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High-throughput analysis of gene regulation, DNA synthesis in Cold Spring Harbor Protocols
Date:2/1/2010

COLD SPRING HARBOR, N.Y. (Mon., Feb. 1, 2010) -- Mapping DNase I hypersensitive sites has long been the standard method for identifying genetic regulatory elements such as promoters, enhancers, silencers, insulators, and locus control regions. Sequences that are nucleosome-depleted, presumably to provide access for transcription factors, are selectively digested by DNase I. Traditional low-throughput methods use Southern blots to then identify these hypersensitive sites. In the February issue of Cold Spring Harbor Protocols (http://www.cshprotocols.org/TOCs/toc2_10.dtl), Gregory Crawford and colleagues from Duke University (http://www.genome.duke.edu/people/faculty/crawford/) present "DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements Across the Genome from Mammalian Cells." DNase-seq is a high-throughput method that identifies DNase I hypersensitive sites across the whole genome by capturing DNase-digested fragments and applying next-generation sequencing techniques. In a single experiment, DNase-seq can identify most active regulatory regions from potentially any cell type, from any species with a sequenced genome. As one of February's featured articles, it is freely available on the journal's website (http://cshprotocols.cshlp.org/cgi/content/full/2010/2/pdb.prot5384).

The incorporation of thymidine analogues, such as 5-bromo-2'-deoxyuridine (BrdU), into newly synthesized DNA is a powerful tool for analysis of DNA replication, repair and other aspects of DNA metabolism. In "Genome-Wide Analysis of DNA Synthesis by BrdU Immunoprecipitation on Tiling Microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae," Oscar Aparicio and colleagues from the University of Southern California (

Contact: David Crotty
crotty@cshl.edu
516-422-4007
Cold Spring Harbor Laboratory
Source:Eurekalert

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