Intrinsic Nucleic Acid-Binding Activity of Chp1 Chromodomain Is Required for Heterochromatic Gene Silencing

Centromeric heterochromatin assembly in fission yeast requires the RNAi pathway. Chp1, a chromodomain (CD) protein, forms the Ago1-containing RNA-induced transcriptional silencing (RITS) complex and recruits siRNA-bound RITS to methylated histone H3 lysine 9 (H3K9me) via its CD. Here, we show that the CD of Chp1 (Chp1-CD) possesses unique nucleic acid-binding activities that are essential for heterochromatic gene silencing. Detailed electrophoretic-mobility shift analyses demonstrated that Chp1 binds to RNA via the CD in addition to its central RNA-recognition motif. Interestingly, robust RNA- and DNA-binding activity of Chp1-CD was strongly enhanced when it was bound to H3K9me, which was revealed to involve a positively charged domain within the Chp1-CD by structural analyses. These results demonstrate a role for the CD that provides a link between RNA, DNA, and methylated histone tails to ensure heterochromatic gene silencing. [Display omitted] ► Chp1-CD possesses unique nucleic-acid binding activities ► These Chp1-CD's activities are strongly enhanced when bound to H3K9me ► A positively charged domain within Chp1-CD is involved in the induced activity ► These nucleic-acid binding activities are required for Chp1's silencing function