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. 2020 Apr 29;21:104. doi: 10.1186/s13059-020-01998-1

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© The Author(s) 2020

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. 4 — Chromatin loops define local-scale functional units of wheat genome architecture. a Integration of Hi-C and ChIP-seq data. A 2D heatmap with the interaction frequency in region chr3B-334500000-337000000 is presented. Black bars represent genes. Dashed circles represent the chromatin loop interactions. b Heatmap presenting the logarithm of odds ratios of all combinations of features of interacting genes (see the “Results” section). Positive log₂(odds ratio) indicates enrichment and negative indicates depletion. c Heatmap presenting the gene expression levels of gene-to-gene loop (GGL) gene pairs. Within each gene pair, each gene was classified into a quartile of expression, and then the number of gene pairs with each combination of quartiles was counted. d Scatterplot of log₂(shoot/root fold change) for pairs of interacting genes associated with a GGL conserved in shoots and roots. Loops (significant interactions) were identified from Hi-C data. e Scatterplots of log₂(shoot/root fold change) for two subsets of loops: weak (first quartile of Z-score) and strong (last quartile of Z-score)