DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.
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.
Crawford
Gregory E
GE
National Human Genome Research Institute, National Institutes of Health, Building 31, Room 4B09, Bethesda, Maryland 20892, USA.
Davis
Sean
S
Scacheri
Peter C
PC
Renaud
Gabriel
G
Halawi
Mohamad J
MJ
Erdos
Michael R
MR
Green
Roland
R
Meltzer
Paul S
PS
Wolfsberg
Tyra G
TG
Collins
Francis S
FS
D002478:Cells, Cultured; D003850:Deoxyribonuclease I / Q000737:chemistry* / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012045:Regulatory Sequences, Nucleic Acid; D012680:Sensitivity and Specificity
D003850:Deoxyribonuclease I