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Heterochromatin formation in fission yeast depends on RNAi machinery and histone-modifying enzymes. One of the key histone-modifying complexes is Clr4-Rik1-Cul4 methyltransferase complex (CLRC), which mediates histone H3K9 methylation, a hallmark for heterochromatin. CLRC is composed of the Clr4 histone methyltransferase, Rik1, Raf1, Raf2 and Pcu4. However, transcriptional regulation of the CLRC subunits is not well understood. In this study, we identified Set3, a core subunit of the Set3/Hos2 histone deacetylase complex (Set3C), as a contributor to the integrity and silencing of heterochromatin at centromeres, telomeres and silent mating-type locus. This novel role of Set3 relies on its PHD finger, but is independent of deacetylase activity or structural integrity of Set3C. Set3 is not located to the centromeric region. Instead, Set3 is targeted to the promoters of  clr4  +  and  rik1  + , probably through its PHD finger. Set3 promotes transcription of  clr4  +  and  rik1  + . Consistently, the protein levels of Clr4 and Rik1 were reduced in the  set3 Δ mutant. The heterochromatin silencing defect in the  set3 Δ mutant could be rescued by overexpressing of  clr4  +  or  rik1  + . Our study suggests transcriptional activation of essential heterochromatin factors underlies the tight regulation of heterochromatin integrity.

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Set3 contributes to heterochromatin integrity by promoting transcription of subunits of Clr4-Rik1-Cul4 histone methyltransferase complex in fission yeast