In Vivo Proximity Labeling for the Detection of Protein–Protein and Protein–RNA Interactions

Accurate
and sensitive detection of protein–protein and protein–RNA
interactions is key to understanding their biological functions. Traditional
methods to identify these interactions require cell lysis and biochemical
manipulations that exclude cellular compartments that cannot be solubilized
under mild conditions. Here, we introduce an in vivo proximity labeling
(IPL) technology that employs an affinity tag combined with a photoactivatable
probe to label polypeptides and RNAs in the vicinity of a protein
of interest in vivo. Using quantitative mass spectrometry and deep
sequencing, we show that IPL correctly identifies known protein–protein
and protein–RNA interactions in the nucleus of mammalian cells.
Thus, IPL provides additional temporal and spatial information for
the characterization of biological interactions in vivo.