Fig. 4

Parent-of-origin allele-specific expression of X-linked genes in human germ cells reveals incomplete X reactivation. a Examples of a somatic cell and germ cells at different developmental stages showing the maternal and paternal expression of SNP-containing autosomal genes (black dots), proper (non-escapee) X-linked genes (red dots) and X-linked genes know to escape inactivation (green dots). b Distribution of pooled allele-specific read counts of SNP-containing XCI-escaping genes (top) and X-proper genes (bottom) on the active and inactive X chromosome per cell type. The average ± standard error of the mean (SEM) is shown for each bin. c Allelic bias of individual autosomes (black) and sex chromosomes (colored by cell type and stage). The sum of maternal and paternal allele-specific read counts of SNP-containing genes per chromosome per single cell shows different degrees of reactivation. Chromosomes are binned per total allelic read counts (gray lines) to counter sequencing depth related technical effects. The yellow area in each bin is the 95% confidence interval as defined by allelic bias in autosomes. X chromosomes in orange circles are from germ cells that fall outside the 95% interval, therefore are significantly non-reactivated. Analysis pipeline depicted in Supplementary Fig. 6a and displayed in log-space in Supplementary Fig. 6b. The read counts of the X chromosome exclude reads from escapee genes. d Percentage of reads from the paternal X chromosome per cell type. Data points corresponding to cells that show significant allelic expression bias on the X chromosome (fell outside the 95% interval in Fig. 4c) are colored. The broken lines indicated the 25% quartiles. e Individual germ cells ranked according to their X chromosome expression bias (reactivation status). Cells are colored according to fetal age (top) and germ cell stage (bottom). X chromosomes in the yellow area are within the 95% confidence interval determined by the autosomes. f Differential gene expression between PGCs that contain X chromosomes with allelic expression bias comparable to autosomes (XaXa) and PGCs that are reactivating the silent X chromosome (XiXa). Red dots (with gene names) were significantly differentially expressed (p < 0.05). P values were calculated using negative binomial distribution and corrected for multiple testing by the Benjamini-Hochberg method