Discovery of Missing Methylation Sites on Endogenous Peptides of Human Cell Lines

Quantitative Analysis of the Protein Methylome Reveals PARP1 Methylation is involved in DNA Damage Response

Protein methylation plays important roles in DNA damage response. To date, proteome-wide profiling of protein methylation upon DNA damage has been not reported yet. In this study, using HILIC affinity enrichment combined with MS analysis, we conducted a quantitative analysis of the methylated proteins in HEK293T cells in response to IR treatment. In total, 235 distinct methylation sites responding to IR treatment were identified, and 38% of them were previously unknown. Multiple RNA-binding proteins were differentially methylated upon DNA damage stress. Furthermore, we identified 14 novel methylation sites in DNA damage response-related proteins. Moreover, we validated the function of PARP1 K23 methylation in repairing IR-induced DNA lesions. K23 methylation deficiency sensitizes cancer cells to radiation and HU-induced replication stress. In addition, PARP1 K23 methylation participates in the resolution of stalled replication forks by regulating PARP1 binding to damaged forks. Taken together, this study generates a data resource for global protein methylation in response to IR-induced DNA damage and reveals a critical role of PARP1 K23 methylation in DNA repair.