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. 2019 Mar 7;10:1109. doi: 10.1038/s41467-019-09041-z

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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. 5 — A Nanog/H3K27me3/Otx2 axis controls LIF-independent self-renewal. a H3K27me3 average levels (reads per million) across 5.15 Mb (mm9: chr14:45346123–50415313, red and blue boxes represent genes on the +and − strands) encompassing the Bmp4 and Otx2 genes that display the two stereotypical behaviours observed in SunTag cells cultured in the presence/absence of LIF/Dox for 3 days. b Heat map of H3K27me3 z-scores of 6,240 H3K27me3 domains identified in SunTag cells cultured as indicated. c Average H3K27me3 (reads per million) across promoter regions of genes upregulated in the absence of LIF and either rescued (left) or not (right) by Nanog. d Correlative analysis of ranked H3K27me3 (left) with gene expression changes (arbitrary units; middle) for transcripts upregulated (top) or downregulated (bottom) in SunTag cells cultured in the presence/absence of LIF/Dox for 3 days. The percentage of genes belonging to rescued (red line) versus non-rescued genes (blue line) in a 500 gene sliding window across the regions of the heat map is shown on the right. e Histogram representing the percentage of undifferentiated (red), mixt (blue) and differentiated (white) colonies (Y-axis) counted after 6 (Passage 1) or 12 (Passage 2) days of clonal growth in the indicated conditions (X-axis). Error bars represent std. dev. (n = 4). f Heat map of the average log2 fold change +Dox/−Dox in gene expression between SunTag cells activating either Nanog or Nanog and Otx2, grown in the absence of LIF and the presence/absence of Dox for 3 days. Genes for which the simultaneous activation of Otx2 compensates the changes observed when only Nanog is induced (FDR < 0.05), are highlighted