Fig. 4

HIF1α binds to and regulates the expression of over 200 lens genes: A Differential gene expression analysis by RNA-seq reveals 219 upregulated genes (log2 fold change FPKM > 0.6, p < 0.05) and 307 downregulated genes (log2 fold change FPKM < − 0.6, p < 0.05) in primary lens cells treated with the HIF1α activator DMOG (1 mM) relative to control untreated cells. B Percent of differentially expressed genes (DEG) (|log2 fold change FPKM| > 0.6, p < 0.05) and non-differentially expressed genes (NON-DEG) (p > 0.05) that have a HIF1α-DNA binding complex. Differentially expressed genes are more significantly associated with HIF1α binding compared to non-differentially expressed genes (X²-test, ***p < 0.001). C Same analysis as (B) but separated by distance between the transcription start site (TSS) and the HIF1α-DNA binding complex. (X²-tests, ***p < 0.001, **p < 0.01, ns p > 0.05). D Heatmap of the top 100 differentially expressed genes sorted by hierarchal clustering. E Percent of upregulated genes, downregulated genes and NON-DEG that have a HIF1α-DNA binding complex. Upregulated and downregulated genes are significantly associated with HIF1α-DNA binding complexes. (X²-test, ***p < 0.001, **p < 0.01). F Same analysis as (E) but separated by distance between the transcription start site (TSS) and the HIF1α-DNA binding complex. (X²-test, ***p < 0.001). (G) Heatmap of differentially expressed (DEGs) and non-differentially expressed (Non-DEGs) genes with a HIF1α-DNA binding complex (DEGs). H Same as (G) but separated by distance from the transcription start site (0-3kbp, 3-10kbp, 10-100kbp, and over 100kbp). I HIF1α CUT&RUN coupled to RNA-seq analysis elucidates a significant relationship between HIF1α binding within 3kbp of the TSS and gene upregulation. In contrast, HIF1α binding between 3-10kbp of the TSS is significantly associated with gene downregulation. J Overlap of number of genes that are significantly upregulated or significantly downregulated and genes with HIF1α-DNA binding complexes within 100kbp of the transcription start site