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. 2020 Nov 16;11:5823. doi: 10.1038/s41467-020-19452-y

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© The Author(s) 2020

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, e Short-read-based reconstruction and epigenomic characterization of the MYCN amplicon in IMR-5/75 (a) and CHP-212 (e) cells. Top to bottom: Hi-C map (color indicating Knight–Ruiz normalized read counts in 25 kb bins), virtual 4C (MYCN viewpoint, v4C), CTCF ChIP-seq, H3K27Ac ChIP-seq, Amplicon reconstruction, copy-number profile, super-enhancer locations (yellow), gene positions (blue). b, f Schematic representation of the class II amplicon described in a, e, showing ectopic enhancers and insulator reshuffling leading to locally disrupted regulatory neighborhoods on the HSR in IMR-5/75 (b) and on ecDNA in CHP-212 (f). c, g Alignment of Hi-C reads to the reconstructed MYCN amplicon in IMR-5/75 (c) and CHP-212 (g) and positions of genes, local MYCN enhancers and CRC-driven super-enhancers on the amplicon. d, h Mapping of the long-read sequencing-based de novo assembly of the MYCN amplicon in IMR-5/75 (d) and CHP-212 (h) on chromosome 2. Source data are provided as a Source Data file.