Histone H3 lysine 9 trimethylation (H3K9me3) is a key epigenetic modification required for heterochromatin formation and maintenance, genome stability and silencing of transposable elements in embryonic stems cells (ESCs). The H3K9-specific methyltransferase (KMT) SETDB1 is vital for mammalian development as it regulates ESCs pluripotency in the early embryo. Here we unravel that SETDB1 undergoes automethylation on two lysines, embedded within its catalytic domain, both in vitro and in cells. Importantly, SETDB1 automethylation is required for mouse ESCs stemness, growth and viability. Hence, transcriptome-wide analyses (RNA-seq) show that the integrity of the two SETDB1 automethylated lysines is required for both coding genes and transposable elements silencing in mESCs. Indeed, our analyses of ChIP-seq show that automethylation-deficient SETDB1 expression leads to a lack of H3K9me3 establishment at target loci. Interestingly, our results point to a model in which SETDB1 auto-methylation paves the path to a subsequent trans-methylation by SUV39H1. This mechanism could regulate not only the SETDB1/SUV39H1 physical interaction (via the SUV39H1 chromodomain), but also cooperation in the establishment and maintenance of both heterochromatin blocks (large domains) and transposable elements silencing. Taken together, my findings uncover a novel mechanism regulating SETDB1 KMT key functions that are key in embryonic stems cells identity maintenance.
