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. 2021 Jul 16;12:4344. doi: 10.1038/s41467-021-24641-4

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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. 5 — a, b H3K27ac HiChIP and ChIP-seq profiles generated in E10.5 mouse brains (a; two biological replicates) and AntNPC (b; both replicates merged), respectively, are shown around the Sox1 locus. Both the Lhx5 TSS and the PE Sox1 (+35 kb) are marked with green vertical lines. Upper panel: heatmap of log2 interaction intensities based on H3K27ac HiChIP data generated in E10.5 mouse brain. Two medium panels: 1D HiChIP signals for H3K27ac in E10.5 mouse brain and H3K27ac, H3K4me3, and CTCF (for potential TAD boundaries) ChIP-seq profiles in AntNPC. Lower two panels: significant (p < 0.01 for E10.5 mouse brains; p < 0.05 for AntNPC; FitHiChIP) interactions were called using the H3K27ac HiChIP PETs (paired-end tags) and loops in which one of the anchors overlaps (±10kb) either the PE Sox1 (+35 kb) or the Lhx5 TSS are shown. c, d Significant (mESC H3K27me3 HiChIP data; p < 0.01; FitHiChIP) interactions between distal PEs (>10 kb from TSS) and ESC bivalent promoters (n = 526) were visualized as pileup plots using H3K27ac HiChIP data generated in H3K27ac HiChIP data generated in E10.5 mouse brain (c) or AntNPC (d). HiChIP interaction matrices were coverage-normalized (unbalanced). HiChIP pairwise interactions are shown 250 kb up- and downstream of each PE and bivalent promoter pair. The numbers in the upper left corners correspond to “loopiness” values (center intensity normalized to the intensity in the corners).