The binding of Chp2's chromodomain to methylated H3K9 is essential for Chp2's role in heterochromatin assembly in fission yeast

PLoS One. 2018 Aug 15;13(8):e0201101. doi: 10.1371/journal.pone.0201101. eCollection 2018.

Abstract

The binding of heterochromatin protein 1 (HP1) to lysine 9-methylated histone H3 (H3K9me) is an essential step in heterochromatin assembly. Chp2, an HP1-family protein in the fission yeast Schizosaccharomyces pombe, is required for heterochromatic silencing. Chp2 recruits SHREC, a multifunctional protein complex containing the nucleosome remodeler Mit1 and the histone deacetylase Clr3. Although the targeting of SHREC to chromatin is thought to occur via two distinct modules regulated by the SHREC components Chp2 and Clr2, it is not clear how Chp2's chromatin binding regulates SHREC function. Here, we show that H3K9me binding by Chp2's chromodomain (CD) is essential for Chp2's silencing function and for SHREC's targeting to chromatin. Cells expressing a Chp2 mutant with defective H3K9me binding (Chp2-W199A) have a silencing defect, with a phenotype similar to that of chp2-null cells. Genetic analysis using a synthetic silencing system revealed that a Chp2 mutant and SHREC-component mutants had similar phenotypes, suggesting that Chp2's function also affects SHREC's chromatin binding. Size-exclusion chromatography of native protein complexes showed that Chp2-CD's binding of H3K9me3 ensures Clr3's chromatin binding, and suggested that SHREC's chromatin binding is mediated by separable functional modules. Interestingly, we found that the stability of the Chp2 protein depended on the Clr3 protein's histone deacetylase activity. Our findings demonstrate that Chp2's H3K9me binding is critical for SHREC function and that the two modules within the SHREC complex are interdependent.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle Proteins / metabolism
  • Escherichia coli
  • Heterochromatin / metabolism*
  • Histones / metabolism*
  • Protein Binding
  • Protein Stability
  • Recombinant Proteins / metabolism
  • Repressor Proteins / metabolism*
  • Schizosaccharomyces
  • Schizosaccharomyces pombe Proteins / metabolism*

Substances

  • CHP2 protein, S pombe
  • Cell Cycle Proteins
  • Clr3 protein, S pombe
  • Heterochromatin
  • Histones
  • Recombinant Proteins
  • Repressor Proteins
  • Schizosaccharomyces pombe Proteins

Grant support

This work was supported by the Swedish Cancer Society (grant number 2008/939), the Swedish Research Council (grant number 521-2011-2437), and Ministry of Education, Culture, Sports, Science and Technology Japan (grant number JP16H01315 and JP17H03713).