Figure 1

HIF-1 preferentially binds to promoters of transcriptionally active genes. (a) Proportional Venn diagrams of genes with mRNA expression significantly (P-value < 0.01) up- or down-regulated after 12 h of hypoxia in U87, HepG2, and MDA-MB231 cells. (b) Results of HIF-1 ChIP-chip analysis on promoter arrays (U87) was highly similar to analysis on whole genome arrays (HepG2). Representative Integrated Genome Browser tracks are shown with the same scale for both cell types. (c) ChIP-quantitative PCR validation of U87 HIF-1 ChIP hits. Data expressed as fold enrichment relative to input (mean ± standard deviation of independent replicates). An increase of more than two-fold (red dashed line) was considered positive for HIF-1 binding. 10 kbUP and 5 kbUP are negative control regions. (d) Approximately half of all genes in the genome are expressed (Present MAS5 call) and half are not expressed (Absent MAS5 call) under normal growth conditions (All) in both cell lines. Upon stabilization by hypoxia, HIF-1 preferentially binds (HIF1-bound) to the promoter of genes that are present under normal growth conditions. Statistical significance determined by Fisher exact test. (e) Genes bound by HIF-1 in U87 or HepG2 cells (HIF1-bound) have higher levels of basal mRNA expression than the normal distribution of all genes (All). Top panel: density plots of genes at indicated mRNA levels. Bottom panel: box plot of all genes (All) compared to genes bound by HIF-1 (HIF1-bound). Statistical significance 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.