Fig. 1

ChIP-seq shows H3K9 methylation is enriched on the inactive X at gene poor regions. Histone ChIP-seq data from 129/CAST F1 Setdb1 ^+/+ Xist ^∆A/+ 129/CAST F1 female MEFs transduced with non-silencing (Nons) hairpin (female, n = 3) and 129/CAST F1 Setdb1 ^+/+ male MEFs transduced with Nons (male n = 3) MEFs. a H3K9me2, H3K9me3 and H3K27me3 ChIP-seq tracks for the entire female X chromosome. Scale bars indicate normalised reads relative to H3, where reads above the axis show enrichment and below depletion. Significance of enrichment or depletion is given by the strength of colour—red is most enriched, blue is most depleted. Location of genes (purple), and peaks called using Seqmonk in-built MACS peak caller (grey) are indicated. b As for a, except for male chromosome X. c Enrichment analysis, showing percentage coverage of H3K9me3 (blue) and H3K27me3 (red) ChIP-seq peaks at 50 kb bins along the Female X chromosome. The Pearson correlation coefficient (r) is indicated. d Number of reads for each histone mark on the Female Xa and Xi, relative to H3. The box indicates the first to third quartile, horizontal line indicates the median, while whiskers extend to the minimum and maximum values. p values shown were determined by Student’s two-tailed paired t test. e Location of ChIP-seq peaks for H3K27me3 (red, n = 3), H3K9me2 (green n = 3) and H3K9me3 (blue n = 3) shown as a merge in female or male MEFs. Location of genes is indicated (purple). A Venn diagram is included to show the colours produced when the various peaks overlap. See also Additional file 2: Figure S2