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Updated: Jun 3, 2025

A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells
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A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells

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Flap endonuclease 1 repairs DNA-protein cross-links via ADP-ribosylation-dependent mechanisms

Yilun Sun1,2,3, Lisa M Jenkins4, Lara H El Touny5

  • 1Department of Pharmacology, Physiology and Drug Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

Science Advances
|January 10, 2025
PubMed

Insights

Formaldehyde exposure creates harmful DNA-protein cross-links (DPCs). A new study identifies flap endonuclease 1 (FEN1) and poly(ADP-ribose) polymerase 1 (PARP1) as key players in repairing these lesions.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • DNA-protein cross-links (DPCs) are highly toxic genomic lesions.
  • Formaldehyde (FA) exposure generates DPCs, and unrepaired DPCs disrupt chromatin, potentially causing neurodegeneration and cancer.
  • The precise nature and repair mechanisms of FA-induced DPCs are not well understood.

Purpose of the Study:

  • To identify proteins involved in FA-induced DPCs.
  • To elucidate the repair pathways for FA- and topoisomerase II (TOP2)-induced DPCs.
  • To investigate the role of poly(ADP-ribose) polymerase 1 (PARP1) and flap endonuclease 1 (FEN1) in DPC repair.

Main Methods:

  • Proteomic profiling of FA-induced DPCs.
  • Investigation of DNA base damage and flap structure formation.
  • Enzymatic assays and biochemical analyses of DPC repair.
  • Analysis of protein-protein interactions and post-translational modifications (PARylation).

Main Results:

  • Flap endonuclease 1 (FEN1) was identified as a key enzyme resolving FA-induced DPCs.
  • FA-induced DPCs involve DNA base damage and 5' flap structures formed via the base excision repair (BER) pathway.
  • FEN1 also repairs enzymatic TOP2-DPCs.
  • Both FA- and TOP2-DPCs are substrates for PARP1-mediated adenosine diphosphate (ADP) ribosylation (PARylation).
  • PARP1-dependent PARylation, including FEN1 PARylation at E285, is crucial for FEN1 recruitment and DPC repair.

Conclusions:

  • This study reveals the protein components of FA-induced DPCs.
  • A novel PARP1-FEN1 nuclease pathway for repairing both FA- and TOP2-DPCs has been uncovered.
  • This pathway highlights a critical mechanism for maintaining genomic integrity against DPC-inducing agents.

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