Additional file 1 of β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation
Creators: name: Mahmood, Syed Raza
name: Said, Nadine Hosny El
name: Gunsalus, Kristin C.
name: Percipalle, Piergiorgio
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1:Fig S1. TAD insulation changes show no correlation with transcription. a) Insulation scores of TADs identified at 50 kb resolution in control condition for each experiment. Insulation scores for the control condition are shown on the x axis and insulation scores for the same domain in the treatment condi- tion are shown on the y axis b) Boxplots showing average log2FoldChange in RNA-Seq expression for genes overlapping differential TADs. Boxes represent first and third quartiles with line in the box showing median and whiskers showing data within 1.5× interquartile range. p-values based on two-tailed, two-sample Wilcoxon-rank sum test. Fig S2. Non-switching compartments contain both up and down regulated genes. a) Volcano plots showing expression, accessibility and compartment of all genes overlapping stable A to B compartments. p-values based on two-tailed Wald test corrected for multiple testing using Benjamini–Hochberg procedure b) Bar plots showing percentage of differentially expressed genes up (log2FC&gt;2 &amp; padj&lt;=0.05) or downregulated (log2FC&lt;-2 &amp; padj&lt;=0.05) in A and B compartments. Fig S3. Compartment switching correlates with changes in chromatin accessibility. a) Volcano plots showing log2FoldChange in accessibility of all ATAC-Seq peaks overlapping stable and switching compartments. p-values based on two-tailed Wald test corrected for multiple testing using Benjamini– Hochberg procedure b) Heatmap showing pearson residuals and pvalue based on Pearson's. Chi-squared test with Yates' continuity correction. DP=Differential Peak (absolute log2FC&gt;=0.5 &amp; p.adj &lt;=0.05), NDP=Non-Differential Peak (absolute log2FC&lt;0.5 or p.adj &gt;0.05) c) Bar plots showing percentage of genic and intergenic differential peaks in switching compartments. Fig S4. Loss of β-actin triggers accumulation of H3K27ac in B to A switching regions. a) β-actin KO over WT Log2FC in rlog/VST normalized H3K27ac counts for each 50kb bin in switching and stable compartments. FIG S5. ABC enhancer predictions lie within recommended parameters in all cell types. Violin plots showing the distribution of average number of enhancers predicted per gene for all datasets. Fig S6. Magnitude of transcriptional change shows limited correlation with number of enhancers gained or lost. Scatierplot showing log2FC in RNA-Seq expression on the y-axis and number of enhancers gained or lost on the x-axis for compartment switching genes. Fig S7. Majority of enhancers in switching regions show zero Activity before or atier switching. Barplots showing the percentage of enhancers showing zero or non-zero Activity in each compartment. Only gained or lost enhancers linked to differentially expressed genes are shown. Fig S8. Gain or loss of enhancers is primarily driven by changes in Activity. Bar plots showing the number of enhancers gained or lost between WT and β-actin KO cells under assumptions of constant Activity or Contact. Only enhancers linked to differentially expressed genes are shown.