DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

Journal Article (Journal Article)

Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including promoters, enhancers, silencers and locus control regions. Although Southern blots are the traditional method of identifying DNase I hypersensitive sites, the conventional manual method is not readily scalable to studying large chromosomal regions, much less the entire genome. Here we describe DNase-chip, an approach that can rapidly identify DNase I hypersensitive sites for any region of interest, or potentially for the entire genome, by using tiled microarrays. We used DNase-chip to identify DNase I hypersensitive sites accurately from a representative 1% of the human genome in both primary and immortalized cell types. We found that although most DNase I hypersensitive sites were present in both cell types studied, some of them were cell-type specific. This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome.

Full Text

Duke Authors

Cited Authors

  • Crawford, GE; Davis, S; Scacheri, PC; Renaud, G; Halawi, MJ; Erdos, MR; Green, R; Meltzer, PS; Wolfsberg, TG; Collins, FS

Published Date

  • July 2006

Published In

Volume / Issue

  • 3 / 7

Start / End Page

  • 503 - 509

PubMed ID

  • 16791207

Pubmed Central ID

  • PMC2698431

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth888


  • eng

Conference Location

  • United States