A multi-scale map of protein assemblies in the DNA damage response

The DNA damage response (DDR) ensures error-free genome replication and transcription and is disrupted in numerous pathologies including cancer, inflammation and aging1–5. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into protein assemblies and complexes, some of which are constitutive, some which emerge de novo or are remodeled in DNA damaging conditions6. Here we integrate multi-conditional protein interaction networks with diverse multi-omics datasets to create a comprehensive map of DDR protein assemblies at multiple scales of analysis. This DNA damage response assembly map (DDRAM) encompasses 336 proteins, of which 57 (17%) are newly implicated in sensing or repair of DNA damage. We establish a requirement for three such factors in homologous recombination, the lipid chaperone FABP5, the actin-depolymerizing factor GSN, and the galectin LGALS7 as part of the BRCA2/PALB2 DNA repair complex. Another 204 (61%) proteins are known DDR factors assigned more specific functions. We find that single-strand DNA repair (SSR) factors segregate into a collection of 18 nested assemblies, which mirrors the function and dynamic aggregation of these factors at sites of DNA damage. One of these factors, CHTF18, localizes in a PARP-dependent manner with dynamics distinct from those in other SSR assemblies. The map is available at ccmi.org/ddram for interactive visualization, query and download.