Extended Data Fig. 4: SPEN is recruited by Xist to active gene promoters and enhancers where it silences transcription and subsequently disengages from chromatin.

a, Bar graph showing the number of SPEN peaks on each chromosome after 0 h, 4 h, 8 h and 24 h of Xist induction in mouse ES cells. b, Annotation of SPEN peaks on autosomes. c, Heat map showing allelic ratios at SPEN peaks during XCI among different X-linked genomic features. d, Violin plot showing expression (RPKM) of genes accumulating SPEN (n = 259) or not accumulating SPEN (n = 689) at their promoters. Genes showing 0 RPKM were excluded from this plot. e, Box plots showing SPEN enrichment after 4 h of Xist induction within promoter windows of genes grouped on the basis of their level of dependency on SPEN for gene silencing (see Fig. 1e). f, Box plots showing SPEN enrichment after 4 h of Xist induction within promoter windows of genes grouped on the basis of whether or not they are silenced at 24 h of Xist induction (see Methods). In d–f, data were analysed using the two-sided Wilcoxon rank-sum test, horizontal lines denote the median, box limits correspond to upper and lower quartiles. g, UCSC Genome Browser allele-specific track showing SPEN binding around Kdm6a, an escaping gene (blue, Cast-Xa; red, B6-Xi; all tracks are scaled identically). h, Bar graphs showing overlap between SPEN-binding sites and the binding sites of four different factors at X-linked enhancers and promoters. i, j, Heat maps showing normalized SPEN enrichment (log₂) at promoters (both replicates are shown) (i) and gene silencing kinetics (allelic ratio) during XCI (j) within three groups of X-linked genes showing different dynamics of SPEN accumulation and loss. k, Schematic of the function of SPEN in XCI. In a–f, h–j, data are from two biological replicates.