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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. 2 — a Plot shows the number of interactions (edges) and the number of interacting HindIII fragments (nodes) for each sub-network in naive and primed PSCs. Each small circle represents a different, individual sub-network. The lower-left quadrant reveals sub-networks that are larger in primed PSCs, and the upper-right quadrant shows the small number of sub-networks that are larger in naive PSCs. The protocadherin (PCDH), histone H1 (HISTH1) and ‘most changing’ (containing diverse genes) sub-networks are highlighted in red. b Multidimensional scaling representation (MDS) of the ‘most changing’ sub-network plotted using the linear genomic distance between nodes as edge weights. The measured stress score of 0.139 indicates there is a reasonable fit between the linear genomic distances and the spacing of the nodes as determined by MDS¹¹¹. c Plot shows the distribution of linear genomic distances between interacting nodes in naive and primed PSCs, binned into long-, mid-, and short-range distances (n = 1000). The box bounds the interquartile range (IQR) divided by the median (horizontal line), and Tukey-style whiskers extend to a maximum of 1.5 × IQR beyond the box. Circles indicate individual outliers. d Plot shows the total number of long-range chromatin interactions identified on all chromosomes in naive and primed PSCs. e Hi-C interaction matrix of chromosome 5 at a resolution of 250 kb with Knight–Ruiz (KR) normalisation; upper right, naive PSCs; lower left, primed PSCs. Areas of contact enrichment were defined separately for naive and primed PSCs using HiCCUPS and each cell-type-specific set of chromatin interactions are highlighted as a black square on their respective heatmap. The two corner numbers indicate the maximum intensity values for the matrix. The tracks below the Hi-C heatmap show the PCHi-C interactions and CHiCAGO scores over the same region. f Heatmap shows the aggregate peak analysis (250 kb resolution) of all naive and primed chromatin interactions genome-wide for naive and primed PSCs. Chromatin interactions >5 Mb from the diagonal were used for the analysis. The ‘peak to lower left’ (P2LL) score denotes the enrichment of the central pixel over the pixels in the lower left quadrant.