Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
05 2021
05 2021
Historique:
received:
02
10
2020
accepted:
26
03
2021
entrez:
8
5
2021
pubmed:
9
5
2021
medline:
28
7
2021
Statut:
ppublish
Résumé
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP-RNA interactions. STAMP does not rely on ultraviolet cross-linking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP-specific and cell-type-specific RNA-protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.
Identifiants
pubmed: 33963355
doi: 10.1038/s41592-021-01128-0
pii: 10.1038/s41592-021-01128-0
pmc: PMC8148648
mid: NIHMS1688158
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
507-519Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM008806
Pays : United States
Organisme : NIGMS NIH HHS
ID : K12 GM068524
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG009889
Pays : United States
Organisme : NINDS NIH HHS
ID : F31 NS111859
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG004659
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008666
Pays : United States
Organisme : NINDS NIH HHS
ID : K22 NS112678
Pays : United States
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