Extended Data Fig. 3: PAX8 and HNF1B support chromatin accessibility at distal enhancers.
From: The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer
a. Relative PAX8 and HNF1B mRNA expression as determined by qRT-PCR in 786-M1A cells. Data points, independent RNA preps (shPAX8 N = 4, shHNF1B N = 3). Mean and SEM. Two-sided Kruskal-Wallis test. b. Western blot showing PAX8 and HNF1B expression in 786-M1A cells (representative image, N = 2). c. ATAC-seq data analysis identifying genomic regions with altered accessibility upon shRNA-mediated PAX8 and HNF1B depletion in 786-M1A cells (two shRNAs with three replicates each). Adjusted two-sided p-values and fold changes derived by DESeq2. d. Heatmap showing ATAC-seq signal in the indicated cell lines for regions with reduced accessibility upon PAX8 and HNF1B depletion, respectively (three replicates for each shRNA). e-f. The most significant de novo DNA motif enriched in the peak set with reduced accessibility upon PAX8 (e) and HNF1B (f) depletion. g. Distribution of ATAC-seq peaks that change upon PAX8 or HNF1B depletion in relation to known transcripts. TTS, transcription termination site. h. Overlap between the peak sets with reduced accessibility upon PAX8 and HNF1B depletion in ccRCC cells and peaks sets characteristic of normal kidney and renal cancer identified by DNAse I hypersensitivity mapping in ref. 29. Top axis, odds ratio of overlap (black), 95% confidence interval. Bottom axis, p-value, one-sided Fisher’s exact test (red). i. Enrichment of known DNA motifs in the peak set that shows reduced accessibility upon PAX8 depletion. j. Enrichment of known DNA motifs in the peak set that shows reduced accessibility upon HNF1B depletion. k. Enrichment of known DNA motifs in the peak set that shows increased accessibility upon PAX8 depletion. l. Enrichment of known DNA motifs in the peak set that shows increased accessibility upon HNF1B depletion. m–n. Mean normalised counts within ccRCC (KIRC)-specific (m) and KIRP-specific (n) ATAC-seq regions in comparison to all other cancer types in the TCGA data set. P-values indicate the significance of enrichment of the de novo PAX8 and HNF1B motifs in the ccRCC and KIRP-specific peak sets. Boxplot, median and interquartile range. Whiskers, data range. N = 26,633 regions for KIRC; N = 68,966 regions for KIRP.
