Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS.
Animals
Base Sequence
Computational Biology
/ methods
Datasets as Topic
Genome-Wide Association Study
/ methods
High-Throughput Nucleotide Sequencing
/ methods
Humans
Nucleic Acid Conformation
Nucleotides
/ chemistry
RNA
/ chemistry
RNA Folding
/ physiology
Saccharomyces cerevisiae
/ genetics
Sequence Analysis, RNA
/ methods
Software
Sulfuric Acid Esters
/ chemistry
Transcriptome
Genome-wide enzymatic probing
RNA folding
RNA secondary structure
RNA structurome
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
9
4
2021
pubmed:
10
4
2021
medline:
23
6
2021
Statut:
ppublish
Résumé
RNA molecules play important roles in almost every cellular process, and their functions are mediated by their sequence and structure. Determining the secondary structure of RNAs is central to understanding RNA function and evolution. RNA structure probing techniques coupled to high-throughput sequencing allow determining structural features of RNA molecules at transcriptome-wide scales. Our group recently developed a novel Illumina-based implementation of in vitro parallel probing of RNA structures called nextPARS.Here, we describe a protocol for the computation of the nextPARS scores and their use to obtain the structural profile (single- or double-stranded state) of an RNA sequence at single-nucleotide resolution.
Identifiants
pubmed: 33835437
doi: 10.1007/978-1-0716-1307-8_4
doi:
Substances chimiques
Nucleotides
0
Sulfuric Acid Esters
0
RNA
63231-63-0
dimethyl sulfate
JW5CW40Z50
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
51-62Commentaires et corrections
Type : ErratumIn
Références
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