Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
29 Nov 2023
29 Nov 2023
Historique:
received:
20
03
2023
accepted:
08
11
2023
medline:
1
12
2023
pubmed:
30
11
2023
entrez:
29
11
2023
Statut:
epublish
Résumé
RNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription. Understanding how RNA folds into secondary and tertiary structures therefore requires methods for determining the structure of cotranscriptional folding intermediates. Cotranscriptional RNA chemical probing methods accomplish this by systematically probing the structure of nascent RNA that is displayed from an RNA polymerase. Here, we describe a concise, high-resolution cotranscriptional RNA chemical probing procedure called variable length Transcription Elongation Complex RNA structure probing (TECprobe-VL). We demonstrate the accuracy and resolution of TECprobe-VL by replicating and extending previous analyses of ZTP and fluoride riboswitch folding and mapping the folding pathway of a ppGpp-sensing riboswitch. In each system, we show that TECprobe-VL identifies coordinated cotranscriptional folding events that mediate transcription antitermination. Our findings establish TECprobe-VL as an accessible method for mapping cotranscriptional RNA folding pathways.
Identifiants
pubmed: 38030633
doi: 10.1038/s41467-023-43395-9
pii: 10.1038/s41467-023-43395-9
pmc: PMC10687018
doi:
Substances chimiques
RNA
63231-63-0
Riboswitch
0
DNA-Directed RNA Polymerases
EC 2.7.7.6
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7839Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM147137
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. The Author(s).
Références
Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):17995-8000
pubmed: 17986617
Nat Protoc. 2009;4(10):1413-21
pubmed: 19745823
Nat Commun. 2020 Sep 10;11(1):4531
pubmed: 32913225
Nat Rev Genet. 2018 Oct;19(10):615-634
pubmed: 30054568
Chem Biol. 2015 Jul 23;22(7):829-37
pubmed: 26144884
RNA. 2003 Jun;9(6):722-33
pubmed: 12756330
Elife. 2018 Jun 07;7:
pubmed: 29877798
Nat Commun. 2022 Jan 11;13(1):207
pubmed: 35017489
Nat Protoc. 2015 Nov;10(11):1643-69
pubmed: 26426499
Nat Chem Biol. 2018 Sep;14(9):887-894
pubmed: 30120360
BMC Bioinformatics. 2010 Mar 15;11:129
pubmed: 20230624
Trends Biochem Sci. 2016 Apr;41(4):293-310
pubmed: 26822487
Methods Mol Biol. 2022;2518:291-330
pubmed: 35666452
Mol Cell. 2015 Jan 22;57(2):317-28
pubmed: 25616067
Nat Protoc. 2016 Aug;11(8):1455-76
pubmed: 27442863
J Chem Phys. 2011 Dec 28;135(24):245101
pubmed: 22225186
J Chem Theory Comput. 2022 Mar 8;18(3):2002-2015
pubmed: 35133833
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Nat Protoc. 2006;1(3):1610-6
pubmed: 17406453
Science. 2012 Jan 13;335(6065):233-235
pubmed: 22194412
Nat Struct Mol Biol. 2016 Dec;23(12):1124-1131
pubmed: 27798597
Bio Protoc. 2021 Sep 05;11(17):e4141
pubmed: 34604447
Nat Methods. 2014 Sep;11(9):959-65
pubmed: 25028896
Mol Cell. 2020 Jan 16;77(2):241-250.e8
pubmed: 31706702
Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6515-20
pubmed: 10823910
J Biol Chem. 2021 Jul;297(1):100812
pubmed: 34023383
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
