Selective interaction of SMCHD1 with chromatin is governed by LRIF1 and SMCHD1 ATPase activity.

The chromosomal protein SMCHD1 is a GHKL ATPase with important roles in epigenetic silencing, including on the inactive X chromosome (Xi). Mutations of SMCHD1 have been linked to facioscapulohumeral muscular dystrophy (FSHD) and Bosma arrhinia microphthalmia syndrome (BAMS). Here, we use live-cell and single-molecule imaging to investigate SMCHD1 interactions with chromatin and its function in epigenetic silencing. We show that chromatin binding of SMCHD1 genome-wide, including on the Xi, is critically dependent on the protein LRIF1 that mediates interaction with H3K9me2/3-modified nucleosomes. Engineered mutations in the GHKL ATPase domain demonstrate that ATP hydrolysis is required for selective enrichment of SMCHD1 at specific chromatin regions, which is critical for X-linked gene silencing. Conversely, gain-of-function BAMS-associated mutations are linked to accelerated Xi recruitment and gene silencing, or increased Xi compaction. Together, our findings advance understanding of SMCHD1 recruitment and function on the Xi and at other target sites in the genome.