Physical Properties of Naked DNA Signal Gene Regulatory Regions

In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. Therefore, DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in the issue, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Here, we have analyzed the physical properties of yeast DNA by a combination of genome-wide nuclease digestion measurements (of both nucleosomal and naked DNA) with molecular dynamics simulations of short DNA fragments