Figure 2. Differential DNAme analysis on Xe distinguishes early from late XIE.

(A) Density plot of probes across X coordinates reveal transition 1 probes (1↓↑, blue) to concentrate irrespective of overall probe density (gray-shaded area), in contrast to fluctuating probes (~, black). KS distances quantify similarity to frequency distribution of the null probe density distribution (* KS test p value = 5.09e–11 for blue transition-1 probes).

(B) Volcano plot of transition-1 differentially methylated probes (DMPs), colored by X coordinate (legend above the plot). Top increasing DMPs annotated by gene name.

(C) DNAme of XIST and FIRRE probes across clusters A–F. Lines to (F) and (G) indicate the position of probes in relation to the genes and their annotated regions (* indicates DMPs from B).

(D) XIST and FIRRE expression (VST + batch-corrected/log2-transformed), respectively, for all samples with available RNA-seq data (all but cluster E).

(E) XIST CpGII/P2 ATAC peak accessibility score over DNAme (β) values, with symbol size indicating XIST expression (VST + batch-corrected/log2-transformed) across all A–F samples with all 3 datapoints.

(F and G) ATAC-seq coverage for XIST and FIRRE, respectively. Horizontal lines below coverage indicate called peaks (gray, black), including differential, closing peaks (red). Bottom panels of (F) and (G) relate DMPs and ATAC peaks to cis-regulatory sites for XIST and FIRRE, respectively.