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. 2023 Jun 5;14:3242. doi: 10.1038/s41467-023-38953-0

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© The Author(s) 2023

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. 3 — a Genome browser view of significant promoter capture Hi-C (PCHi-C) interactions (blue arcs) for Hoxa2, chromatin accessibility (ATAC-seq, purple), and ChIP-seq profile for H3K27ac (blue) in the mandibular process (Md) and second pharyngeal arch (PA2) cranial neural crest cells (CNCCs) at E10.5, and in E12.5 and E14.5 pinna CNCCs in a 2 Mb region of chromosome 6 (50,502,806–52,500,000 bp). PCHi-C interactions with a CHiCAGO score ≥5 are visualized. The color intensity of an arc indicates the CHiCAGO score, with a maximum value of 20 (i.e., interactions having a score ≥20 are shown in dark blue). Only interactions with Hoxa2 are shown. Bottom, ChIP-seq binding sites for Hoxa2⁵⁷, Pbx, and Meis⁵⁸ in PA2 at E11.5. b Hi-C interaction heatmaps at 25 kb resolution in a 2.2 Mb region of chromosome 6, including the Hoxa cluster (50,442,417–52,636,150 bp) in Md and PA2 CNCCs at E10.5, and in pinna CNCCs at E12.5 and E14.5. TAD separation scores are called with HiCExplorer’s hicFindTADs (shown as blue lines). Additional gray lines show the TAD scores for different window sizes. The blue highlight marks the domain encompassing the Hoxa cluster and Evx1 (chr6:52,145,433–52,327,518). Arrows indicate the location of a TAD boundary between Hoxa2 and HIRE1/HIRE2. Arrowheads highlight inter-TAD interactions between Hoxa2 and HIRE1/HIRE2. c Virtual 4C profiles derived from PCHi-C of E10.5 Md (black) and PA2 (green) CNCCs and pinna CNCCs at E12.5 (blue) and E14.5 (red) on the Hoxa2 promoter bait. The same chromosomal region is displayed for panels a, c. For better readability, genomic coordinates are only displayed below panel c and within the Hoxa cluster only show Hoxa2 genomic position. d Zoom in on virtual 4C profiles of panel c at HIRE1 and HIRE2 (chr6:50779503 − 51183201). Bottom, ChIP-seq binding sites for Hoxa2⁵⁷, Pbx, and Meis⁵⁸ in PA2 at E11.5. In a–d, HIRE1 and HIRE2 are highlighted by yellow boxes. The Hoxa2 locus is highlighted in yellow (a) or green (b). Black boxes at the top of panels a and b show the Hoxa2 super-enhancer 1–5 (SE1–5) in PA2 CNCCs at E10.5.