SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells.

ABSTRACT: RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs,

SUBMITTER: Aydin J 

PROVIDER: S-EPMC10954451 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature