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TY - JOUR AU - Dorschner, Michael O AU - Hawrylycz, Michael AU - Humbert, Richard AU - Wallace, James C AU - Shafer, Anthony AU - Kawamoto, Janelle AU - Mack, Joshua AU - Hall, Robert AU - Goldy, Jeff AU - Sabo, Peter J AU - Kohli, Ajay AU - Li, Qiliang AU - McArthur, Michael AU - Stamatoyannopoulos, John A PY - 2004 DA - 2004/12/01 TI - High-throughput localization of functional elements by quantitative chromatin profiling JO - Nature Methods SP - 219 EP - 225 VL - 1 IS - 3 AB - 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. SN - 1548-7105 UR - https://doi.org/10.1038/nmeth721 DO - 10.1038/nmeth721 ID - Dorschner2004 ER -