Journal
NUCLEIC ACIDS RESEARCH
Volume 49, Issue 11, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab156
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Funding
- National Key R&D Program of China [2016YFA0501403, 2018YFC0910302, 2017YFA0505002]
- National Key Laboratory of Proteomics [SKLP-K201706]
- National Natural Science Foundation of China [32088101, 21675172]
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RNA-protein interactions are crucial in biological regulation, and the development of the PP method for RNA tagging and RNP enrichment has enabled successful screening and analysis of RBPs.
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. [GRAPHICS] .
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