Base excision repair in nucleosomes lacking histone tails

DNA Repair (Amst). 2005 Feb 3;4(2):203-9. doi: 10.1016/j.dnarep.2004.09.011.


Recently, we developed an in vitro system using human uracil DNA glycosylase (UDG), AP endonuclease (APE), DNA polymerase beta (pol beta) and rotationally positioned DNA containing a single uracil associated with a 'designed' nucleosome, to test short-patch base excision repair (BER) in chromatin. We found that UDG and APE carry out their catalytic activities with reduced efficiency on nucleosome substrates, showing a distinction between uracil facing 'out' or 'in' from the histone surface, while DNA polymerase beta (pol beta) is completely inhibited by nucleosome formation. In this report, we tested the inhibition of BER enzymes by the N-terminal 'tails' of core histones that take part in both inter- and intra-nucleosome interactions, and contain sites of post-translational modifications. Histone tails were removed by limited trypsin digestion of 'donor' nucleosome core particles and histone octamers were exchanged onto a nucleosome-positioning DNA sequence containing a single G:U mismatch. The data indicate that UDG and APE activities are not significantly enhanced with tailless nucleosomes, and the distinction between rotational settings of uracil on the histone surface is unaffected. More importantly, the inhibition of pol beta activity is not relieved by removal of the histone tails, even though these tails interact with DNA in the G:U mismatch region. Finally, inclusion of X-ray cross complement group protein 1 (XRCC1) or Werner syndrome protein (WRN) had no effect on the BER reactions. Thus, additional activities may be required in cells for efficient BER of at least some structural domains in chromatin.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA Glycosylases / metabolism
  • DNA Helicases / metabolism
  • DNA Polymerase beta / antagonists & inhibitors
  • DNA Polymerase beta / metabolism
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism
  • DNA-Binding Proteins / metabolism
  • Exodeoxyribonucleases
  • Histones / genetics
  • Histones / metabolism*
  • Humans
  • Nucleosomes / metabolism*
  • RecQ Helicases
  • Uracil-DNA Glycosidase
  • Werner Syndrome Helicase
  • X-ray Repair Cross Complementing Protein 1


  • DNA-Binding Proteins
  • Histones
  • Nucleosomes
  • X-ray Repair Cross Complementing Protein 1
  • XRCC1 protein, human
  • DNA Polymerase beta
  • Exodeoxyribonucleases
  • DNA Glycosylases
  • Uracil-DNA Glycosidase
  • DNA Helicases
  • RecQ Helicases
  • WRN protein, human
  • Werner Syndrome Helicase
  • DNA-(Apurinic or Apyrimidinic Site) Lyase