Extended Data Figure 8: 3D DNA FISH and integrative ATAC–seq/RNA-seq analysis in ΔFT NPCs.
From: Structural organization of the inactive X chromosome in the mouse
a, Top left, scheme of the DNA FISH probe sets (a–b: inside the same mega-domain, b–c: across the boundary). Bottom, loci detected by probe set b–c are more interacting in the ΔFT than in the wild-type Xi chromosome both in Hi-C (left) and in 3D-DNA FISH (right), showing loss of mega-domain boundary. *P < 2 × 10−4, **P < 1 × 10−5 (Wilcoxon’s rank sum test corrected with Bonferroni for multiple hypothesis testing). Right, sample RNA/DNA FISH images showing that signals from probe set b–c are more overlapping on the ΔFT Xi than on the wild-type Xi chromosome. Two biological replicates were analysed. b, Chromosome-wide ATAC–seq and RNA-seq signal generated with ambiguous (mm9), 129- and Cast-specific reads in wild-type NPCs and ΔFT NPCs, showing global loss of chromatin accessibility on the ΔFT Xi chromosome except at the X-inactivation centre (Xic) region and constitutive escape genes. Dotted line indicates the position of the mega-domain boundary. c, Zoomed-in view of a region on the ΔFT Xi chromosome encompassing the Xic showing Hi-C interactions, RNA-seq and ATAC–seq signal. ATAC–seq from wild-type NPCs is included for reference (previously shown in Fig. 1).
