Localized accessibility of critical DNA sequences to the regulatory machinery is a key requirement for regulation of human genes. Here we describe a high-resolution, genome-scale approach for quantifying chromatin accessibility by measuring DNase I sensitivity as a continuous function of genome position using tiling DNA microarrays (DNase-array). We demonstrate this approach across 1% (∼30 Mb) of the human genome, wherein we localized 2,690 classical DNase I hypersensitive sites with high sensitivity and specificity, and also mapped larger-scale patterns of chromatin architecture. DNase I hypersensitive sites exhibit marked aggregation around transcriptional start sites (TSSs), though the majority mark nonpromoter functional elements. We also developed a computational approach for visualizing higher-order features of chromatin structure. This revealed that human chromatin organization is dominated by large (100–500 kb) 'superclusters' of DNase I hypersensitive sites, which encompass both gene-rich and gene-poor regions. DNase-array is a powerful and straightforward approach for systematic exposition of the cis-regulatory architecture of complex genomes.
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This work was supported by grants from the US National Institute of General Medical Sciences and the National Human Genome Research Institute to J.A.S. and W.S.N.
R.D.G. is an employee of NimbleGen Systems, a manufacturer of microarrays, which potentially stands to benefit from the results published in this article.
Reproducibility of DNase-array. (PDF 31 kb)
Conventional validation of DNase-array. (PDF 3110 kb)
Shown are location (chromosome, position) of 2,690 DHSs and distance of each to 5′ and 3′ ends of the nearest known gene, mRNA, and spliced EST from the UCSC database. (PDF 226 kb)
Comparison of DNase-array and conventional Southern validation assays. (PDF 116 kb)
Primer sequences referred to in Methods and Supplementary Methods. (PDF 53 kb)
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