CUT&ID for simultaneous profiling of protein–DNA and protein–protein interactions

Abstract

We developed CUT&ID to simultaneously profile the native genomics and proteomics associations of any endogenous target, in a single workflow with no need for transgenesis. CUT&ID is enabled by a fusion protein of TurboID, protein A/G, and micrococcal nuclease, which drives sequential target recognition, proximal protein biotinylation, and DNA cleavage in living cells. CUT&ID is broadly applicable, works on fresh, frozen, or fixed nuclei, and provides high signal-to-noise genomics and proteomics identification across all types of gene regulators tested, including histone modifications, transcription factors, and non-DNA-binding proteins. CUT&ID’s streamlined protocol yields a dual readout from 1 million cells per sample, making it an attractive alternative to existing methodologies.