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ChIRP-MS: RNA-Directed Proteomic Discovery

  • Ci Chu
  • Howard Y. Chang
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1861)

Abstract

Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-ms) is a novel technique for studying endogenous ribonucleoprotein complexes. ChIRP-ms is robust across a wide range of expression level, from abundant housekeeping RNAs (e.g., spliceosomal U RNAs) to relatively lowly expressed RNAs (e.g., Xist). In vivo RNA–protein interactions are chemically cross-linked, and purified using biotinylated antisense oligonucleotides against RNA of interest. Coprecipitated proteins are gently eluted, and identified by mass-spectrometry (for discovery) or by western blotting (for validation).

Key words

lncRNA RNA-binding proteins Mass-spec 

Notes

Acknowledgments

This work was supported by the Singapore Agency for Science, Technology, and Research (A*STAR to C.C.) and the US National Institutes of Health and Howard Hughes Medical Institute. (H.Y.C.).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Stanford University School of MedicineStanfordUSA

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