TREX reveals proteins that bind to specific RNA regions in living cells.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
received:
21
08
2023
accepted:
16
01
2024
medline:
13
3
2024
pubmed:
20
2
2024
entrez:
19
2
2024
Statut:
ppublish
Résumé
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
Identifiants
pubmed: 38374261
doi: 10.1038/s41592-024-02181-1
pii: 10.1038/s41592-024-02181-1
pmc: PMC10927567
doi:
Substances chimiques
RNA
63231-63-0
RNA-Binding Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
423-434Subventions
Organisme : Medical Research Council
ID : MR/P009417/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/W001500/1
Pays : United Kingdom
Organisme : Academy of Medical Sciences
ID : SBF006\1026
Pays : United Kingdom
Informations de copyright
© 2024. The Author(s).
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