Non-coding transcription can trigger histone post-translational modifications 
forming specialized chromatin. In fission yeast, heterochromatin formation 
requires RNAi and the histone H3K9 methyltransferase complex CLRC, composed of 
Clr4, Raf1, Raf2, Cul4, and Rik1. CLRC mediates H3K9 methylation and siRNA 
production; it also displays E3-ubiquitin ligase activity in vitro. DCAFs act as 
substrate receptors for E3 ligases and may couple ubiquitination with histone 
methylation. Here, structural alignment and mutation of signature WDxR motifs in 
Raf1 indicate that it is a DCAF for CLRC. We demonstrate that Raf1 promotes H3K9 
methylation and siRNA amplification via two distinct, separable functions. The 
association of the DCAF Raf1 with Cul4-Rik1 is critical for H3K9 methylation, 
but dispensable for processing of centromeric transcripts into siRNAs. Thus the 
association of a DCAF, Raf1, with its adaptor, Rik1, is required for histone 
methylation and to allow RNAi to signal to chromatin.