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      High-resolution mapping and characterization of open chromatin across the genome.

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          Abstract

          Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. We employed high-throughput sequencing and whole-genome tiled array strategies to identify DNase I HS sites within human primary CD4+ T cells. Combining these two technologies, we have created a comprehensive and accurate genome-wide open chromatin map. Surprisingly, only 16%-21% of the identified 94,925 DNase I HS sites are found in promoters or first exons of known genes, but nearly half of the most open sites are in these regions. In conjunction with expression, motif, and chromatin immunoprecipitation data, we find evidence of cell-type-specific characteristics, including the ability to identify transcription start sites and locations of different chromatin marks utilized in these cells. In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure.

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          Author and article information

          Journal
          Cell
          Cell
          Elsevier BV
          1097-4172
          0092-8674
          Jan 25 2008
          : 132
          : 2
          Affiliations
          [1 ] Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA.
          Article
          S0092-8674(07)01613-3 NIHMS106456
          10.1016/j.cell.2007.12.014
          2669738
          18243105
          c4510e21-56f3-4d1d-a3ba-33ac684585e2
          History

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