Mechanisms governing interaction of the chromosomal protein SMCHD1 with chromatin determined by live-cell and single molecule imaging

The chromosomal protein SMCHD1 is a GHKL-ATPase that plays important roles in epigenetic silencing, including on the inactive X chromosome (Xi) and at the D4Z4 macrosatellite linked to regulation of DUX4 expression in the disorders FSHD2 and BAMS. In this study we use live-cell and single-molecule imaging approaches to investigate SMCHD1 interactions with chromatin and its function in epigenetic silencing. We show that chromatin binding of SMCHD1 genome wide, including on Xi, is critically dependent on the protein LRIF1 that mediates interaction with H3K9me2/3 modified nucleosomes. Using engineered mutations in the GHKL ATPase domain we show that ATP hydrolysis is required for SMCHD1 function on chromatin and gene silencing, but is dispensable for chromatin binding. A gain of function mutation, G137E, that occurs in BAMS patients, results in accelerated Xi recruitment and greater Xi chromosome compaction. Together, our findings advance mechanistic understanding of SMCHD1 function on Xi and at other target sites in the genome.