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.
Highlights
Epigenetic changes affect genome function without an alteration of the DNA sequence, and they can be inherited by daughter cells and sometimes by offspring
heterochromatin protein 1 (HP1)-family proteins recognize histone H3 methylated on lysine 9 (H3K9me) via their CD [6,9], which consists of four ß-strands and an α-helix and it recognizes H3K9me through an aromatic cage formed by three conserved residues (Fig 1A, underlined) [6]
isothermal titration calorimetry (ITC) showed that Chp2-CD bound the H3K9me3 peptide with an affinity of KD = 4.37 ± 0.91 μM (Fig 1C, left panel), which agrees with previous reports [10]
Summary
Epigenetic changes affect genome function without an alteration of the DNA sequence, and they can be inherited by daughter cells and sometimes by offspring. Epigenetic changes in the genome are important in many diseases, including cancer, diabetes type II, and obesity [1,2].
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