Nature Methods1, 219 - 225 (2004)
Published online: 18 November 2004; | doi:10.1038/nmeth721
High-throughput localization of functional elements by quantitative chromatin profiling
Michael O Dorschner1, Michael Hawrylycz1, Richard Humbert1, James C Wallace1, Anthony Shafer1, Janelle Kawamoto1, Joshua Mack1, Robert Hall1, Jeff Goldy1, Peter J Sabo1, Ajay Kohli2, Qiliang Li2, Michael McArthur1
& John A Stamatoyannopoulos1
1
Department of Molecular Biology, Regulome, 2211 Elliott Avenue, Suite 600, Seattle, Washington 98121, USA.
2
Division of Medical Genetics, University of Washington, K−253 Health Sciences Building, Box 357720, 1705 NE Pacific Street, Seattle, Washington 98105, USA.
Correspondence should be addressed to John A Stamatoyannopoulos jstam@regulome.com
Identification of functional, noncoding elements that regulate transcription in the context of complex genomes is a major goal of modern biology. Localization of functionality to specific sequences is a requirement for genetic and computational studies. Here, we describe a generic approach, quantitative chromatin profiling, that uses quantitative analysis of in vivo chromatin structure over entire gene loci to rapidly and precisely localize cis-regulatory sequences and other functional modalities encoded by DNase I hypersensitive sites. To demonstrate the accuracy of this approach, we analyzed 300 kilobases of human genome sequence from diverse gene loci and cleanly delineated functional elements corresponding to a spectrum of classical cis-regulatory activities including enhancers, promoters, locus control regions and insulators as well as novel elements. Systematic, high-throughput identification of functional elements coinciding with DNase I hypersensitive sites will substantially expand our knowledge of transcriptional regulation and should simplify the search for noncoding genetic variation with phenotypic consequences.
MORE ARTICLES LIKE THIS
These links to content published by NPG are automatically generated.
Natureproducts is an online service detailing information about specific
products used in this article, you can view the product descriptions, request
information and compare with other similar products. The products
used are listed in alphabetical order.
300 kilobases of human genome sequence from diverse gene loci and cleanly delineated functional elements corresponding to a spectrum of classical cis-regulatory activities including enhancers, promoters, locus control regions and insulators as well as novel elements. Systematic, high-throughput identification of functional elements coinciding with DNase I hypersensitive sites will substantially expand our knowledge of transcriptional regulation and should simplify the search for noncoding genetic variation with phenotypic consequences.
FastStart buffer (Roche)
