Figure 3

Cell-type specific gene expression predicts HIF-1 binding. For the indicated genes, IGB tracks for HIF-1, RNA Pol II, H3K4 me3 and H3K27 me3 are shown with identical scales between cell types. Representative data are shown for (a) HIF-1 hits common to both cell types, (b) HIF-1 ChIP hits unique to HepG2 or (c) U87 cells, and (d) HIF-1 binding sites reported in the literature but not bound in either cell type. (e) ChIP-qPCR analysis of HIF-1, H3K4 me3, RNA Pol II, and H3K27 me3 at the indicated loci. For HIF-1, H3K4 me3, and RNA Pol II ChIP, results are normalized to negative control regions located 5 kb and 10 kb upstream of the vascular endothelial growth factor (VEGF) gene. For H3K27 me3 ChIP, results are normalized to the promoter regions of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and aldolase A (ALDOA) genes. Data expressed as mean ± SD of independent replicates. (f) A set of well-validated HIF-1 target genes were partitioned based on whether HIF-1 binding was observed (U87-bound) or absent (U87-unbound) in U87 cells. Binding of HIF-1 is highly correlated with H3K4 me3 modification, RNA Pol II occupancy, and basal mRNA production. Statistical significance was determined by Student's t-test. For box plots, the median is indicated by a dark bar, the box bounds the lower and upper quartiles, the whiskers define the data range, and the notches represent the 95% confidence interval.