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. 2023 Jun 6;14:3303. doi: 10.1038/s41467-023-38429-1

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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, b Examples of genes of various sizes where the TSS is in the A compartment while the TTS is in the B compartment. GRO-seq signal is shown as an indicator of the gene’s transcription status. Black rectangles indicate regions of TSSs that reside in the A compartment. c Sizes of genes with concordant (labeled A/A & green) or discordant (labeled A/B & purple) compartments. * indicates p < 2.2e-16 two-sided Wilcoxon Rank Sum, n = 6021 (AA) and 510 (AB). Source data are provided as a Source Data file. d Percentage of TTSs that localize to the B compartment for genes of various sizes that have the TSS in the A compartment. Source data are provided as a Source Data file. e Average profile of the eigenvector at discordant genes. The vertical line indicates the distance where the average eigenvector value equals zero. f Pausing Index of genes with concordant (labeled A/A & green) or discordant (labeled A/B & purple) compartments. * indicates p < 2.2e-16 two-sided Wilcoxon Rank Sum, n = 6021 (AA) and 510 (AB). Source data are provided as a Source Data file. g Percentage of TTS that localize to the B compartment for genes with different pausing statuses and have the TSS in A. Source data are provided as a Source Data file. h Scaled average profiles of the compartment eigenvector for elongating (blue) or paused (red) discordant genes. The vertical line indicates the distance where the average eigenvector value equals zero.