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The DNA-encoded nucleosome organization of a eukaryotic genome
Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition withExpand
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These dataExpand
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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factorExpand
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The accessible chromatin landscape of the human genome
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencersExpand
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FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity toExpand
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Evidence for nucleosome depletion at active regulatory regions genome-wide
The identification of nuclease-hypersensitive sites in an active globin gene and in the 5′ regions of fruit fly heat shock genes first suggested that chromatin changes accompany gene regulation inExpand
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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biologyExpand
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An integrated encyclopedia of DNA elements in the human genome
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project hasExpand
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Integrating regulatory motif discovery and genome-wide expression analysis
We propose motif regressor for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding andExpand
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Unlocking the secrets of the genome
Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at the crucial functional elements of fly and worm genomes could change that. TheExpand
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