Figure 3. Different genes show different kinetics of silencing associated with their chromosomal position and Xist “entry” site localization.

(a) X-linked genes are clustered based on their silencing kinetics as “early” (silenced at 16-cell or earlier), “intermediate” (silenced at 32-cell), “late” (silenced at blastocyst), “biased” (maternally biased) and “escapee” (Esc, not silenced). The allelic ratio of each gene represents the number of reads mapped on the paternal genome divided by the total number of reads mapped and is represented at 4-cell, 16-cell, 32-cell and blastocyst stages from single female blastomeres. Further information is provided in Supplementary Table 1 and Online Methods. n= 137 X-linked genes (89 with consistent silencing kinetics between BC and CB crosses and 48 BC or CB-specific).

(b) Parental expression ratios of X-linked genes in female blastocysts in BC and CB strains. Each dot represents a single gene. The upper and lower sections represent data respectively from BC and CB embryos. Xist is represented by a red dot. Green and orange dots represent genes that escape from early XCI respectively in both strains or in strain-specific manner. Further information on escapees is found in Supplementary Table 2. n= 125 common X-linked genes.

(c) Box plot representing the distribution of the genomic distances to Xist locus (in Mb) for the different clusters of genes. “Transcription Start Site (TSS) of each gene has been used to measure the distance to Xist. p<0.05 corresponds to * by Dunn’s test.”

(d) Allelic expression of X-linked genes classified by their relative position to Xist “entry” sites (as identified during XCI induction in ESCs²⁰): “inside” (TSS located in a Xist “entry” site), “next to” (TSS located less than 100 kb to an “entry” site) and “outside” (over 100 kb from an “entry” site). By Dunn’s test; p<0.05 corresponds to *. Consistent or strain-specific genes have been used.

Boxplot represent median with lower and upper quartiles.