Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.

ABSTRACT: Methods for the systematic study of subcellular RNA localization are limited, and their development has lagged behind that of proteomic tools. We combined APEX2-mediated proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced crosslinking to simultaneously profile the proteome and the transcriptome bound by RNA-binding proteins in any given subcellular compartment. Our approach is fractionation independent and allows study of the localization of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied by proteins, in a cellular-compartment-specific manner. We used our method, Proximity-CLIP, to profile RNA and protein in the nucleus, in the cytoplasm, and at cell-cell interfaces. Among other insights, we observed f

SUBMITTER: Benhalevy D 

PROVIDER: S-EPMC6289640 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature