In vivo crosslinking and effective 2D enrichment for interactome studies of the nucleosome

Cross-linking mass spectrometry has evolved as a powerful technique to study protein-protein interactions and to provide structural information over the past decades. Low reaction efficiencies, and complex matrices lead to challenging system wide crosslink analysis. In this study, we improved and streamlined an Azide-A-DSBSO based in vivo crosslinking workflow employing two orthogonal effective enrichment steps: Affinity enrichment and size exclusion chromatography (SEC). Combined, they allow an effective pulling of DSBSO containing peptides and remove the background of linear as well as mono-linked peptides. We found that the analysis of a single SEC fraction is effective to yield ∼90% of all crosslinks, which is important whenever measurement time is limited, and sample throughput is crucial. Our workflow resulted in more than 5000 crosslinks from K562 cells and generated a comprehensive PPI network from whole cells as well as nuclear extracts. From 393 PPI found within the nucleus, 56 have not yet been reported in the STING database and are representing a valuable resource for investigating new molecular mechanisms and provide complementary data for future studies. We further show, that by applying DSBSO to nuclear extracts we yield more crosslinks on lower abundant proteins and showcase this on the DEAD-box RNA helicase DDX39B which is predominantly expressed in the nucleus. Our data indicates that DDX39B is present in monomeric and dimeric form together with DDX39A within the nuclear extracts analyzed.