Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in
RNA structure
amino acid starvation
riboswitch
stress response
transcription attenuation
translation control
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
20
04
2020
accepted:
28
06
2020
pubmed:
3
7
2020
medline:
6
10
2020
entrez:
3
7
2020
Statut:
ppublish
Résumé
RNA structure influences numerous processes in all organisms. In bacteria, these processes include transcription termination and attenuation, small RNA and protein binding, translation initiation, and mRNA stability, and can be regulated via metabolite availability and other stresses. Here we use Structure-seq2 to probe the in vivo RNA structurome of
Identifiants
pubmed: 32611709
pii: rna.075986.120
doi: 10.1261/rna.075986.120
pmc: PMC7491331
doi:
Substances chimiques
Amino Acids
0
Bacterial Proteins
0
RNA, Bacterial
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
1431-1447Subventions
Organisme : NIGMS NIH HHS
ID : F32 GM128311
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM098399
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM127064
Pays : United States
Informations de copyright
© 2020 Ritchey et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Références
J Bacteriol. 2001 Oct;183(20):5795-802
pubmed: 11566976
J Bacteriol. 2002 May;184(9):2500-20
pubmed: 11948165
J Bacteriol. 2004 Jan;186(2):278-86
pubmed: 14702295
RNA. 2017 Jul;23(7):995-1011
pubmed: 28396576
Elife. 2017 Jan 31;6:
pubmed: 28139975
Nature. 2013 Aug 15;500(7462):363-6
pubmed: 23892783
Nat Struct Biol. 2003 Sep;10(9):701-7
pubmed: 12910260
Structure. 2013 Nov 5;21(11):2025-32
pubmed: 24095061
Methods. 2018 Jul 1;143:12-15
pubmed: 29410279
Int J Med Microbiol. 2014 Mar;304(2):150-5
pubmed: 24462007
Curr Genet. 2016 Feb;62(1):125-8
pubmed: 26458398
Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3083-8
pubmed: 12626738
FEBS Lett. 2010 Jan 21;584(2):318-24
pubmed: 19932103
Nucleic Acids Res. 2014 Jan;42(Database issue):D459-71
pubmed: 24225315
BMC Bioinformatics. 2010 Mar 15;11:129
pubmed: 20230624
Adv Microb Physiol. 2001;44:35-91
pubmed: 11407115
Curr Opin Microbiol. 2005 Apr;8(2):203-7
pubmed: 15802253
Biochim Biophys Acta. 2002 Sep 13;1577(2):240-50
pubmed: 12213655
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12057-62
pubmed: 14523230
Genome Biol. 2019 Dec 30;20(1):300
pubmed: 31888698
Methods Mol Biol. 2019;1933:305-341
pubmed: 30945195
Cell. 2009 Feb 20;136(4):615-28
pubmed: 19239884
Nucleic Acids Res. 2018 Jan 4;46(D1):D743-D748
pubmed: 29788229
Annu Rev Microbiol. 2016 Sep 8;70:361-74
pubmed: 27607554
Annu Rev Microbiol. 2014;68:45-60
pubmed: 24742053
Nat Microbiol. 2016 Jan 11;1:15007
pubmed: 27571753
Theory Biosci. 2012 Dec;131(4):281-5
pubmed: 22872506
J Bacteriol. 1995 Jul;177(13):3771-80
pubmed: 7601843
J Biol Chem. 2015 Sep 18;290(38):23336-47
pubmed: 26229106
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nature. 2014 Jan 30;505(7485):696-700
pubmed: 24270811
Curr Opin Microbiol. 2004 Apr;7(2):126-31
pubmed: 15063848
Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8227-32
pubmed: 24843172
Cell. 2018 Mar 22;173(1):181-195.e18
pubmed: 29551268
Biosci Biotechnol Biochem. 2009 Feb;73(2):245-59
pubmed: 19202299
Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7237-42
pubmed: 27298343
Genome Biol. 2015 Jan 13;16:1
pubmed: 25583448
Nature. 2014 Jan 30;505(7485):701-5
pubmed: 24336214
J Biol Chem. 2008 Jul 18;283(29):20117-25
pubmed: 18390551
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
pubmed: 12824337
Plant Cell. 2012 Nov;24(11):4346-59
pubmed: 23150631
J Bacteriol. 1993 Dec;175(23):7581-93
pubmed: 8244927
Nucleic Acids Res. 2010 Oct;38(19):6637-51
pubmed: 20525796
Nucleic Acids Res. 2017 Oct 13;45(18):10811-10823
pubmed: 28977401
J Mol Biol. 2010 Dec 17;404(5):803-18
pubmed: 20951706
Annu Rev Genet. 2005;39:47-68
pubmed: 16285852
BMC Microbiol. 2019 Mar 22;19(1):66
pubmed: 30902049
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
PLoS One. 2015 Apr 02;10(3):e0121945
pubmed: 25835001
Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12170-12175
pubmed: 30413617
RNA Biol. 2011 Jan-Feb;8(1):82-9
pubmed: 21282981
J Biol Chem. 1998 Aug 7;273(32):20494-503
pubmed: 9685405
Environ Microbiol. 2013 Feb;15(2):313-24
pubmed: 22672726
J Bacteriol. 1995 Nov;177(22):6362-70
pubmed: 7592410
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Mol Microbiol. 1998 Nov;30(4):737-49
pubmed: 10094622
Genes Dev. 2003 Nov 1;17(21):2688-97
pubmed: 14597663
PLoS Genet. 2015 Oct 23;11(10):e1005613
pubmed: 26495981
Mol Gen Genet. 2001 Feb;264(6):913-23
pubmed: 11254139
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
Science. 2004 Oct 8;306(5694):275-9
pubmed: 15472076
RNA. 2020 Apr;26(4):492-511
pubmed: 31937672
Nucleic Acids Res. 2017 Aug 21;45(14):e135
pubmed: 28637286
Peptides. 2001 Oct;22(10):1555-77
pubmed: 11587785
Annu Rev Microbiol. 2009;63:27-44
pubmed: 19385727
Nat Commun. 2018 Mar 29;9(1):1289
pubmed: 29599443
Science. 2016 Apr 8;352(6282):aad9822
pubmed: 27120414