J Am Chem Soc. 2018 Aug 15;140(32):10067-10070
pubmed: 30063835
J Phys Chem B. 2018 Aug 2;122(30):7484-7496
pubmed: 29985608
Biochemistry. 2019 Feb 5;58(5):401-410
pubmed: 30081631
Curr Opin Struct Biol. 2008 Jun;18(3):321-9
pubmed: 18547802
RNA. 2018 Feb;24(2):143-148
pubmed: 29114018
Mol Cell. 2022 May 5;82(9):1708-1723.e10
pubmed: 35320755
Nucleic Acids Res. 2003 Nov 15;31(22):6473-80
pubmed: 14602905
J Biol Chem. 2020 May 8;295(19):6401-6412
pubmed: 32209658
Nat Chem Biol. 2019 Nov;15(11):1067-1076
pubmed: 31636437
J Am Chem Soc. 2008 Dec 3;130(48):16178-80
pubmed: 18998638
Mol Cell. 1998 Jun;1(7):1033-42
pubmed: 9651586
Proc Natl Acad Sci U S A. 2021 Nov 9;118(45):
pubmed: 34740970
Nat Chem Biol. 2017 Sep;13(9):968-974
pubmed: 28719589
Curr Opin Struct Biol. 2019 Dec;59:151-158
pubmed: 31521910
Genome Biol. 2018 Aug 14;19(1):113
pubmed: 30107842
Nucleic Acids Res. 1990 Dec 25;18(24):7465
pubmed: 2259646
Nat Protoc. 2007;2(10):2608-23
pubmed: 17948004
Mol Cell. 2017 Jan 19;65(2):220-230
pubmed: 27989440
Nucleic Acids Res. 2017 Jul 7;45(12):e109
pubmed: 28398514
Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6052-6057
pubmed: 29784782
Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):
pubmed: 34782462
Mol Cell. 2021 Feb 18;81(4):870-883.e10
pubmed: 33453165
Bioinformatics. 2019 Dec 15;35(24):5103-5112
pubmed: 31389563
Nature. 2012 May 13;486(7401):85-9
pubmed: 22678284
Nat Struct Mol Biol. 2015 Sep;22(9):679-85
pubmed: 26280533
Nat Methods. 2021 Mar;18(3):249-252
pubmed: 33619392
RNA. 2023 Nov;29(11):1658-1672
pubmed: 37419663
Proc Natl Acad Sci U S A. 1959 Apr;45(4):482-99
pubmed: 16590404
J Mol Biol. 2021 Jul 9;433(14):166975
pubmed: 33811916
Nucleic Acids Res. 2013 May;41(9):e102
pubmed: 23511969
Nat Commun. 2023 Nov 29;14(1):7839
pubmed: 38030633
Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82
pubmed: 6159633
Nature. 2020 Jun;582(7812):438-442
pubmed: 32555469
Annu Rev Biophys Biomol Struct. 2006;35:161-75
pubmed: 16689632
Structure. 2015 Aug 4;23(8):1375-1381
pubmed: 26118534
RNA. 2015 May;21(5):1042-52
pubmed: 25805860
Nat Biotechnol. 2021 Mar;39(3):347-356
pubmed: 33077962
Bioinformatics. 2012 Nov 15;28(22):3006-8
pubmed: 22976082
J Am Chem Soc. 2005 Mar 30;127(12):4223-31
pubmed: 15783204
Nucleic Acids Res. 2017 Sep 19;45(16):9716-9725
pubmed: 28934475
Nucleic Acids Res. 2023 Sep 8;51(16):8744-8757
pubmed: 37334863
PLoS Comput Biol. 2010 Jun 24;6(6):e1000823
pubmed: 20589081
Elife. 2018 Mar 05;7:
pubmed: 29504937
Nat Rev Genet. 2023 Mar;24(3):178-196
pubmed: 36348050
Nat Methods. 2017 Jan;14(1):75-82
pubmed: 27819661
Nat Struct Mol Biol. 2005 Dec;12(12):1130-6
pubmed: 16273104
Anal Biochem. 2013 Apr 15;435(2):181-6
pubmed: 23399535
RNA. 2013 Nov;19(11):1461-73
pubmed: 24131802
Biosci Biotechnol Biochem. 2010;74(9):1925-30
pubmed: 20834159
Nucleic Acids Res. 2021 Feb 26;49(4):e19
pubmed: 33095878
Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13858-63
pubmed: 25205807
Nucleic Acids Res. 2017 Aug 21;45(14):e135
pubmed: 28637286
Mol Cell Probes. 2005 Jun;19(3):203-5
pubmed: 15797821
Science. 2012 Oct 19;338(6105):397-400
pubmed: 23087247