The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation

Nucleic Acids Res. 2024 Jun 24;52(11):6424-6440. doi: 10.1093/nar/gkae445.

Abstract

TIMELESS (TIM) in the fork protection complex acts as a scaffold of the replisome to prevent its uncoupling and ensure efficient DNA replication fork progression. Nevertheless, its underlying basis for coordinating leading and lagging strand synthesis to limit single-stranded DNA (ssDNA) exposure remains elusive. Here, we demonstrate that acute degradation of TIM at ongoing DNA replication forks induces the accumulation of ssDNA gaps stemming from defective Okazaki fragment (OF) processing. Cells devoid of TIM fail to support the poly(ADP-ribosyl)ation necessary for backing up the canonical OF processing mechanism mediated by LIG1 and FEN1. Consequently, recruitment of XRCC1, a known effector of PARP1-dependent single-strand break repair, to post-replicative ssDNA gaps behind replication forks is impaired. Physical disruption of the TIM-PARP1 complex phenocopies the rapid loss of TIM, indicating that the TIM-PARP1 interaction is critical for the activation of this compensatory pathway. Accordingly, combined deficiency of FEN1 and the TIM-PARP1 interaction leads to synergistic DNA damage and cytotoxicity. We propose that TIM is essential for the engagement of PARP1 to the replisome to coordinate lagging strand synthesis with replication fork progression. Our study identifies TIM as a synthetic lethal target of OF processing enzymes that can be exploited for cancer therapy.

MeSH terms

  • Cell Cycle Proteins* / genetics
  • Cell Cycle Proteins* / metabolism
  • DNA / genetics
  • DNA / metabolism
  • DNA Ligase ATP / genetics
  • DNA Ligase ATP / metabolism
  • DNA Repair
  • DNA Replication*
  • DNA, Single-Stranded* / genetics
  • DNA, Single-Stranded* / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Flap Endonucleases / genetics
  • Flap Endonucleases / metabolism
  • Humans
  • Intracellular Signaling Peptides and Proteins* / genetics
  • Intracellular Signaling Peptides and Proteins* / metabolism
  • Poly (ADP-Ribose) Polymerase-1* / genetics
  • Poly (ADP-Ribose) Polymerase-1* / metabolism
  • X-ray Repair Cross Complementing Protein 1 / genetics
  • X-ray Repair Cross Complementing Protein 1 / metabolism

Substances

  • Cell Cycle Proteins
  • DNA
  • DNA Ligase ATP
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • FEN1 protein, human
  • Flap Endonucleases
  • Intracellular Signaling Peptides and Proteins
  • LIG1 protein, human
  • Okazaki fragments
  • PARP1 protein, human
  • Poly (ADP-Ribose) Polymerase-1
  • TIMELESS protein, human
  • X-ray Repair Cross Complementing Protein 1
  • XRCC1 protein, human