Distribution of DHSs, CpG islands, and transcription factor binding site (TFBS)-associated DHSs on different chromosomes.

<p>(A) Distribution of DHSs on the annotated genome. DHS peaks were mapped to each chromosome, and the densities of sites per Mb were determined (blue bars). (B) CpG island-related peaks on different chromosomes in the experimental sample, and controls 1 and 2. Controls 1 & 2 are two independent HeLaS3 DHS datasets downloaded from the UCSC website: DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington [<a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase</a>]. Numbers of CpG island-associated peaks in the experimental sample were significantly higher than in the two positive controls. (C) TFBS-related DHS peaks on the chromosomes from the experimental Short DHS DNA (Sample), and controls 1 and 2. Numbers of TFBS-associated DHS peaks were significantly higher in the Short DHS DNA than in the two controls.