Issue 15, 2023

Transcriptome-wide identification of single-stranded RNA binding proteins

Abstract

RNA–protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA–protein interactions.

Graphical abstract: Transcriptome-wide identification of single-stranded RNA binding proteins

Supplementary files

Article information

Article type
Edge Article
Submitted
20 Feb 2023
Accepted
07 Mar 2023
First published
24 Mar 2023
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY-NC license

Chem. Sci., 2023,14, 4038-4047

Transcriptome-wide identification of single-stranded RNA binding proteins

R. Zhao, X. Fang, Z. Mai, X. Chen, J. Mo, Y. Lin, R. Xiao, X. Bao, X. Weng and X. Zhou, Chem. Sci., 2023, 14, 4038 DOI: 10.1039/D3SC00957B

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