Binding of PHF1 Tudor to H3K36me3 enhances nucleosome accessibility

Nat Commun. 2013:4:2969. doi: 10.1038/ncomms3969.

Abstract

The Tudor domain of human PHF1 recognizes trimethylated lysine 36 of histone H3 (H3K36me3). This interaction modulates the methyltransferase activity of the PRC2 complex and has a role in retention of PHF1 at DNA damage sites. We have previously determined the structural basis for the association of Tudor with a methylated histone peptide. Here we detail the molecular mechanism of binding of the Tudor domain to the H3KC36me3-nucleosome core particle (H3KC36me3-NCP). Using a combination of TROSY NMR and FRET, we show that Tudor concomitantly interacts with H3K36me3 and DNA. Binding of the PHF1 Tudor domain to the H3KC36me3-NCP stabilizes the nucleosome in a conformation in which the nucleosomal DNA is more accessible to DNA-binding regulatory proteins. Our data provide a mechanistic explanation for the consequence of reading of the active mark H3K36me3 by the PHF1 Tudor domain.

Publication types

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

MeSH terms

  • DNA / chemistry
  • DNA Damage
  • DNA-Binding Proteins / chemistry*
  • Fluorescence Resonance Energy Transfer
  • Histones / chemistry*
  • Humans
  • Lysine / chemistry
  • Magnetic Resonance Spectroscopy
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism*
  • Peptides / chemistry
  • Polycomb-Group Proteins
  • Protein Binding
  • Protein Structure, Tertiary
  • Transcription Factors / chemistry*

Substances

  • DNA-Binding Proteins
  • Histones
  • Nucleosomes
  • PHF1 protein, human
  • Peptides
  • Polycomb-Group Proteins
  • Transcription Factors
  • DNA
  • Lysine