Finding Footprints in the Genome

The idea behind this method is simple: genomic DNA that is bound by proteins is shielded from DNase I, an enzyme that digests the DNA, leaving an intact DNA fragment. This DNA fragment is a footprint of the protein, corresponding in size to the bound region. The sequence of the footprint reveals the binding sequence of the protein and therefore often allows the identification of the regulatory proteins.

John Stamatoyannopoulos and colleagues scaled this approach to a genome-wide level by using a technique for massively parallel sequencing of the DNase I-cleaved genomic DNA. They systematically mapped all footprints across the yeast genome and analyzed them for new and known protein binding patterns. As a result the authors were able to draw an intricate map of regulatory proteins along the entire yeast DNA.

This technique can be adapted to any organism with a sequenced genome and will allow new insights into the fine-scale architecture of genome regulation.

Author contact:

John Stamatoyannopoulos (University of Washington, Seattle, WA, USA)
E-mail: jstam@u.washington.edu

Abstract available online.

(C) Nature Methods press release.

Message posted by: Trevor M. D'Souza