The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome

Michal R Gdula,Daniella Moralli,Greta Pintacuda,Michael Mcclellan,Skirmantas Kriaucionis,Wolf Reik,Felix Krueger,Tatyana B Nesterova,Neil Brockdorff,Jonathan Godwin,Ye Zhan,Catherine M Green,Hakan Ozadam,Edith Heard,Job Dekker

doi:10.1038/s41467-018-07907-2

Abstract

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Here we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contributes to this unique chromosome architecture. Specifically, allelic mapping of the transcriptome and epigenome in SmcHD1 mutant cells reveals the appearance of sub-megabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me3. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells, additionally adopt features of active X chromosome higher-order chromosome architecture, including A/B compartments and partial restoration of TAD boundaries. Xi chromosome architecture changes also occurred following SmcHD1 knockout in a somatic cell model, but in this case, independent of Xi gene derepression. We conclude that SmcHD1 is a key factor in defining the unique chromosome architecture of Xi.

Highlights

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains
H3K27me[3] depleted regions extend beyond the boundaries of activated genes (Supplementary Fig. 5b), and in some cases do not include known genes (Supplementary Fig. 5c). Together these results suggest that modified epigenomic features in SmcHD1 mutant cells correlate with domains in which Xi genes are activated
Allelic ChIP-seq analysis of SmcHD1 on Xi shows strong enrichment over gene-dense domains. This pattern mirrors the localisation of Xist RNA and Xist-dependent histone modifications[49,50], and is consistent with a previous study using a human cell line that reported a requirement for ongoing XIST RNA expression to maintain SMCHD1 enrichment on Xi36

Summary

Introduction

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Allelic mapping of the transcriptome and epigenome in SmcHD1 mutant cells reveals the appearance of submegabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me[3]. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells, adopt features of active X chromosome higher-order chromosome architecture, including A/B compartments and partial restoration of TAD boundaries. CTCF8–13, are in large part absent on Xi, being replaced instead by two large mega-domains that are separated by a hinge that encompasses the DXZ4 repeat sequence[14,15,16,17,18] The basis for this unique TAD structure is not well understood, but is thought to depend, at least in part, on ongoing expression of Xist RNA17.

Methods

Results

Conclusion