Fig. 4
Setdb1 depletion results in losses of H3K9me2, H3K9me3 and DNA methylation spread along the inactive X chromosome. a–c ChIP-seq data from 129/CAST F1 MEFs: Setdb1 +/+ Xist ∆A/+ transduced with Nons (female) (n = 3) or Setdb1 +/gt Xist ∆A/+ transduced with shSetdb1.6 (Setdb1 depleted) (n = 2) MEFs and Male Setdb1 +/+ X/Y MEFs transduced with Nons (male) (n = 3). The female and male samples are as shown in Fig. 1. a Peaks per Mb of chromosome for H3K9me2, H3K9me3 and H3K27me3, X chromosome shown separately to the X chromosome. b Location of genes (purple), peaks of H3K27me3 (red, n = 3), H3K9me2 (green n = 3), H3K9me3 (blue n = 3), as a merge of all three histone marks in female or Setdb1 depleted MEFs, as determined by ChIP-seq, derived from a Seqmonk browser track. c H3K9me2, H3K9me3 and H3K27me3 shown for the X inactivation centre (XIC). The genes within the XIC are shown, and beneath peaks called by Seqmonk in-built MACS peak caller as grey bars. Seqmonk tracks are also shown, where the height of the track indicates the read number related to H3. Significance of enrichment or depletion is given by the strength of colour—red is most enriched, blue is most depleted. d–f eRRBS data from the same samples as a–c. d Depletion of mC for individual CpGs on the Xa and Xi in Female (n = 3) and Setdb1 depleted female samples (n = 2), for CpGs within CGIs on the X chromosome (Student’s two-tailed t test) as log2(mC/C). Dotted line indicates median for Xi in Female. e Average %mC along the width of a CGI after normalising for CGI length for CpGs falling within CGIs on the X only. f Location on the Xi of the CpGs with significantly altered mC levels, with genes (purple), CGIs (grey), CpGs gaining mC (red) and CpGs losing mC (blue) upon Setdb1 depletion indicated, derived from a Seqmonk browser track. See also Additional files 10: Figure S9, 11: Figure S10