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. 2021 Apr 7;12:2098. doi: 10.1038/s41467-021-22201-4

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© The Author(s) 2021

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. 6 — a Heatmap shows the percentage of OSN sites that fall within each of the ChromHMM-defined chromatin states. Columns 1 and 2 indicate OSN sites that are common to both naive and primed PSCs; columns 3 and 4 are OSN sites that are specific to either naive or primed PSCs; columns 5 and 6 represent random regions that do not contain OSN sites. b, c ChIP-seq data for H3K27ac, OCT4, SOX2 and NANOG in b naive and c primed PSCs. Metaplots (upper) and heatmaps (lower) show normalised ChIP-seq read counts within a 4 kb peak-centred window. Regions were subsetted into active enhancers (naive, n = 43,966; primed, n = 54,633), bivalent enhancers (naive, n = 1,998; primed, n = 5,502) and inactive enhancers (naive, n = 117,609; primed, n = 127,146) based on ChromHMM-defined chromatin states, and ranked by H3K27ac signal. d Heatmap shows the log2 odds ratio for the associated changes in OSN occupancy and promoter–enhancer interactions in primed compared to naive PSCs. e Table shows the highest-ranking (by adjusted P-value, one-tailed Fisher’s exact test) transcription factor motifs that are enriched at OSN sites in naive compared to primed PSCs. Four motifs associated with transcription factors that are not expressed in naive PSCs (log2 RPKM < 0) were removed from the list: KLF1, NR2F1, ZNF354C and VDR. f Bar chart shows the percentage of OSN-bound enhancers that contain each of the identified transcription factor motifs in naive and primed PSCs. g Enrichment of TFAP2C ChIP-seq signal across OSN peaks and the 2 kb up- and downstream regions.