Extended Data Fig. 8: Loss of the E-repeat prevents continued gene silencing in differentiating ES cells.

a, Histograms of nascent transcription pattern of indicated X-linked genes (Rnf12 (Rlim), Atrx, Mecp2, Gpc4 and Chic1) in undifferentiated wild-type and ΔE ES cells, demonstrating that heterozygous deletion of the E-repeat does not interfere with X-linked gene expression in undifferentiated ES cells (n = 60, from one experiment). b, Representative epifluorescence images of cells counted in a. Tsix, the antisense transcript of Xist, was also detected here to identify both X chromosomes. Co-localized foci appear yellow. c, Histograms of nascent expression patterns of the X-linked genes Gpc4 and Atrx in wild-type and ΔE cells displaying an Xis t^MS2-coated X chromosome (n = 50), across 5 days of differentiation. These data were derived from an independent differentiation from that shown in Fig. 2c. d, Histograms of nascent expression patterns of indicated X-linked genes in wild-type and ΔE cells displaying an Xis t^MS2-coated X chromosome (n = 50), across 7 days of differentiation derived from an independent differentiation from that shown in c and Fig. 2c. e, Histogram of nascent expression patterns of the X-linked gene Tsix in wild-type and ΔE cells across 5 days of differentiation. Note that these data were not scored relative to Xist^MS2 expression (that is, the monoallelic Tsix signal can be derived from either the 129 or cas allele (n = 70, except for the ΔE cells at day 5 with only 47 cells counted).