PARP1-mediated 5’ flap dynamics facilitate Okazaki fragment maturation

Abstract/Summary Precise regulation of enzyme recruitment during Okazaki fragment maturation (OFM) is essential for faithful and efficient lagging-strand DNA synthesis. Emerging evidence suggests that PARP1 contributes to OFM yet its specific functions remain unclear. Here, we define context-dependent functions of PARP1 during OFM. Under physiological conditions, PARP1 co-localizes with PCNA in early S phase and restrains Pol δ–PCNA– mediated strand-displacement DNA synthesis, thereby preventing the formation of long 5′ flaps, which is refractory to FEN1 cleavage. On the other hand, in LIG1-deficient cells, in which DNA nicks and unexpectedly long 5′ flaps accumulate, PARP1 promotes the recruitment of LIG3 to catalyze OF ligation and DNA2 to facilitate long 5′ flap processing. Collectively, our findings uncover previously unrecognized roles of PARP1 in regulating 5′ flap dynamics to ensure efficient OFM and cell viability. Highlights PARP1 plays context-dependent regulatory functions in Okazaki fragment maturation (OFM). PARP1 controls strand displacement DNA synthesis by the PCNA-Polδ complex to dictate generation of short over long RNA-DNA flaps during canonic OFM. PARP1 senses unligated Okazaki fragments in DNA Ligase 1 deficient cells and suppresses unwanted conversion of DNA nicks into 5’ flaps. Processing of unligated nicks or flaps by DNA ligase 3 or DNA2, respectively in LIG1 deficient cells depends on PARP1. PARP1 inhibitors induce synthetic lethality with DNA ligase 1 or DNA2 inhibition.