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. 2024 Apr 2;43(9):1799–1821. doi: 10.1038/s44318-024-00089-2

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© The Author(s) 2024

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 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/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) PCA plot showing a low-dimensional representation of dynamic transcriptome analysis (DTA) samples without negative control. (B) Distribution of mRNA synthesis rate values measured by DTA separated into synthesis quartiles. (C) Box plots showing residence time distributions (y-axis) for all GTFs (x-axis) within the indicated synthesis quartile. Values for reliably fast sites (<1 min) were randomly generated for plotting purposes and are highlighted by the gray area. The middle line represents the median, the lower and upper edges of the boxes represent the first and third quartiles, and the whiskers represent the 1.5 * interquartile range. P values represent the results of Kruskal–Wallis tests for a given GTF. P value symbols (Wilcoxon test): n.s. p ≥ 0.05, *p ≤ 0.05, **p ≤ 0.01, ***p < 0.001, ****p ≤ 0.0001. Number of observations (n): TBP- Q1: 216, Q2: 324, Q3: 427, Q4: 605; TFIIA- Q1: 239, Q2: 320, Q3: 397, Q4: 426; TFIIB Q1: 302, Q2: 486, Q3: 581, Q4: 606; TFIIF- Q1: 253, Q2: 358, Q3: 432, Q4: 517; TFIIE- Q1: 416, Q2: 584, Q3: 610, Q4: 553. (D) Violin plots showing the distributions of log₂ transformed transcription efficiency (TE, y-axis) for each GTF (x-axis). TE indicates the number of mRNA molecules synthesized during one binding event. The points show the medians of the log₂ transformed TE values. Mean and median TE values are shown above the plots. Number of observations (n): TBP = 1572, TFIIA = 1382, TFIIB = 1975, TFIIF = 1560, TFIIE = 2163. (E) PCA plot showing a low-dimensional representation of gene targets based on GTF residence times. Each gray point is a gene, color map shows the mean synthesis rate of genes under a given area. The percentage within the axis labels indicates the percentage of variance explained by a given PC. (F) Pearson’s correlation coefficients (y-axis) between the indicated PCs (panel title) and GTF (x-axis) residence times. (G) Pearson’s correlation coefficients (y-axis) between PCs (x-axis) and synthesis rates. Source data are available online for this figure.