed: 11470405
J Cell Biol. 2002 Jan 7;156(1):41-51
pubmed: 11781334
Nat Rev Mol Cell Biol. 2002 Mar;3(3):195-205
pubmed: 11994740
Nucleic Acids Res. 2002 Dec 15;30(24):5452-64
pubmed: 12490714
EMBO J. 2004 Aug 18;23(16):3346-55
pubmed: 15282548
Biophys J. 2004 Dec;87(6):4153-62
pubmed: 15377515
Biol Cell. 2005 Jan;97(1):87-96
pubmed: 15601260
Nature. 2005 Nov 24;438(7067):512-5
pubmed: 16306994
Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1557-62
pubmed: 16432185
Mol Cell Biol. 2006 Sep;26(17):6584-97
pubmed: 16914741
Nat Neurosci. 2006 Oct;9(10):1265-73
pubmed: 16980965
Mol Cell Proteomics. 2007 May;6(5):798-811
pubmed: 17289661
Mol Cell Biol. 2007 Aug;27(15):5365-80
pubmed: 17548472
Mol Cell Biol. 2007 Dec;27(23):8340-51
pubmed: 17893325
RNA. 2009 Jan;15(1):104-15
pubmed: 19029303
Cell. 2009 Feb 20;136(4):719-30
pubmed: 19239891
Genes Dev. 2010 Jan 15;24(2):148-58
pubmed: 20080952
Cell. 2010 Apr 2;141(1):129-41
pubmed: 20371350
RNA. 2010 Nov;16(11):2277-90
pubmed: 20876833
Nat Methods. 2011 Feb;8(2):165-70
pubmed: 21240280
Curr Opin Cell Biol. 2012 Apr;24(2):202-10
pubmed: 22278045
J Cell Biol. 2012 Mar 19;196(6):801-10
pubmed: 22412018
PLoS One. 2012;7(4):e35034
pubmed: 22523568
Nucleic Acids Res. 2012 Aug;40(14):6873-86
pubmed: 22547390
Cell. 2012 Jun 8;149(6):1393-406
pubmed: 22658674
Cell Rep. 2012 Feb 23;1(2):179-84
pubmed: 22832165
Genes Dev. 2012 Sep 1;26(17):1885-90
pubmed: 22948660
J Neurochem. 2013 Mar;124(5):670-84
pubmed: 23121659
Biol Open. 2012 May 15;1(5):488-97
pubmed: 23213441
Science. 2013 Mar 15;339(6125):1328-1331
pubmed: 23371551
Nat Methods. 2013 Apr;10(4):277-8
pubmed: 23538861
Biol Chem. 2013 Aug;394(8):1077-90
pubmed: 23640942
J Biol Chem. 2013 Jul 12;288(28):20361-8
pubmed: 23720759
Dev Neurobiol. 2014 Mar;74(3):319-332
pubmed: 23897586
Science. 2014 Jan 24;343(6169):422-4
pubmed: 24458643
PLoS One. 2014 Mar 17;9(3):e92349
pubmed: 24637809
Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):E2453-61
pubmed: 24927568
Trends Neurosci. 2014 Sep;37(9):470-9
pubmed: 25012293
J Cell Sci. 2015 Mar 1;128(5):1001-10
pubmed: 25588836
J Cell Sci. 2015 May 15;128(10):1922-33
pubmed: 25908858
Methods Cell Biol. 2015;129:153-170
pubmed: 26175438
Proteomics. 2016 Oct;16(19):2503-2518
pubmed: 27329485
Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6877-E6886
pubmed: 27791158
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1875-E1884
pubmed: 28223507
Transcription. 2017 May 27;8(3):185-192
pubmed: 28301294
RNA. 2017 Aug;23(8):1290-1302
pubmed: 28476952
Nat Commun. 2017 Jun 06;8:15690
pubmed: 28585547
RNA. 2017 Oct;23(10):1582-1591
pubmed: 28698239
Mol Cell. 2018 Feb 1;69(3):354-369
pubmed: 29395060
Nat Methods. 2018 Mar;15(3):207-212
pubmed: 29400715
Curr Protoc Protein Sci. 2018 Feb 21;91:19.23.1-19.23.15
pubmed: 29516480
Mol Cell. 2018 Jun 7;70(5):854-867.e9
pubmed: 29883606
Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):E9697-E9706
pubmed: 30254174
Cell. 1986 May 9;45(3):407-15
pubmed: 3698103
J Cell Biol. 1994 Oct;127(2):441-51
pubmed: 7929587
EMBO J. 1993 Feb;12(2):595-600
pubmed: 8440248
J Cell Biol. 1997 Mar 24;136(6):1263-70
pubmed: 9087442
Mol Cell Biol. 1997 Apr;17(4):2158-65
pubmed: 9121465
J Neurosci. 1998 Jan 1;18(1):251-65
pubmed: 9412505
Science. 1998 Apr 24;280(5363):585-90
pubmed: 9554849