RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting

Significance The biogenesis, processing, function, and degradation of cellular RNAs depend critically on their protein interaction partners. Systematic analysis of the protein interactome of specific RNAs of interest inside living cells can therefore enable a better understanding of many biological processes. We developed two complementary methods for tagging endogenous proteins in the vicinity of specific cellular RNAs, for subsequent identification by mass spectrometry. When applied to the human telomerase RNA, our methods recovered known interaction partners as well as unexpected hits, including an enzyme that catalyzes RNA posttranscriptional modification to influence telomerase activity. The technology introduced by our study should facilitate future investigations into RNA–protein interactions in living cells.