Details

Autor(en) / Beteiligte

• Stamatoyannopoulos, John A
• Sabo, Peter J
• Kuehn, Michael S
• Thurman, Robert
• Johnson, Brett E
• Johnson, Ericka M
• Cao, Hua
• Yu, Man
• Rosenzweig, Elizabeth
• Goldy, Jeff
• Haydock, Andrew
• Weaver, Molly
• Shafer, Anthony
• Lee, Kristin
• Neri, Fidencio
• Humbert, Richard
• Singer, Michael A
• Richmond, Todd A
• Dorschner, Michael O
• McArthur, Michael
• Hawrylycz, Michael
• Green, Roland D
• Navas, Patrick A
• Noble, William S

Titel

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

Ist Teil von

• Nature methods, 2006-07, Vol.3 (7), p.511-518

Ort / Verlag

United States: Nature Publishing Group

Erscheinungsjahr

2006

Quelle

MEDLINE

Beschreibungen/Notizen

• 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% ( approximately 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.