Fig. 6
Depleting polycomb repressive complex 1 (PRC1) or heterogeneous nuclear ribonucleoprotein K (HNRNPK) disrupts S1/S2 compartments in Smchd1−/− mouse embryonic fibroblasts (MEFs). a H2AK119ub enrichment profiles across the X chromosome. Gray areas, unmappable regions. Also shown are Xist CHART (capture hybridization analysis of RNA target) profiles, the locations of Class I genes (red bars), and S1/S2 compartments inSmchd1−/− MEFs. Δ, Smchd1−/− minus wild type (WT). Shown are “comp” tracks (compiled from all reads) of H2AK119ub ChIP-seq (chromatin immunoprecipitation followed by deep sequencing). Allele-specific tracks have been deposited to Gene Expression Omnibus (GEO) (GSE116413). b Box plots comparing the difference in H2AK119ub density between WT and Smchd1−/− cells of each 200-kb bin in S1 vs. S2 compartments. P values are given by the Wilcoxon’s rank-sum test (unpaired, one-sided). Midline, median. Top and bottom of the box, first and third quartile. Whiskers, extension from the top or bottom to the furthest datum within 1.5 times the interquartile range. c Depth-corrected chromatin interaction maps of the inactive X chromosome (Xi) in WT MEFs treated with control (Scramble) small interfering RNA (siRNA), and Smchd1−/− MEFs treated with control, RING1A/RING1B (PRC1 KD), or HNRNPK (HNRNPK KD) siRNA binned at 200-kb resolution (top) and the corresponding Pearson’s correlation maps (bottom). Gray-shaded areas, unmappable regions. Also see Supplementary Fig. 13a for the active X chromosome (Xa) maps. d Principal component 1 (PC1) and PC2 values of the Xi. Regions with positive PC1 values represent the S1 compartment or the telomeric megadomain. Gray-shaded areas, unmappable regions. Also see Supplementary Fig. 13b for PCs of the Xa. e Bar plots displaying the fraction of long-range interactions (>10 Mb) that span the Dxz4 megadomain boundary (“inter-megadomain” interactions) under different conditions. Two replicates were analyzed, with P values determined by the t test (unpaired, one-sided). Error bars, s.d.
