The Methyltransferase Activity of Clr4Suv39h Triggers RNAi Independently of Histone H3K9 Methylation

SummaryIn fission yeast, the pericentromeric dg and dh repeats are transcribed and give rise to small interfering RNAs (siRNAs) by a mechanism that depends on the Clr4suv39h histone H3 lysine 9 (H3K9) methyltransferase. Here, we show that Clr4 activity promotes the assembly of a tripartite complex composed of the Clr4-containing CLRC complex and complexes involved in siRNA generation. However, unlike dh siRNAs, dg siRNAs accumulate to near wild-type levels in cells with H3K9 substitutions that cannot be methylated. Thus, Clr4 activity controls siRNA amplification from the different repeat regions by different mechanisms, H3K9 methylation dependent versus independent. Furthermore, artificial tethering of Rik1, a core subunit of the CLRC complex, to a euchromatic RNA mediates RNAi-dependent silencing that partially bypasses the requirement for other CLRC subunits. These findings establish Rik1 as a key link between CLRC and RNAi and reveal distinct centromeric siRNA amplification mechanisms that depend on the Clr4 methyltransferase activity.

Graphical AbstractFigure optionsDownload high-quality image (219 K)Download as PowerPoint slideHighlights
► Clr4Suv39h methyltransferase activity promotes its association with RNAi
► siRNA generation from centromeric dg and dh repeats depends on Clr4 activity
► dg siRNA generation occurs independently of H3K9 methylation
► The Rik1 protein links the RITS and RDRC RNAi complexes to the Clr4 complex, CLRC