Fig. 4

Maternal deletion of Smchd1 results in failed silencing of the Xi in E14.5 placentae despite normal Xist expression. a Xist expression separated by maternal allele, paternal allele or total counts (without haplotyping, i.e. maternal + paternal + non-allele-specific reads) in female \(\textit{Smchd1}^{mat\Delta }\) or wt E14.5 placentae. The reads are shown as a proportion of the total library size (counts per million, CPM) before haplotyping. b Differential gene expression between \(\textit{Smchd1}^{\textit{het}}\) and \(\textit{Smchd1}^{wt}\) E14.5 placentae, and \(\textit{Smchd1}^{mat\Delta }\) and \(\textit{Smchd1}^{wt}\) in E14.5 placentae split by alleles. X-linked genes are coloured, differentially expressed genes that pass the genome-wide 5% FDR are circled. Average expression in \(\hbox {log}_{2}\) cpm. The paternal X is the inactive X is mouse placenta. Median log2-fold change of X-linked genes is plotted as a coloured horizontal line. c Overlap between X-linked genes that are significantly differentially expressed in \(\textit{Smchd1}^{\textit{het}}\) and in \(\textit{Smchd1}^{mat\Delta }\) placentae. d Comparison of the \(\hbox {log}_{2}\)-fold changes of the differentially expressed paternal X-linked alleles common to the \(\textit{Smchd1}^{\textit{het}}\) and \(\textit{Smchd1}^{mat\Delta }\) placentae. p = 8e−5, paired t-test. e Distribution of CpG island methylation on the Xi and Xa in \(\textit{Smchd1}^{mat\Delta }\) and \(\textit{Smchd1}^{wt}\) E14.5 female placentae. Xi: p < 1e−6; Xa: p = 2e−5; paired t-tests. n = 4 MMTV-Cre \(\textit{Smchd1}^{mat\Delta }\) and n = 5 wt; n = 6 het and littermate n = 4 wt control E14.5 placentae