Intrinsically disordered region of Clr4/Suv39 regulates its enzymatic activity and ensures heterochromatin spreading

Methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin, is catalyzed by Clr4/Suv39. Clr4/Suv39 contains two conserved domains-an N-terminal chromodomain and a C-terminal catalytic domain-connected by an intrinsically disordered region (IDR). Several mechanisms have been proposed to regulate Clr4/Suv39 activity, but how it is regulated under physiological conditions remains largely unknown. We found that the N-terminus of Clr4 interacts with its C-terminal catalytic domain and represses its enzymatic activity. Detailed biochemical analyses revealed that basic amino acid residues in the IDR are involved in this interaction. Amino acid substitutions of these residues weakened this interaction, thereby promoting Clr4 activity in vitro. Interestingly, cells expressing mutant Clr4 with these substitutions showed a silencing defect, which suggested additional roles of the IDR in vivo. Genetic analysis revealed that the IDR functions in H3K9me spreading and that this activity is functionally linked to the RNAi pathway. We also showed that Clr4 binds to RNAs via the IDR and that RNA attenuates Clr4 autoinhibition in vitro. Furthermore, the IDR was found to contribute to the targeting of nucleosomal substrates in vitro. These results reveal a novel function of the Clr4/Suv39 IDR in regulating its enzymatic activity and heterochromatin spreading.