PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome

Nat Commun. 2019 Dec 17;10(1):5751. doi: 10.1038/s41467-019-13641-0.

Abstract

The poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear. We characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks, which reveal that PARP1 associates faster with (γ)H2A.X- versus H2A-nucleosomes, resulting in a higher affinity for the former, which is maximal for γH2A.X-nucleosome that is also the activator eliciting the greatest poly-ADP-ribosylation catalytic efficiency. The enhanced activities with γH2A.X-nucleosome coincide with increased accessibility of the DNA termini resulting from the H2A.X-Ser139 phosphorylation. Indeed, H2A- and (γ)H2A.X-nucleosomes have distinct stability characteristics, which are rationalized by mutational analysis and (γ)H2A.X-nucleosome core crystal structures. This suggests that the γH2A.X epigenetic marker directly facilitates DNA repair by stabilizing PARP1 association and promoting catalysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic Helix-Loop-Helix Transcription Factors / genetics
  • Basic Helix-Loop-Helix Transcription Factors / isolation & purification
  • Basic Helix-Loop-Helix Transcription Factors / metabolism*
  • Biocatalysis
  • Crystallography, X-Ray
  • DNA Breaks, Double-Stranded
  • DNA Repair / genetics*
  • Epigenesis, Genetic
  • Histones / chemical synthesis
  • Histones / metabolism*
  • Histones / ultrastructure
  • Models, Molecular
  • Nerve Tissue Proteins / genetics
  • Nerve Tissue Proteins / isolation & purification
  • Nerve Tissue Proteins / metabolism*
  • Nucleosomes / metabolism*
  • Nucleosomes / ultrastructure
  • Poly (ADP-Ribose) Polymerase-1 / genetics
  • Poly (ADP-Ribose) Polymerase-1 / isolation & purification
  • Poly (ADP-Ribose) Polymerase-1 / metabolism*
  • Poly ADP Ribosylation / genetics
  • Recombinant Proteins / genetics
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism

Substances

  • Basic Helix-Loop-Helix Transcription Factors
  • H2AX protein, human
  • Histones
  • NPAS1 protein, human
  • Nerve Tissue Proteins
  • Nucleosomes
  • Recombinant Proteins
  • PARP1 protein, human
  • Poly (ADP-Ribose) Polymerase-1