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Identifying and Characterizing Regulatory Sequences in the Human Genome with Chromatin Accessibility Assays

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Program in Computational Biology and Bioinformatics, Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA
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Depts of Genetics and Biology, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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Author to whom correspondence should be addressed.
Genes 2012, 3(4), 651-670; https://doi.org/10.3390/genes3040651
Received: 16 May 2012 / Revised: 17 August 2012 / Accepted: 25 September 2012 / Published: 15 October 2012
(This article belongs to the Special Issue Junk DNA' is not Junk)
After finishing a human genome reference sequence in 2002, the genomics community has turned to the task of interpreting it. A primary focus is to identify and characterize not only protein-coding genes, but all functional elements in the genome. The effort includes both individual investigators and large-scale projects like the Encyclopedia of DNA Elements (ENCODE) project. As part of the ENCODE project, several groups have identified millions of regulatory elements in hundreds of human cell-types using DNase-seq and FAIRE-seq experiments that detect regions of nucleosome-free open chromatin. ChIP-seq experiments have also been used to discover transcription factor binding sites and map histone modifications. Nearly all identified elements are found in non-coding DNA, hypothesizing a function for previously unannotated sequence. In this review, we provide an overview of the ENCODE effort to define regulatory elements, summarize the main results, and discuss implications of the millions of regulatory elements distributed throughout the genome. View Full-Text
Keywords: open chromatin; DNaseI; transcriptional regulation; ENCODE open chromatin; DNaseI; transcriptional regulation; ENCODE
MDPI and ACS Style

Sheffield, N.C.; Furey, T.S. Identifying and Characterizing Regulatory Sequences in the Human Genome with Chromatin Accessibility Assays. Genes 2012, 3, 651-670.

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