Fig. 6: BMAL1 chromatin occupancy correlates with BMAL1-dependent expression.

A, C Venn diagrams depicting the numbers of genomic sites (“peaks”) identified in chromatin fragments isolated by CUT&RUN procedure from 786O cells using antibodies recognizing BMAL1 (blue) or HIF2α (red, pink) that are associated with genes that were detected in RNA prepared from 786O cells expressing shRNA targeting a control sequence (shControl) or BMAL1 (shBMAL1). B, D Heatmaps depicting differentially expressed genes (DEGs) associated with the chromatin binding sites bound by BMAL1 and/or HIF2α depicted in (A, B) as indicated. (FDR < 0.1 by DESeq2 for shControl vs. shARNT or shControl vs. shBMAL1). E Pathway enrichment in HIF2a-occupied genes grouped by BMAL1 occupancy and impact of shBMAL1. The x-axis represents the Enrichment Ratio, and the y-axis represents enriched GOBP pathways for genes associated with HIF2α peaks in 786O cells expressing shControl with at least 5 genes, FDR < 0.05, and fold enrichment >2. Expression of these genes was increased or decreased in 786O cells expressing shBMAL1 compared to 786O cells expressing shControl. Source data are provided as a Source Data file.