Extended Data Fig. 7: Phospho-HDAC6 LLPS condensates disruption induces transcriptional reprogramming in TNBCs.
Related to Fig. 6. a. Genomic binding patterns of Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) and Pol II ChIP-seq with or without Nexturastat A treatment, centered around peak regions and 1 kb upstream and downstream of lost, common and new peaks. b. Box plots displaying the consistency of ATAC-seq and Pol II ChIP-seq signal. X-axis is grade of log2 (fold change) of ATAC signal and Y-axis is log2 (fold change) of pol II occupancy. The boxplots represent the median values and quartiles, and the whiskers represent the maximum and minimum values. P values were calculated by one-way ANOVA with multiple comparisons. c. Heatmap showing binding pattern of ATAC-seq and Pol II ChIP-seq surrounding new peaks. d-e. Volcano plot displaying the changes in gene expression following Nexturastat A, HPOB, Tubastatin A treatment or knockdown of HDAC6 in MDA-MB231 cells. Gene expression differences were assessed using DESeq2, which models read counts with a negative binomial distribution and uses two-tailed Wald tests to identify differentially expressed genes between conditions. f. Heatmap displaying the expression levels of differentially expressed genes, including tumor suppressor genes, proto-oncogenes, and immunomodulators, in MDA-MB-231 cells with or without Nexturastat A treatment. g-h. Gene set enrichment analysis (GSEA) enrichment plot showing the pathway of Antigen Processing and Presentation (GO:0019882) and TNFα Signaling via NF-κB for Nexturastat A treatment versus control and shHDAC6 versus shCtrl. GSEA was performed using a two-tailed non-parametric permutation-based method. Genes were first ranked by their correlation with the phenotype. P values in d-e were calculated by two-tailed Wald tests and g-h was performed using a two-tailed non-parametric permutation-based method. N = 3 biologically independent experiments.
