The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription

Mol Cell Biol. 2007 Nov;27(21):7475-85. doi: 10.1128/MCB.01314-07. Epub 2007 Sep 4.

Abstract

We explored the mechanisms of chromatin compaction and transcriptional regulation by poly(ADP-ribose) polymerase 1 (PARP-1), a nucleosome-binding protein with an NAD(+)-dependent enzymatic activity. By using atomic force microscopy and a complementary set of biochemical assays with reconstituted chromatin, we showed that PARP-1 promotes the localized compaction of chromatin into supranucleosomal structures in a manner independent of the amino-terminal tails of core histones. In addition, we defined the domains of PARP-1 required for nucleosome binding, chromatin compaction, and transcriptional repression. Our results indicate that the DNA binding domain (DBD) of PARP-1 is necessary and sufficient for binding to nucleosomes, yet the DBD alone is unable to promote chromatin compaction and only partially represses RNA polymerase II-dependent transcription in an in vitro assay with chromatin templates (approximately 50% of the repression observed with wild-type PARP-1). Furthermore, our results show that the catalytic domain of PARP-1, which does not bind nucleosomes on its own, cooperates with the DBD to promote chromatin compaction and efficient transcriptional repression in a manner independent of its enzymatic activity. Collectively, our results have revealed a novel function for the catalytic domain in chromatin compaction. In addition, they show that the DBD and catalytic domain cooperate to regulate chromatin structure and chromatin-dependent transcription, providing mechanistic insights into how these domains contribute to the chromatin-dependent functions of PARP-1.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Catalytic Domain*
  • Cattle
  • Chromatin / chemistry*
  • Chromatin / genetics*
  • Chromatin / ultrastructure
  • DNA / metabolism*
  • Drosophila
  • Histones / metabolism
  • Humans
  • Microscopy, Atomic Force
  • Mutant Proteins / isolation & purification
  • Mutant Proteins / metabolism
  • Poly(ADP-ribose) Polymerases / chemistry*
  • Poly(ADP-ribose) Polymerases / isolation & purification
  • Poly(ADP-ribose) Polymerases / metabolism*
  • Protein Binding
  • Protein Structure, Tertiary
  • Repressor Proteins / metabolism
  • Structure-Activity Relationship
  • Transcription, Genetic*

Substances

  • Chromatin
  • Histones
  • Mutant Proteins
  • Repressor Proteins
  • DNA
  • Poly(ADP-ribose) Polymerases