Methylation of lysine 9 in histone H3 directs alternative modes of highly dynamic interaction of heterochromatin protein hHP1β with the nucleosome

J Biol Chem. 2012 Sep 28;287(40):33756-65. doi: 10.1074/jbc.M112.390849. Epub 2012 Jul 19.

Abstract

Binding of heterochromatin protein 1 (HP1) to the histone H3 lysine 9 trimethylation (H3K9me3) mark is a hallmark of establishment and maintenance of heterochromatin. Although genetic and cell biological aspects have been elucidated, the molecular details of HP1 binding to H3K9me3 nucleosomes are unknown. Using a combination of NMR spectroscopy and biophysical measurements on fully defined recombinant experimental systems, we demonstrate that H3K9me3 works as an on/off switch regulating distinct binding modes of hHP1β to the nucleosome. The methyl-mark determines a highly flexible and very dynamic interaction of the chromodomain of hHP1β with the H3-tail. There are no other constraints of interaction or additional multimerization interfaces. In contrast, in the absence of methylation, the hinge region and the N-terminal tail form weak nucleosome contacts mainly with DNA. In agreement with the high flexibility within the hHP1β-H3K9me3 nucleosome complex, the chromoshadow domain does not provide a direct binding interface. Our results report the first detailed structural analysis of a dynamic protein-nucleosome complex directed by a histone modification and provide a conceptual framework for understanding similar interactions in the context of chromatin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biotinylation
  • Calorimetry / methods
  • Chromatin / chemistry
  • Chromatin / metabolism
  • Chromobox Protein Homolog 5
  • Chromosomal Proteins, Non-Histone / chemistry*
  • DNA / chemistry
  • Epigenesis, Genetic
  • Histones / chemistry*
  • Histones / metabolism
  • Humans
  • Lysine / chemistry*
  • Magnetic Resonance Spectroscopy / methods
  • Methylation
  • Nucleosomes / chemistry*
  • Nucleosomes / metabolism
  • Protein Binding
  • Protein Structure, Tertiary
  • Schizosaccharomyces / metabolism

Substances

  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Histones
  • Nucleosomes
  • Chromobox Protein Homolog 5
  • DNA
  • Lysine