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. 2022 Apr 11;23:91. doi: 10.1186/s13059-022-02662-6

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© The Author(s) 2022

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 8 — Co-segregation of enhancers with target genes in vLADs or cLADs. a Identification of H3K27ac enhancers used in this study. b Size distribution of the GeneHancer double-elite enhancers considered in this study; thick bar, median; thin bars, 25–75% percentile; cross, mean. c Proportions of H3K27ac enhancers in LADs (gray shades) or i-LADs (green shades) at T00, T24, and T72, which are targeted to genes localized in indicated LAD classes (x axis); see Additional file 2, Table S7 for numbers of enhancers localized in each LAD class. d Distribution of gene start-enhancer distances for enhancers targeted to DE genes in all LAD classes; distances are from enhancer center to gene start sites, upstream (negative values) or downstream (positive values) of the gene start sites. e Box plot of gene start-enhancer center distances; bar, median; cross, mean; box, 25–75% percentile; whiskers, min-max. f Proportions of upstream and downstream enhancers. g H3K4me1 and H3K27ac levels at enhancers located in i-LADs, vLADs, and cLADs (all time points aggregated). vLAD enhancers are defined as enhancers in a vLAD at ≥ 1 time point in the 0–72-h time course; cLAD enhancers are in cLADs at all time points; i-LAD enhancers are in i-LADs at all time points; mean ChIP-seq read counts normalized to library size across all time points. h H3K27ac and H3K4me1 levels at enhancers in i-LADs, vLADs, and cLADs (all time points aggregated); bar, median; cross, mean; box, 25–75% percentile; whiskers, min-max. H3K27ac **P = 0.0049, ***P = 0.0002; H3K4me1 **P = 0.0023; unpaired two-tailed t-tests with Welch’s correction. i H3K27ac and H3K4me1 levels at enhancers of repressed cLAD genes (all time points aggregated)