The phosphoproteomic landscape of the DNA damage response

The DNA damage response (DDR) comprises an intricate network of protein-protein interactions and signaling pathways activated by DNA lesions and genomic instability. Central to this response is protein phosphorylation, which orchestrates DNA repair, cell cycle checkpoint activation, and chromatin organization. The response of the human phosphoproteome to different DNA damage-inducing agents and the functional role of regulated phosphorylation sites remains insufficiently characterized. Here, we systematically profiled the cellular phosphoproteome following exposure to eleven DNA damage-inducing agents that humans encounter physiologically or during cancer therapy. We identified a core set of DNA damage responsive phosphorylation sites, along with DDR signatures associated with DNA double strand breaks, replication stress and a pleiotropic response. Regulated phosphorylation sites are enriched within intrinsically disordered regions (IDRs), often forming clusters of nearby modifications that can affect IDR conformations or overlap with short linear interaction motifs. We discover that the RNA damage response predominantly shapes the changes induced by reactive aldehyde formaldehyde, alkylating agent methyl methanesulfonate and oxidative stress. Finally, we demonstrate that the proteasome-associated ubiquitin E3 ligase UBE3A is targeted by ATM and ATR kinases, thus linking proteasome regulation with the DDR.