Figure 5

DNase I hypersensitive sites (DHS) are enriched at promoters of oncogenes and tumor suppressor loci in the colorectal cancer genome. (A) Sucrose gradient purification of DHS fragments resolved on High-resolution Bio-Anaylzer gels before deep sequencing. (B) Left: distribution analysis and overlap between HeLa DHS and HeLa CENP-A; and SW480 DHS and SW480 CENP-A. Right: Genomic locations of CENP-A hotspots coinciding with DHS shown as a percentage of total, color-coded as in (B). (C) DHS identified in this study wholly belong to the large compendium of DHS identified by ENCODE in 129 cell lines. (D) Examples of DHS profiles for individual genes demonstrate that the promoters of some oncogenes are preferentially accessible in SW480 cancer cells. The gene for CENP-A itself has an increased DHS peak over its promoter in SW80 cells, correlating with increase in mRNA and protein levels for CENP-A in SW480 cells.