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. 2023 Apr 6;55(5):841–851. doi: 10.1038/s41588-023-01366-2

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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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Extended Data Fig. 8 — (a) Scatterplot of effects of full SOX9 depletion for 3 h (x-axis) versus 24 h (y-axis) on nascent transcription, as assayed by SLAM-seq, for all SOX9-dependent genes (that is responding to full SOX9 depletion for 48 h in RNA-seq). Y = x line in red. (b) Effects of full SOX9 depletion on transcription of COL2A1, a known direct target of SOX9. Points represent SLAM-seq counts from biological replicates, adjusted p-value calculated by DESeq2. (c, d) For all REs responding to full depletion of SOX9 at 48 h, the effects of 3 h (c) or 24 h (d) full SOX9 depletion on chromatin accessibility (ATAC-seq, x-axis) or H3K27ac levels (ChIP-seq, y-axis) is plotted. (e) Distributions of observed (left) or predicted (right) fold-changes vs full SOX9 dosage at each concentration, stratified based on direction of transcriptional response to full SOX9 depletion (colors). N of groups by color: red, 184; grey, 10,339; blue, 197. Points and error bars represent median and 25th and 75th percentiles of distribution. ** p = 2.1e-12, *** p < 2.2e-16, two-sided Kruskal-Wallis test comparing the three groups. (f) Examples of predictions for a buffered (left) or sensitive (right) gene. (g) Median absolute deviation between observed and predicted dosage response curves for transcriptionally downregulated genes, stratified by number of SOX9-downregulated REs within 100 kb of TSS. Spearman rho for correlation and associated two-sided p-value are shown. N of groups from left to right: 227, 238, 173, 162, 105, 77, 55, 35, 32, 26, 49. Boxplot center represents median, box bounds represent 25th and 75th percentiles, and whiskers represent 5th and 95th percentiles. (h) Median ED₅₀ of REs within 100 kb of the TSS of transcriptionally downregulated genes stratified by sensitivity to SOX9 dosage. N of groups from left to right: 27, 27, 27, 28. Points and error bars represent median and 95% confidence intervals as computed by bootstrap (see Methods). All reported correlation coefficients in this figure are Spearman rho values.