The UHRF1 protein interacts with the RFTS domain of DNMT1. UHRF1 is a multi-domain protein with E3 ligase activity, which has been shown to be required for the degradation of DNMT1 and can bind to histone H3 methylated on lysine 9. Consequently, UHRF1 mediates cross talk between DNA Chelerythrine Chloride methylation and post-translational modification of histones, specifically H3K9 methylation. Thus a clear link between the RFTS domain of DNMT1, an E3 ligase and chromatin modification has been established; it is likely that RFTS domains mediate similar interactions in other eukaryotes. We set out to characterise the RFTS domain of Raf2 and its role in centromeric heterochromatin formation. We show that the RFTS domain of Raf2 can be modelled on that of DNMT1 and that specific residues within this domain are crucial for heterochromatin integrity. We demonstrate that alteration of particular residues within the RFTS domain disrupts a direct interaction between the Raf2 and the Cul4 subunit of CLRC. Furthermore, although heterochromatin is disrupted, the generation of siRNA remains unperturbed, suggesting that Raf2 has separable roles in chromatin modification and siRNA production. Thus we have identified the RFTS domain of Raf2 as a protein interaction module crucial for heterochromatin integrity and centromere function. CLRC has two major functions in heterochromatin formation: it possesses histone methyltransferase activity via Clr4 and mediates siRNA production. In wild-type fission yeast, these processes are coupled to direct heterochromatin formation to specific location such as centromeres, telomeres and the silent mating-type locus, and prohibit silencing elsewhere. Cells expressing only mutant histone H3 are unable to methylate K9 of H3 and do not form heterochromatin, however such cells continue to produce a low level of siRNAs homologous to centromeric repeats. This suggests that the CLRC complex plays a role in promoting siRNA production, independently of H3K9 methylation. Deletion of any CLRC component results in loss of both H3K9 methylation and siRNA production, yet point mutations within CLRC components Raf1 and Cul4 exhibit separable functions with Hydroxychloroquine Sulfate respect to chromatin modification and siRNA generation.