SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice

Abstract

Stable silencing of the inactive X chromosome (Xi) in female mammals is critical for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher order chromatin structure of the Xi, the underlying mechanism is largely obscure. Here we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells (EpiSCs) and mouse embryonic fibroblasts (MEFs) in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a critical role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

“… 36 , 99 This included LRIF1, SMCHD1 (SMHD1), TIF1B/TRIM28/KAP1, and replication fork proteins (MCM2-7 and HUWE1) ( Figure 6 E), all of which are annotated SUMOylated proteins 101 and known or putative SETDB1-linked factors. 33 , 102 , 103 , 104 , 105 …”

“…SMCHD1 is a known reader of H3K9me3, which functions in X chromosome and repeat silencing. 78 , 79 , 81 , 105 , 118 We thus propose that targeting DAXX–H3.3–H4 to different regions of the genome provides a mechanism to direct de novo assembly of H3K9me3 marked heterochromatin ( Figure 7 ). This nucleosome assembly pathway could both support other silencing systems (e.g., H3K9me3 read-write, DNA methylation, and sequence-dependent histone methyltransferase recruitment) and act as a seed for heterochromatin formation.…”

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

“…Upon bait normalization, our results revealed that DAXX forms a substantial number of SUMO dependent interactions ( Figure S5E ), which reflect the SUMO dependent recruitment of DAXX to subnuclear compartments including PML bodies (Corpet et al , 2020; Lin et al , 2006). We identified SUMOylation as a mechanism for DAXX to connect with SMCHD1/SMHD1, LRIF1, TIF1B/TRIM28/KAP1 and replication fork proteins (MCM2-7, HUWE1) ( Figure 6C ), which are identified as SUMOylated proteins (Hendriks et al, 2014) and known or putative SETDB1-linked factors (Ichihara et al, 2021; Keniry et al, 2016; Nozawa et al, 2013; Schultz et al, 2002; Teng et al , 2021). These factors were either marginally enriched with DAXX ABM (TIF1B, SMCHD1, LRIF1 and HUWE1) or not affected (MCM2-7).…”

Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells

“…Upon request, data can be available by the corresponding author. The previously published dataset used for this study is available at GEO under the following accessions: GSE201189 (42).…”