Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

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Abstract

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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Figure 1: Approach for high-resolution mapping of accessible chromatin in human cells using DNase-array.
Figure 2: Chromatin accessibility at both megabase and fine scale.
Figure 3: Regulatory elements of the Th2 cytokine cluster.
Figure 4: Genomic distribution of DNase I hypersensitive sites relative to genes and transcripts.
Figure 5: Higher-order chromatin features revealed by DNase-array.

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Acknowledgements

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.

Author information

Correspondence to John A Stamatoyannopoulos.

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Competing interests

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.

Supplementary information

Supplementary Fig. 1

Reproducibility of DNase-array. (PDF 31 kb)

Supplementary Fig. 2

Conventional validation of DNase-array. (PDF 3110 kb)

Supplementary Table 1

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)

Supplementary Table 2

Comparison of DNase-array and conventional Southern validation assays. (PDF 116 kb)

Supplementary Table 3

Primer sequences referred to in Methods and Supplementary Methods. (PDF 53 kb)

Supplementary Methods (PDF 104 kb)

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