Automethylation-induced conformational switch in Clr4/Suv39h maintains epigenetic stability

Histone H3 lysine 9 methylation (H3K9me) mediates heterochromatic gene silencing and is important for genome stability and regulation of gene expression(1–4). The establishment and epigenetic maintenance of heterochromatin involve the recruitment of H3K9 methyltransferases to specific sites on DNA followed by the recognition of pre-existing H3K9me by the methyltransferase and methylation of proximal histone H3(5-11). This positive feedback loop must be tightly regulated to prevent deleterious epigenetic gene silencing. Extrinsic anti-silencing mechanisms involving histone demethylation or boundary elements help limit inappropriate H3K9me spreading(12–15). However, how H3K9 methyltransferase activity is locally restricted or prevented from initiating random H3K9me leading to aberrant gene silencing and epigenetic instability is not fully understood. Here we reveal an autoinhibited conformation in the conserved fission yeast S. pombe H3K9 methyltransferase Clr4/Suv39h that plays a critical role in preventing aberrant heterochromatin formation. Biochemical and X-ray crystallographic data show that an internal loop in Clr4 inhibits its catalytic activity by blocking the histone H3K9 substrate-binding pocket, and that automethylation of specific lysines in this loop promotes a conformational switch that enhances Clr4 H3K9 methylation activity. Mutations predicted to disrupt this regulation lead to aberrant H3K9me, loss of heterochromatin domains, and growth inhibition, demonstrating the importance of Clr4 intrinsic inhibition and auto-activation in regulating H3K9me deposition and preventing epigenetic instability. Conservation of the Clr4 autoinhibitory loop in other H3K9 methyltransferases, and automethylation of a corresponding lysine in the human SUV39H2 homolog(16), suggest that the mechanism described here is broadly conserved.