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Article
Nature Methods - 3, 511 - 518 (2006)
Published online: 21 June 2006; | doi:10.1038/nmeth890

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

Peter J Sabo1, 6, Michael S Kuehn1, 2, 6, Robert Thurman1, 2, Brett E Johnson2, Ericka M Johnson2, Hua Cao2, Man Yu2, Elizabeth Rosenzweig2, Jeff Goldy1, Andrew Haydock1, Molly Weaver1, Anthony Shafer1, Kristin Lee1, Fidencio Neri1, Richard Humbert1, Michael A Singer3, Todd A Richmond3, Michael O Dorschner1, Michael McArthur4, Michael Hawrylycz5, Roland D Green3, Patrick A Navas2, William S Noble1 & John A Stamatoyannopoulos1

1  Department of Genome Sciences, University of Washington, 1705 NE Pacific St., Box 357730, Seattle, Washington 98195, USA.

2  Division of Medical Genetics, Department of Medicine, University of Washington, 1705 NE Pacific St., Box 357730, Seattle, Washington 98195, USA.

3  Nimblegen Systems, Inc., 1 Science Court, Madison, Wisconsin 53711, USA.

4  Department of Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.

5  Allen Institute for Brain Sciences, 551 N. 34th Street, Seattle, Washington 98103, USA.

6  These authors contributed equally to this work.

Correspondence should be addressed to John A Stamatoyannopoulos jstam@u.washington.edu

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% (approx30 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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DNA microarray (Nimblegen)
DNase I (Roche)
LE-80 Ultracentrifuge (Beckman)
PCR purification (Qiagen)
random nonamer oligonucleotides (TriLink Biotechnologies)
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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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