JMJD1B-mediated FEN1 demethylation allows timely switching of Okazaki fragment maturation core enzymes to avoid mutagenic flap ligation by PARP1-LIG3

Efficient and faithful Okazaki fragment maturation (OFM) depends on the PCNA-coordinated actions of core enzymes Pol{delta}, FEN1, and LIG1. We demonstrate that Pol{delta}, FEN1, and LIG1 sequentially but not simultaneously bind to PCNA in mammalian cells. The association of FEN1 with PCNA, which lies at the center of this orderly program, is mediated by FEN1 R192 methylation, which is also crucial for preventing premature loading of LIG1. Conversely, FEN1 demethylation by the recently identified arginine demethylase JMJD1B promotes FEN1 dissociation from PCNA and LIG1 recruitment. Disruption of the sequential PCNA binding program in R192Q or Jmjd1b-/- cells results in unprocessed 5 flaps that prevent OFM and induction of PARP1-dependent recruitment of LIG3, which has flap ligation activity to join incompletely processed OFs. This alternative OFM process supports cell survival but causes duplications and other DNA mutations. Our findings define fundamental and alternative DNA replication processes underlying mutagenesis and cell survival. HighlightsO_LIThe core enzymes involved in Okazaki fragment maturation (OFM), DNA polymerase {delta} (Pol{delta}), flap endonuclease 1 (FEN1), and ligase 1 (LIG1), sequentially bind to the scaffold protein PCNA for their concerted actions C_LIO_LIFEN1 R192 methylation enables FEN1 binding to PCNA; JMJD1B-mediated FEN1 arginine demethylation provokes FEN1 exit from PCNA and LIG1 recruitment C_LIO_LIFEN1 R192Q mutation and JMJD1B deficiency oppositely alter dynamic PCNA interactions with FEN1 and LIG1 and result in distinct OFM DNA intermediate structures C_LIO_LIActivation of PARP1 at replication forks due to disruption of the sequential PCNA binding program induces LIG3-mediated alternative mutagenic 5 flap ligation for survival. C_LI