Reconstitution of heterochromatin spreading on designer chromatin reveals a two-state activation mechanism for the histone methyltransferase Suv39h1

Specialized chromatin domains contribute to nuclear organization and the regulation of gene expression. Gene-poor regions are demarcated by the activity of the histone methyltransferase, Suv39h1, which di- and trimethylates lysine 9 of histone H3 (H3K9me2/3). A positive feedback loop is hardwired into the domain architecture of Suv39h1, enabling it to spread H3K9me2/3 over extended heterochromatic regions. However, little is known about how feedback loops operate on complex biopolymers such as chromatin, in part because of the difficulty in obtaining suitable substrates. Here we describe the synthesis of multi-domain ‘designer chromatin’ templates and their application to dissecting Suv39h1 regulation. We uncover a two-step activation switch where H3K9me3 recognition and subsequent anchoring of the enzyme to chromatin allosterically promotes methylation activity, and confirm that this mechanism contributes to chromatin recognition in cells. We propose that this mechanism serves as a paradigm in chromatin biochemistry since it enables highly dynamic sampling of chromatin state combined with targeted modification of desired genomic regions.