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

Abstract

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.

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Acknowledgements

We thank E. Margulies and the Multiple Species Alignment group from the ENCODE consortium for kindly providing the sequence conservation track. We also thank S. Anderson, A. Elkahloun, and the National Human Genome Research Institute Microarray core for excellent technical assistance. This research was supported by the Intramural Research Program of the US National Human Genome Research Institute, National Institutes of Health.

Author information

Competing interests

R.G. is employed by NimbleGen Systems.

Correspondence to Francis S Collins.

Supplementary information

  1. Supplementary Fig. 1

    Control to rule out sequence bias of DNaseI enzyme. (PDF 368 kb)

  2. Supplementary Table 1

    Positive predictive value (PPV) of DNase-chip as assessed by real-time (RT) PCR. (DOC 43 kb)

  3. Supplementary Protocol

    DNase-chip protocol. (DOC 31 kb)

  4. Supplementary Methods (DOC 39 kb)

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Figure 1: DNase-chip protocol.
Figure 2: Confirmatory real-time PCR analysis.
Figure 3: Comparison of DNase-chip and MPSS data for CD4+ T cells.
Figure 4: Identification of cell type–specific DNase I hypersensitive sites.
Figure 5: Location of DNase I hypersensitive sites relative to the annotated genome.
Figure 6: Expression of genes relative to proximity to DNase I hypersensitive sites.