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, Stamatoyannopoulos John A
Department of Genome Sciences, University of Washington, 1705 NE Pacific St., Box 357730, Seattle, Washington 98195, USA.
Nat Methods. 2006 Jul;3(7):511-8. doi: 10.1038/nmeth890.
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.
关键DNA序列对调控机制的局部可及性是人类基因调控的关键要求。在此，我们描述了一种高分辨率、全基因组规模的方法，通过使用平铺式DNA微阵列（DNase-array）测量作为基因组位置连续函数的DNase I敏感性来量化染色质可及性。我们在人类基因组的1%（约30 Mb）范围内展示了这种方法，在其中我们以高敏感性和特异性定位了2690个经典的DNase I超敏感位点，还绘制了染色质结构的更大规模模式。DNase I超敏感位点在转录起始位点（TSS）周围呈现明显聚集，尽管大多数标记的是非启动子功能元件。我们还开发了一种计算方法来可视化染色质结构的高阶特征。这揭示了人类染色质组织由DNase I超敏感位点的大（100 - 500 kb）“超级簇”主导，这些超级簇既包含基因丰富区域，也包含基因贫乏区域。DNase-array是一种用于系统阐述复杂基因组顺式调控结构的强大且直接的方法。
