Extended Data Fig. 3: Contribution to the kinetics of X-chromosome reactivation.
(A) Representation of the Gene Ontology analysis of Biological process performed on the best correlated genes with X-linked gene reactivation (adj.p-value ≤ 0.05) (Supplementary Data 3). Correlation and anti-correlation between gene expression levels (autosomes and X chromosomes) and the percentage of X-linked gene reactivation (allelic ratio >0.15 and <0.85 for X-linked genes) were measured using two-sided Pearson’s correlation and the Benjamini–Hochberg correction. (B) Comparison of reactivation timing for 7 X-linked genes between our study (129 x Mus musculus castaneus PGCs) and published scRT-PCR digested by restriction enzyme (Mus musculus domesticus x Mus musculus mollossinus PGCs) 21. In the extracted data from Sugimoto and Abe, an arbitrary threshold of ≥ 50% of biallelic cells has been applied to consider the gene reactivated. (C) Distance to escapee genes. Distribution of genomic distances to escapees (Mb) for each X-linked gene reactivation class. The transcription start site (TSS) of each gene was used to measure the distance from the closest escaping gene. No significant differences were found between reactivation classes by the KW test (p-value = 0.13), despite very late-reactivated genes being statistically further to escapees than early-reactivated genes by MW test (p-value = 0.02). Boxplots represent the medians with lower and upper quartiles. (D) Reactivation classes in female PGCs compared to the in vitro PGC-like cell system 32. (E) Xist RNA entry sites are regions of the X chromosome showing early accumulation of Xist RNA upon initiation of X-chromosome inactivation and are thought to be the closest to the Xist locus in 3D spatial proximity. Allelic expression of X-linked genes classified on the basis of their relative position to Xist RNA entry sites (as identified during XCI induction in ESC 6): inside (TSS located inside a Xist RNA site, 17 informative genes), next to (TSS located less than 100 kb away from an entry site, 17 informative genes) and outside (over 100 kb from an entry site, 163 informative genes). Box plots represent medians (centre lines) with lower and upper quartiles (box limits). Whiskers represent 1.5× the interquartile range. Outliers are represented by dots.
