qXL-MS raw data for "Capturing the Hierarchically Assorted Modules of Protein-protein Interaction in the Organized Nucleome"

Nuclear proteins are major constituents and key regulators of the topological organization of nucleome and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of nuclear protein interactions, the double chemical-crosslinking coupled with mass spectrometry (in vivo XL-MS) analysis was integrated with the dimethyl-labelling to generate a qXL-MS workflow, which consequently identified 5,340 cross-linked peptides (or crosslinks) from the nuclei of soybean seedlings. These crosslinks were converted into 1,297 nuclear protein-protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared to those in repositories. There were 250 and 26 novel interactors of histones and nucleolar box C/D snoRNP complex, respectively. Modulomic analysis of the Arabidopsis orthoglous PPIs constructed 27 and 24 master nuclear protein-protein interaction modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region (IDR)-containing proteins, respectively. These NPIMs successfully captured the previously reported nuclear protein complexes and nuclear bodies in nucleus. Surprisingly, these NPIMs are hierarchically assorted into 4 higher order communities in nucleomic graph, including Genome and Nucleolus Community. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene hormone-specific module variants participating in a broad range of nuclear events. It is capable of capturing both nuclear protein complexes and nuclear bodies, of constructing the topological architectures of both PPI modules and module variants in nucleome and of probably mapping the protein compositions of biomolecular condensates.