A new sub‐pathway of long‐patch base excision repair involving 5′ gap formation

Base excision repair (BER) is one of the most frequently used cellular DNA repair mechanisms and modulates many human pathophysiological conditions related to DNA damage. Through live cell and in vitro reconstitution experiments, we have discovered a major sub‐pathway of conventional long‐patch BER that involves formation of a 9‐nucleotide gap 5′ to the lesion. This new sub‐pathway is mediated by RECQ1 DNA helicase and ERCC1‐XPF endonuclease in cooperation with PARP1 poly(ADP‐ribose) polymerase and RPA. The novel gap formation step is employed during repair of a variety of DNA lesions, including oxidative and alkylation damage. Moreover, RECQ1 regulates PARP1 auto‐(ADP‐ribosyl)ation and the choice between long‐patch and single‐nucleotide BER, thereby modulating cellular sensitivity to DNA damage. Based on these results, we propose a revised model of long‐patch BER and a new key regulation point for pathway choice in BER. Synopsis DNA base excision repair (BER) is essential for coping with highly frequent oxidative and alkylation base damage. Identification of a novel sub‐pathway argues for a revision of mammalian long‐patch BER models and suggests a new key regulation point in BER pathway choice. Live cell and in vitro reconstitution experiments reveal formation of a 9‐nucleotide gap 5′ to the lesion. Gap formation happens during repair of various DNA lesions, including oxidative and alkylation damage. Gap formation involves the specific actions of PARP1, RECQ1 helicase, RPA and ERCC1‐XPF endonuclease. RECQ1 inhibits PARP1 auto‐PARylation to suppress single‐nucleotide BER in favor of gap‐mediated long‐patch BER. Graphical Abstract Formation of a ssDNA gap and involvement of PARP1, RECQ1 and ERCC1‐XPF in response to various forms of oxidative and alkylation damage challenge current models of mammalian base excision repair.