Fig. 1: Transcriptional dosage compensation of X-linked genes in mouse pluripotent stem cell lines with X-chromosome monosomy.

a Schematic depiction of cells with different sex chromosome complements (XX, XY, and XO) and the corresponding expected upregulation status of the X chromosome (gray: not upregulated, green: upregulated). b, c Violin plots of the mean normalized gene expression from the Mus (b) and Cast (c) allele of all expressed X-linked genes in X^CastX^Mus (green), X^CastO^Mus (blue), X^MusO^Cast (orange), and X^MusY (yellow) cells. Dashed line indicates the mean value of XX cells, serving as a reference line for expected expression without upregulation. Each dot represents a cell. P-values were calculated via the Tukey HSD test (two-sided, with Tukey–Kramer correction for multiple comparisons). d, e Violin plots of the mean X:A ratio of the Mus (d) and Cast (e) allele in X^CastX^Mus, X^CastO^Mus, X^MusO^Cast, and X^MusY cells. The dashed line indicates the mean value of XX cells, serving as a reference line for expected expression without upregulation. Each dot represents a cell. P-values were calculated using the Tukey HSD test (two-sided, with Tukey–Kramer correction for multiple comparisons). f Normalized expression in X^CastX^Mus iPSCs of genes annotated as upregulated (in XO and XY cells, n = 103, green) or non-upregulated (n = 168, gray). P-value was calculated using a two-sided Student’s t-test. g Schematic overview of the experimental set-up used to generate allele-specific ChIP-seq data⁵⁷. h, i Line plots showing the promoter enrichment of repressive (h) and active (i) histone modifications on the active Cast allele during XCI inactivation, and thus XCU induction. Promoter enrichment was quantified as the mean counts per 10 million (CP10M) in the 1 kb region upstream of the TSS (as shown for the 24 h time point in Supplementary Figs. 3d and 4c). Mean enrichment is plotted for the promoters of upregulated (green) and non-upregulated (gray) genes separately, with shaded areas indicating the standard error. P-values comparing enrichment at 0 and 24 h were calculated using two-sided paired t-tests, corrected for multiple testing with the Benjamini–Hochberg method, and shown to the right of each gene set.