Architecture of a polycomb nucleoprotein complex

Mol Cell. 2006 Oct 6;24(1):91-100. doi: 10.1016/j.molcel.2006.08.007.


Polycomb group (PcG) epigenetic silencing proteins act through cis-acting DNA sequences, named Polycomb response elements (PREs). Within PREs, Pleiohomeotic (PHO) binding sites and juxtaposed Pc binding elements (PBEs) function as an integrated DNA platform for the synergistic binding of PHO and the multisubunit Polycomb core complex (PCC). Here, we analyzed the architecture of the PHO/PCC/PRE nucleoprotein complex. DNase I footprinting revealed extensive contacts between PHO/PCC and the PRE. Scanning force microscopy (SFM) in combination with DNA topological assays suggested that PHO/PCC wraps the PRE DNA around its surface in a constrained negative supercoil. These features are difficult to reconcile with the simultaneous presence of nucleosomes at the PRE. Indeed, chromatin immunoprecipitations (ChIPs) and nuclease mapping demonstrated that PREs are nucleosome depleted in vivo. We discuss the implications of these findings for models explaining PRE function.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites / physiology
  • Chromatin Immunoprecipitation
  • DNA / chemistry
  • DNA / metabolism
  • DNA Footprinting
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Drosophila / genetics
  • Drosophila / metabolism
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / metabolism
  • Epigenesis, Genetic
  • Gene Expression Regulation / physiology
  • Microscopy, Atomic Force
  • Models, Genetic
  • Nucleic Acid Conformation
  • Nucleosomes / metabolism
  • Polycomb-Group Proteins
  • Protein Structure, Tertiary
  • Repressor Proteins / chemistry
  • Repressor Proteins / metabolism*
  • Repressor Proteins / ultrastructure
  • Response Elements*
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism


  • DNA-Binding Proteins
  • Drosophila Proteins
  • Nucleosomes
  • Polycomb-Group Proteins
  • Repressor Proteins
  • Transcription Factors
  • pho protein, Drosophila
  • DNA