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. 2019 Dec 12;10:5688. doi: 10.1038/s41467-019-13604-5

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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. 4 — a GSEA of genes located at BA-switching regions. All human genes were ranked by expression fold changes (FC), calculated as expression levels of genes in OIS cells divided by those in growing cells (blue distribution). For this GSEA, the difference in PCA scores between OIS and growing cells was calculated for each BA-switching region, and the top 300 genes present at the regions with the largest difference in PCA scores were analyzed. NES, normalized enrichment score. b GSEA of genes located at AB-switching regions (n = 263). c ChIP-seq enrichment of the indicated proteins and epigenetic marks for the respective compartmental categories in growing (G) and OIS cells. Five hundred genomic regions (40 kb bins) were randomly sampled from each compartmental category, and distributions of average ChIP enrichments are shown as boxplots (central bar represents the median with boxes indicating the upper and lower quartiles, and whiskers extend to the data points, which are no more than 1.5× the interquartile range from the box; outliers shown as circles). ChIP-seq data for the epigenetic marks and LMNB1 were previously published^47,70. d An example of how BA transitions of small B compartments change the compartmental organization upon OIS. PCA scores in growing and OIS cells are plotted along a 50 Mb region in chromosome 4. BA transitions upon OIS are indicated by arrows. ChIP-seq data for CAP-H2, H3K4me3, H3K9me3, and LMNB1 are shown beneath. e Same as panel d, but a 5 Mb region with a single BA transition (dotted) is shown. f GO analysis of the 96 genes that are present at BA-switching regions and significantly upregulated upon OIS. These genes were cross-referenced with genes involved in specific biological processes to test the significance of their overlap (Fisher exact test).