Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

Nature Methods
Kristopher BrannanGene Yeo

Abstract

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.

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Citations

Aug 7, 2021·Molecular Cell·Mariavittoria PizzingaAnne E Willis
Jul 4, 2021·Molecular Cell·Jaclyn M EinsteinGene W Yeo
Aug 18, 2021·The International Journal of Biochemistry & Cell Biology·Eugenia LicariPaola Falletta
Sep 10, 2021·Nature·Michael VanInsbergheAlexander van Oudenaarden

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Software Mentioned

Cell Ranger
RBP
cutadapt
Cellranger
bamtobed
Integrative genome viewer ( IGV )
findMotifsGenome
STAMP
Samtools
metaPlotR

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