Probing RNA structure in vivo.

Models, Molecular Molecular Structure Nucleic Acid Conformation RNA / chemistry RNA Folding Sulfuric Acid Esters / chemistry

Journal

Current opinion in structural biology
ISSN: 1879-033X
Titre abrégé: Curr Opin Struct Biol
Pays: England
ID NLM: 9107784

Informations de publication

Date de publication:
12 2019
Historique:
received: 05 04 2019
revised: 26 07 2019
accepted: 30 07 2019
pubmed: 16 9 2019
medline: 4 8 2020
entrez: 16 9 2019
Statut: ppublish

Résumé

RNA structure underpins many essential functions in biology. New chemical reagents and techniques for probing RNA structure in living cells have emerged in recent years. High-throughput, genome-wide techniques such as Structure-seq2 and DMS-MaPseq exploit nucleobase modification by dimethylsulfate (DMS) to obtain complete structuromes, and are applicable to multiple domains of life and conditions. New reagents such as 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), glyoxal, and nicotinoyl azide (NAz) greatly expand the capabilities of nucleobase probing in cells. Additionally, ribose-targeting reagents in selective 2'-hydroxyl acylation and primer extension (SHAPE) detect RNA flexibility in vivo. These techniques, coupled with crosslinking nucleobases in psoralen analysis of RNA interactions and structures (PARIS), provide new and diverse ways to elucidate RNA secondary and tertiary structure in vivo and genome-wide.

Identifiants

DOI: 10.1016/j.sbi.2019.07.008 PMID: 31521910 PMC: PMC6888943
pubmed: 31521910
pii: S0959-440X(18)30217-3
doi: 10.1016/j.sbi.2019.07.008
pmc: PMC6888943
mid: NIHMS1536643
pii:
doi:

Substances chimiques

Sulfuric Acid Esters 0
RNA 63231-63-0
dimethyl sulfate JW5CW40Z50

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Review

Langues

eng

Sous-ensembles de citation

IM

Pagination

151-158

Subventions

Organisme : NIGMS NIH HHS
ID : R35 GM127064
Pays : United States

Informations de copyright

Copyright © 2019 Elsevier Ltd. All rights reserved.

