An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition. Issue 11 (10th March 2021)

• Record Type: Journal Article
• Authors: Zhang, Zheng; Liu, Tong; Dong, Hangyan; Li, Jian; Sun, Haofan; Qian, Xiaohong; Qin, Weijie
• Is Part Of: Nucleic acids research. Volume 49:Issue 11(2021)
• Page Start: e65
• Page End: e65
• Publication Date: 2021-03-10
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab156
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: RNA-protein interactions play key roles in epigenetic, transcriptional and posttranscriptional regulation. To reveal the regulatory mechanisms of these interactions, global investigation of RNA-binding proteins (RBPs) and monitor their changes under various physiological conditions are needed. Herein, we developed a psoralen probe (PP)-based method for RNA tagging and ribonucleic-protein complex (RNP) enrichment. Isolation of both coding and noncoding RNAs and mapping of 2986 RBPs including 782 unknown candidate RBPs from HeLa cells was achieved by PP enrichment, RNA-sequencing and mass spectrometry analysis. The dynamics study of RNPs by PP enrichment after the inhibition of RNA synthesis provides the first large-scale distribution profile of RBPs bound to RNAs with different decay rates. Furthermore, the remarkably greater decreases in the abundance of the RBPs obtained by PP-enrichment than by global proteome profiling suggest that PP enrichment after transcription inhibition offers a valuable way for large-scale evaluation of the candidate RBPs. Graphical Abstract: