Fig. 5

Ablating Xist RNA does not reveal S1/S2 compartments despite failed structural maintenance of chromosomes hinge domain containing 1 (SMCHD1) recruitment. a Schematic representation of the epigenetic status of the inactive X chromosome (Xi) in wild-type (WT), Smchd1^−/−, and Xi^ΔXist fibroblasts. b Immuno-RNA-fluorescent in situ hybridization (Immuno-RNA-FISH) for SMCHD1 and Xist on WT [Xi^WT, 2lox(Xist+)] and Xi^ΔXist fibroblasts. Scale bar, 10 μm. c Depth-corrected chromatin interaction maps of the Xi in WT, Smchd1^−/_, and Xi^ΔXist fibroblasts binned at 200-kb resolution (top) and the corresponding Pearson’s correlation maps (bottom). Gray-shaded areas, unmappable regions. Also see Supplementary Fig. 2a for active X chromosome (Xa) maps. Note that in the Xi maps of Xi^ΔXist fibroblasts, the “super-loops” (arrowheads) formed by association between Xi regions exhibiting ATAC-seq (assay for transposase-accessible chromatin using sequencing) accessibility, BRG1 binding, cohesin binding, and topologically associated domain (TAD)-like structures not seen on the WT Xi can also be observed. Please see our reanalysis⁶⁸ of Hi-C data from the same Xi^ΔXist fibroblasts²¹ for in-depth description. d Principal component 1 (PC1) and PC2 values of the Xi. Gray-shaded areas, unmappable regions. Also see Supplementary Fig. 2b for PCs of the Xa. e Bar plots displaying the fraction of long-range interactions (>10 Mb) that span the megadomain boundary (“inter-megadomain” interactions) on the Xa and Xi in WT and Xi^ΔXist fibroblasts. Two replicates were analyzed, with P -values determined by the t test (unpaired, one-sided). Error bars, s.d. f Immuno-RNA-FISH for H2AK119ub and Xist on WT [2lox(Xist+)] and Xi^ΔXist fibroblasts. Number of cells with Xist clouds and co-localizing H2AK119ub foci is shown. Scale bar, 5 μm. g Immuno-RNA-FISH for H2AK119ub and Xist on WT and Smchd1^−/− MEFs. Number of cells with H2AK119ub foci co-localizing with Xist clouds is shown. Scale bar, 5 μm