DNase-chip: A High Resolution Method to Identify DNaseI Hypersensitive Sites using Tiled Microarrays

Authors

Gregory Crawford

Summary

Mapping DNaseI hypersensitive (HS) sites is an accurate method of identifying the location of gene regulatory elements, including promoters, enhancers, silencers, and locus control regions. While Southern blots have been the traditional method of identifying DNaseI HS 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 DNaseI HS sites for any region of interest, or potentially for the entire genome, by using tiled microarrays. We have used DNase-chip to identify DNaseI HS sites accurately from a representative 1% of the human genome in both primary and immortalized cell types. We find that although most HS sites are present in both cell types studied, some are cell type specific. This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome.

Further details

The protocol was published on Protocol Exchange in 2006. To see the entire protocol, click on the source link.

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