Abstract

DNA-protein crosslinks (DPCs) are among the most ubiquitous and detrimental DNA lesions which arise from exposure to metabolic stresses, drugs, or crosslinking agents such as formaldehyde (FA). FA is a cellular by-product of methanol metabolism, histone demethylation, lipid peroxidation as well as environmental pollutants. Failure to repair FA-induced DPCs blocks nearly all chromatin-based processes including replication and transcription, leading to immunodeficiencies, neurodegeneration, and cancer. Yet, it remains largely unknown how the cell repairs DPCs. The study of DPC repair is impeded by our incomprehension of the types of proteins crosslinked by FA due to the lack of techniques to identify the DPCs. Here, we designed a novel bioassay to profile FA-induced DPCs by coupling cesium chloride differential ultracentrifugation with HPLC-mass spectrometry (MS). Using the method, we revealed the proteome of FA-induced DPCs in human cells and found that the most abundant proteins that form DPCs are PARP1, topoisomerases I and II, methyltransferases, DNA and RNA polymerases, histones, as well as ribosomal proteins. To identify enzymes that repair DPCs, we carried out RNA interference screening and found that downregulation of flap endonuclease 1 (FEN1) rendered cells hypersensitive to FA. Since FEN1 possesses 5-flap endonuclease activity, we hypothesized that FA induces DPC-conjugated 5-flap DNA fragments that can be processed by FEN1. Indeed, we demonstrate that FA damages DNA bases that are converted into 5-flap via the base excision pathway (BER). We also observed that the damaged DNA bases were colocalized with DPCs and FEN1. Mechanistically, we showed that FEN1 repairs FA-induced DPCs in vivo and cleaves 5-flap DNA substrate harboring DPC mimetic in vitro. We also found that FEN1 repairs enzymatic topoisomerase II (TOP2)-DPCs induced by their inhibitors etoposide and doxorubicin independently of the BER pathway, and that FEN1 and the DPC-targeting protease SPRTN act as parallel pathways for the repair of both FA-induced non-enzymatic DPCs and etoposide-induced enzymatic TOP2-DPCs. Notably, we found that FA-induced non-enzymatic DPCs and enzymatic TOP2-DPCs are promptly modified by poly-ADP-ribosylation (PARylation), a post-translational modification catalyzed by PARP1, a key DNA damage response effector that acts by PARylating both DNA damage sites and DNA repair proteins. We performed immunoprecipitation (IP) assays with anti-PAR antibody for HPLC-MS and identified FEN1 as a PARylation substrate. Next, we showed that PARylation of DPC substrates signaled FEN1 whereas PARylation of FEN1 drove FEN1 to DPC sites. Finally, using the enzymatic labeling of the terminal ADP-ribose-MS method, we identified the E285 residue of FEN1 as a dominant PARylation site, which appeared to be required for FEN1 relocation to DPCs. Taken together, our work not only unveiled the identities of FA-induced DPCs but also discovered an unprecedented PARP1-FEN1 nuclease pathway as a universal and imperative mechanism to repair the miscellaneous DPCs and prevent DPC-induced genomic instability.