Light induced targeting enables proteomics on endogenous condensates

Endogenous condensates with transient constituents are notoriously difficult to study with common biological assays like mass-spectrometry and other proteomics profiling. Here we report a method for light-induced targeting of endogenous condensates (LiTEC) in living cells. LiTEC combines the identification of molecular zip codes that target the endogenous condensates with optogenetics to enable controlled and reversible partitioning of an arbitrary cargo, such as enzymes commonly used in proteomics, into the condensate in a blue light dependent manner. We demonstrate a proof of concept by combining LiTEC with proximity-based biotinylation (BioID) and uncover putative components of transcriptional condensates in mouse embryonic stem cells. Our approach opens the road to genome-wide functional studies of endogenous condensates. Overall design: To test the effect of LiTEC on transcription, global RNA-seq was performed with and without blue-light exposure (30 min, ~3.42 mW/cm^2) on wildtype mESCs and LiTEC mESCs. To check how transcription changes over time, RNAs were extracted on 0 hour, 1 hour and 4 hour after 30 min of blue light exposure (or without blue light exposure)