Viral RNA structure analysis using DMS-MaPseq.

Genome, Viral High-Throughput Nucleotide Sequencing / methods Mutagens / chemistry Mutation / drug effects Nucleic Acid Conformation / drug effects RNA Viruses / genetics RNA, Viral / chemistry Reverse Transcriptase Polymerase Chain Reaction / methods Sequence Analysis, RNA / methods Sulfuric Acid Esters / chemistry
Chemical probing DMS-MaPseq Dimethyl sulfate Next-generation sequencing RNA structure

Journal

Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302

Informations de publication

Date de publication:
01 11 2020
Historique:
received: 13 08 2019
revised: 31 03 2020
accepted: 01 04 2020
pubmed: 7 4 2020
medline: 14 9 2021
entrez: 7 4 2020
Statut: ppublish

Résumé

RNA structure is critically important to RNA viruses in every part of the replication cycle. RNA structure is also utilized by DNA viruses in order to regulate gene expression and interact with host factors. Advances in next-generation sequencing have greatly enhanced the utility of chemical probing in order to analyze RNA structure. This review will cover some recent viral RNA structural studies using chemical probing and next-generation sequencing as well as the advantages of dimethyl sulfate (DMS)-mutational profiling and sequencing (MaPseq). DMS-MaPseq is a robust assay that can easily modify RNA in vitro, in cell and in virion. A detailed protocol for whole-genome DMS-MaPseq from cells transfected with HIV-1 and the structure of TAR as determined by DMS-MaPseq is presented. DMS-MaPseq has the ability to answer a variety of integral questions about viral RNA, including how they change in different environments and when interacting with different host factors.

Identifiants

DOI: 10.1016/j.ymeth.2020.04.001 PMID: 32251733 PMC: PMC7541462
pubmed: 32251733
pii: S1046-2023(19)30227-0
doi: 10.1016/j.ymeth.2020.04.001
pmc: PMC7541462
mid: NIHMS1585690
pii:
doi:

Substances chimiques

Mutagens 0
RNA, Viral 0
Sulfuric Acid Esters 0
dimethyl sulfate JW5CW40Z50

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

68-75

Subventions

Organisme : NIAID NIH HHS
ID : R21 AI134365
Pays : United States

Informations de copyright

Published by Elsevier Inc.

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Auteurs

Phillip Tomezsko (P)

Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Program in Virology, Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA.

Harish Swaminathan (H)

Whitehead Institute for Biomedical Research, Cambridge, MA, USA.

Silvi Rouskin (S)

Whitehead Institute for Biomedical Research, Cambridge, MA, USA. Electronic address: srouskin@wi.mit.edu.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome viral › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Actions chimiques et utilisations › Actions toxiques › Noxas › Mutagènes › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Virus › Virus à ARN › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN viral › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Techniques d'amplification d'acides nucléiques › Réaction de polymérisation en chaîne › RT-PCR › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Viral RNA structure analysis using DMS-MaPseq.
questionsmedicales.fr › Composés chimiques organiques › Composés du soufre › Acides du soufre › Acides sulfuriques › Sulfates organiques › Viral RNA structure analysis using DMS-MaPseq.