In this research we study precise nature of the DNA lesions underlying formaldehyde toxicity and their consequences on DNA replication.
Formaldehyde is a highly reactive endogenous metabolite increasingly recognized as a major source of genome instability. While its genotoxicity has been traditionally attributed to DNA crosslinking, the precise nature of the DNA lesions and their consequences on DNA replication remain poorly understood. Using Xenopus egg extracts, we find that formaldehyde induces chromatin-associated lesions that predominantly consist of protein-protein crosslinks, leaving the DNA intact. These chromatin lesions include histone-histone crosslinks and impede replication fork progression, causing replication stress during S phase. We find that the replisome, assisted by the RTEL1 helicase, can autonomously bypass these lesions without involving DNA breakage or canonical crosslink repair pathways. However, in mitotic-like extracts, formaldehyde damaged chromatin triggers TRAIP-dependent fork breakage and microhomology mediated end joining by Pol?. We further identify the Fanconi anemia nuclease XPF as a key mediator of this process. Complementary cell-based assays confirm that formaldehyde does not induce point mutations but instead promotes large-scale structural variants, consistent with mitotic fork collapse. Collectively, our findings reveal a previously unrecognized class of chromatin-associated lesions induced by formaldehyde and highlight their distinct consequences on DNA replication across cell cycle phases.
Formaldehyde is a highly reactive endogenous metabolite increasingly recognized as a major source of genome instability. While its genotoxicity has been traditionally attributed to DNA crosslinking, the precise nature of the DNA lesions and their consequences on DNA replication remain poorly understood. Using Xenopus egg extracts, we find that formaldehyde induces chromatin-associated lesions that predominantly consist of protein-protein crosslinks, leaving the DNA intact. These chromatin lesions include histone-histone crosslinks and impede replication fork progression, causing replication stress during S phase. We find that the replisome, assisted by the RTEL1 helicase, can autonomously bypass these lesions without involving DNA breakage or canonical crosslink repair pathways. However, in mitotic-like extracts, formaldehyde damaged chromatin triggers TRAIP-dependent fork breakage and microhomology mediated end joining by Pol?. We further identify the Fanconi anemia nuclease XPF as a key mediator of this process. Complementary cell-based assays confirm that formaldehyde does not induce point mutations but instead promotes large-scale structural variants, consistent with mitotic fork collapse. Collectively, our findings reveal a previously unrecognized class of chromatin-associated lesions induced by formaldehyde and highlight their distinct consequences on DNA replication across cell cycle phases.