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DNase I assay gets a face lift

Nature Reviews Genetics volume 7, page 590 (2006)Cite this article

For the past 25 years, the access we have had to active chromatin has been predominantly afforded by DNase I — an enzyme that preferentially snips accessible and presumably active promoters and enhancers. This traditional approach has now been given a makeover — by marrying it to microarrays two groups have now come up with related ways of turning the DNase I assay into a high-resolution genome-scale effort.

In both methods, DNA is digested by DNase I in the conventional manner. Then, in the DNase-chip method of Crawford et al., the cut ends of the DNA are each ligated to a biotinylated tag: these are then captured by a streptavidin column, washed off, labelled and then hybridized to the microarray. The technique devised by Peter Sabo and co-workers, called DNase-array, rests on the assumption that short stretches of open chromatin are likely to be cut not just once, but twice by DNase I in close proximity. This time the short fragments are separated by size on a sucrose gradient, and then isolated, labelled and hybridized to the microarray.

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ORIGINAL RESEARCH PAPERS

  1. Crawford, G. E. et al. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nature Methods 3, 503–509 (2006)

    Article  CAS  Google Scholar 

  2. Sabo, P. J. et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3, 511–518 (2006)

    Article  CAS  Google Scholar 

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Authors
  1. Tanita Casci
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Casci, T. DNase I assay gets a face lift. Nat Rev Genet 7, 590 (2006). https://doi.org/10.1038/nrg1927

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  • DOI: https://doi.org/10.1038/nrg1927

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