Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
18 11 2021
18 11 2021
Historique:
accepted:
20
09
2021
revised:
15
09
2021
received:
05
08
2021
pubmed:
12
10
2021
medline:
28
12
2021
entrez:
11
10
2021
Statut:
ppublish
Résumé
RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.
Identifiants
pubmed: 34634799
pii: 6389609
doi: 10.1093/nar/gkab885
pmc: PMC8599799
doi:
Substances chimiques
RNA-Binding Proteins
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
11868-11882Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM090056
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM128441
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009443
Pays : United States
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
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