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. 2019 Jul 16;10:3129. doi: 10.1038/s41467-019-11171-3

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — Integrated analysis of key pathways in Xist-mediated silencing. a, b PCA analysis of biological replicates of ChrRNA-seq analysis for all uninduced and Xist-induced experiments in iXist-Chr3 (a) and iXist-ChrX (b) for WT and mutants. c Cluster analysis and heatmap for silencing efficiency of ChrX genes in selected mutant mESCs, as indicated after 1 day of Xist RNA induction. Gene order is ranked by silencing efficiency in WT iXist-ChrX cells. Chromatin signature defined by ChromHMM is shown below. d Silencing levels in different mutants in iXist-ChrX cells illustrated as one-sided Wilcoxon rank-sum significance. Bar charts illustrate separate significance scores for genes classified according to pre-existing active (pre-active) and H3K27me3 (pre-H3K27me3) chromatin signatures, corrected for sample size. Error bars indicate significance range for 180 permutations. e Correlation analysis for topological distance and silencing efficiency for WT and selected mutant mESCs in iXist-ChrX model. Ninety-five per cent of the population is encircled. Spearman correlation and p values are indicated below