Site-specific Acetylation of Histone H3 Decreases Polymerase β Activity on Nucleosome Core Particles in Vitro

J Biol Chem. 2016 May 20;291(21):11434-45. doi: 10.1074/jbc.M116.725788. Epub 2016 Mar 31.

Abstract

Histone posttranslational modifications have been associated with changes in chromatin structure necessary for transcription, replication, and DNA repair. Acetylation is one of the most studied and best characterized histone posttranslational modifications, but it is not known if histone acetylation modulates base excision repair of DNA lesions in chromatin. To address this question, we generated nucleosome core particles (NCPs) containing site-specifically acetylated H3K14 or H3K56 and measured repair of uracil and single-nucleotide gaps. We find that H3K56Ac and H3K14Ac do not significantly contribute to removal of uracils by uracil DNA glycosylase regardless of the translational or rotational position of the lesions within NCPs. In repair of single-nucleotide gaps, however, the presence of H3K56Ac or H3K14Ac in NCPs decreases the gap-filling activity of DNA polymerase β near the dyad center, with H3K14Ac exhibiting stronger inhibition. To a lesser extent, H3K56Ac induces a similar effect near the DNA ends. Moreover, using restriction enzyme accessibility, we detect no changes in NCP structure or dynamics between H3K14Ac-NCPs and WT-NCPs containing single-nucleotide gaps. Thus, acetylation at H3K56 and H3K14 in nucleosomes may promote alternative gap-filling pathways by inhibiting DNA polymerase β activity.

Keywords: DNA damage; DNA glycosylase; DNA polymerase; base excision repair (BER); histone acetylation; nucleosome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Acetylation
  • Animals
  • DNA Polymerase beta / antagonists & inhibitors
  • DNA Polymerase beta / metabolism*
  • DNA Repair
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism
  • Histones / chemistry*
  • Histones / metabolism*
  • Humans
  • Kinetics
  • Models, Molecular
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism*
  • Protein Processing, Post-Translational
  • Uracil / metabolism
  • Uracil-DNA Glycosidase / metabolism
  • Xenopus laevis

Substances

  • Histones
  • Nucleosomes
  • Uracil
  • DNA Polymerase beta
  • Uracil-DNA Glycosidase
  • APEX1 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase

Associated data

  • PDB/IKX5