Références

Mol Cell. 2012 Oct 26;48(2):169-81
pubmed: 22981864
RNA. 1995 Jun;1(4):351-62
pubmed: 7493314
Nucleic Acids Res. 1987 Nov 25;15(22):9109-28
pubmed: 2446263
Methods Enzymol. 1989;180:192-212
pubmed: 2482414
Bioinformatics. 2017 Jan 15;33(2):306-308
pubmed: 27663500
BMC Bioinformatics. 2010 Mar 15;11:129
pubmed: 20230624
Nat Chem Biol. 2018 Mar;14(3):276-283
pubmed: 29334380
RNA. 2019 Jan;25(1):147-157
pubmed: 30341176
Nucleic Acids Res. 2017 Jun 20;45(11):6805-6821
pubmed: 28383682
Nat Protoc. 2018 Jun;13(6):1181-1195
pubmed: 29725122
Trends Cell Biol. 2018 Dec;28(12):999-1013
pubmed: 29910081
J Mol Biol. 1989 Nov 20;210(2):265-80
pubmed: 2532257
RNA. 2017 Feb;23(2):169-174
pubmed: 27879433
Nucleic Acids Res. 2016 Nov 2;44(19):9426-9437
pubmed: 27369378
Nature. 2014 Jan 30;505(7485):696-700
pubmed: 24270811
J Am Chem Soc. 2015 Feb 11;137(5):2107-15
pubmed: 25611135
Methods. 2016 Jul 1;103:34-48
pubmed: 27064082
Nat Methods. 2014 Sep;11(9):959-65
pubmed: 25028896
Nature. 2015 Mar 26;519(7544):486-90
pubmed: 25799993
Cell. 2018 Mar 22;173(1):181-195.e18
pubmed: 29551268
Nature. 2014 Jan 30;505(7485):701-5
pubmed: 24336214
Biochemistry. 2017 Sep 5;56(35):4713-4721
pubmed: 28820243
Science. 1992 Jun 5;256(5062):1416-9
pubmed: 1604315
PLoS Genet. 2015 Dec 08;11(12):e1005668
pubmed: 26646615
Brief Funct Genomics. 2010 Mar;9(2):178-89
pubmed: 20352660
Cell Rep. 2015 Jul 28;12(4):554-61
pubmed: 26190100
Cell. 1986 May 9;45(3):407-15
pubmed: 3698103
Nature. 1981 Feb 26;289(5800):751-8
pubmed: 7007895
Biochemistry. 2014 May 20;53(19):3237-47
pubmed: 24818530
Genome Res. 2013 Feb;23(2):377-87
pubmed: 23064747
Q Rev Biophys. 2016 Jan;49:e10
pubmed: 27658939
RNA. 2018 Dec;24(12):1615-1624
pubmed: 30143552
Nat Struct Mol Biol. 2019 Apr;26(4):322-330
pubmed: 30886404
RNA. 2013 Jul;19(7):958-70
pubmed: 23697550
Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12170-12175
pubmed: 30413617
Nat Chem Biol. 2013 Jan;9(1):18-20
pubmed: 23178934
Mol Plant. 2018 Apr 2;11(4):607-622
pubmed: 29409859
Nucleic Acids Res. 1998 Jul 15;26(14):3449-50
pubmed: 9649634
RNA. 1995 Jun;1(4):363-74
pubmed: 7493315
Nucleic Acids Res. 2019 Jan 10;47(1):43-55
pubmed: 30476193
Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82
pubmed: 6159633
RNA. 2019 Jan;25(1):135-146
pubmed: 30389828
Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 6:Unit 6.1
pubmed: 18428862
RNA. 2018 Jan;24(1):114-124
pubmed: 29030489
J Am Chem Soc. 2005 Mar 30;127(12):4223-31
pubmed: 15783204
Biochim Biophys Acta. 2014 Oct;1839(10):908-918
pubmed: 24583553
Proc Natl Acad Sci U S A. 1972 Nov;69(11):3115-8
pubmed: 4564202
Cell. 2016 May 19;165(5):1267-1279
pubmed: 27180905
Nat Methods. 2017 Jan;14(1):75-82
pubmed: 27819661
Anal Biochem. 2013 Apr 15;435(2):181-6
pubmed: 23399535
Methods. 2018 Jul 1;143:12-15
pubmed: 29410279
Biochemistry. 2017 Jul 11;56(27):3422-3433
pubmed: 28657303
Biophys J. 2017 Jul 25;113(2):290-301
pubmed: 28625696
Nature. 2015 Feb 26;518(7540):560-4
pubmed: 25719671
Science. 2001 May 4;292(5518):883-96
pubmed: 11283358
Nucleic Acids Res. 2017 Aug 21;45(14):e135
pubmed: 28637286
PeerJ. 2018 Dec 18;6:e6136
pubmed: 30627482

Auteurs

David Mitchell (D)

Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address: dxm492@psu.edu.

Sarah M Assmann (SM)

Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address: sma3@psu.edu.

Philip C Bevilacqua (PC)

Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address: pcb5@psu.edu.

Articles similaires

Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases.

Arpine Sokratian, Ye Zhou, Meltem Tatli et al.
1.00
alpha-Synuclein Humans Animals Mice Lewy Body Disease

Biological functions and molecular mechanisms of exosome-derived circular RNAs and their clinical implications in digestive malignancies: the vintage in the bottle.

Yuanyan Lou, Jianing Yan, Qingqing Liu et al.
1.00
Humans RNA, Circular Exosomes Cell Proliferation Epithelial-Mesenchymal Transition

Mutational analysis of Phanerochaete chrysosporium´s purine transporter.

Mariana Barraco-Vega, Manuel Sanguinetti, Gabriela da Rosa et al.
1.00
Phanerochaete Fungal Proteins Purines Aspergillus nidulans DNA Mutational Analysis

iDNA-ITLM: An interpretable and transferable learning model for identifying DNA methylation.

Xia Yu, Cui Yani, Zhichao Wang et al.
1.00
DNA Methylation Humans DNA Animals Machine Learning

Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles moléculaires › Probing RNA structure in vivo.
questionsmedicales.fr › Phénomènes chimiques › Structure moléculaire › Probing RNA structure in vivo.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Probing RNA structure in vivo.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Probing RNA structure in vivo.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Pliage de l'ARN › Probing RNA structure in vivo.
questionsmedicales.fr › Composés chimiques organiques › Composés du soufre › Acides du soufre › Acides sulfuriques › Sulfates organiques › Probing RNA structure in vivo.