Fig. 6: Protein-level dosage compensation is induced within regions of monosomic expression on the X chromosome.

a Copy number-corrected protein abundance for all X-linked proteins in X^CastX^Mus, X^MusY and X^CastO^Mus ESCs. The mean (of n = 127 proteins) per biological replicate from a single clone is depicted with a dot, with the corresponding 95% confidence intervals shown as error bars. The dashed line indicates the mean value of X^CastX^Mus cells, serving as a reference line for expected expression without upregulation. b, c Volcano plots displaying the differential protein expression analysis of X-linked proteins between X^MusY and X^CastX^Mus samples (b) and between X^CastO^Mus and XX samples (c) (n = 3). Each dot represents a protein. P-values were calculated from copy number-corrected protein quantifications using Tukey’s HSD test (two-sided, with Tukey–Kramer correction for multiple comparisons). Significantly up and downregulated proteins are highlighted in red and blue, respectively (α < 0.05, log₂(fold change) > 0.5 or < −0.5, respectively). d Barplot displaying the proportion of upregulated genes per chromosome. The X chromosome is highlighted in green. e Barplot showing the proportion of complex-forming proteins in the upregulated (green) and non-upregulated (gray) protein lists. P-values were calculated via the Chi-square test. f Scatter plot showing the correlation between upregulation at RNA and protein level. Each dot represents a gene/protein. For both levels, the fold change between X^CastO^Mus and half of the X^CastX^Mus level is shown for each gene. Genes are colored according to their upregulation status at both (orange), either (blue or green) or neither (gray) levels. Shaded area indicates 95% confidence interval. g, h Scatter plots separated by region showing the mean copy number-corrected abundance levels of proteins encoded by genes located outside (g) and within (h) region E and K for X^CastX^Mus, X^MusY, X^CastO^Mus ESCs, and ESCs with the corresponding deletion. Each dot represents a biological replicate from a single clone. The dashed line represents the average abundance levels from the X^CastX^Mus samples. i Heatmap showing the z-scores of copy-number-corrected protein quantifications for X-linked proteins upregulated in both X^CastY and X^CastO^Mus samples compared to X^CastX^Mus. Proteins are ordered by genomic locations, with deletions E and K highlighted in light blue and pink, respectively. Proteins expected to be upregulated are highlighted with a box.