The ENCODE Project

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RESEARCH HIGHLIGHTS GENOMICS The ENCODE project The second, genome-wide phase of a particular product (for instance, a protein ENCODE-defined functional element in at the Encyclopedia of DNA Elements or noncoding RNA) or has a consistent bio- least one examined cell type; an even larger (ENCODE) project is being reported. chemical property (for instance, being bound fraction (99%) lies nearby such an element The function of most of the human by protein or having a particular biochemical (within 1.7 kilobases). An examination of genome is unknown. Protein-coding genes mark). previously identified disease-associated account for only a small fraction (about 3%) The laboratories in the ENCODE Project single-nucleotide polymorphisms shows that of the total genome sequence; most func- Consortium have developed and applied a they are enriched in ENCODE-annotated tional genomic sequences are likely to have huge range of sequencing-based techniques regions, suggesting hypotheses for functional regulatory roles. Understanding human to map functional elements across the consequences of single-nucleotide polymor- gene organization and regulation and their genome. To put it succinctly, the ENCODE phisms that can be further tested. impact on normal and disease phenotypes project has mapped chromatin state and The data generated by ENCODE are vast requires that functional elements be mapped structure, three-dimensional genome organi- and can be only very briefly summarized and annotated across the genome. This is the zation, DNA methylation, transcription fac- here. The collected ENCODE papers may goal of the ENCODE project. tor binding, RNA transcription and protein be examined at http://www.encodeproject. The initial 5-year pilot phase of the proj- expression genome wide. Experiments were org/ENCODE/pubs.html or explored with ect focused on 1% of the human genome conducted in multiple cell types, with the a dedicated visualization tool at http://www. sequence. The second 5-year phase of highest priority given to widely studied cell nature.com/ENCODE/. ENCODE, which began in 2007 and is now lines but with the list also including a human Natalie de Souza coming to fruition, has extended the analy- embryonic stem cell line and, in some cases, RESEARCH PAPERS sis of functional elements genome wide. A primary cells. The ENCODE Project Consortium. An integrated functional element as defined by ENCODE It is striking that a large fraction (80%) encyclopedia of DNA elements in the human genome. is a genomic sequence that either encodes of the genome overlaps with at least one Nature 489, 57–74 (2012). © 2012 Nature America, Inc. All rights reserved. America, Inc. © 2012 Nature npg 1046 | VOL.9 NO.11 | NOVEMBER 2012 | NATURE METHODS.

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ENCODE Regions Identification of Higher-Order Functional Domains in the Human
Downloaded from www.genome.org on August 14, 2007 Identification of higher-order functional domains in the human ENCODE regions Robert E. Thurman, Nathan Day, William S. Noble and John A. Stamatoyannopoulos Genome Res. 2007 17: 917-927 Access the most recent version at doi:10.1101/gr.6081407 Supplementary "Supplemental Research Data" data http://www.genome.org/cgi/content/full/17/6/917/DC1 References This article cites 45 articles, 17 of which can be accessed free at: http://www.genome.org/cgi/content/full/17/6/917#References Article cited in: http://www.genome.org/cgi/content/full/17/6/917#otherarticles Open Access Freely available online through the Genome Research Open Access option. Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here Notes To subscribe to Genome Research go to: http://www.genome.org/subscriptions/ © 2007 Cold Spring Harbor Laboratory Press Downloaded from www.genome.org on August 14, 2007 Methods Identification of higher-order functional domains in the human ENCODE regions Robert E. Thurman,1,2 Nathan Day,3 William S. Noble,2,3 and John A. Stamatoyannopoulos2,4 1Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; 2Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 3Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains.
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Developing and Implementing an Institute-Wide Data Sharing Policy Stephanie OM Dyke and Tim JP Hubbard*
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Estimating the Number of Unseen Variants in the Human Genome
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The ENCODE (Encyclopedia of S DNA Elements) Project
GGENESENES IN INAACTIONCTION VIEWPOINT ECTION The ENCODE (ENCyclopedia Of S DNA Elements) Project PECIAL The ENCODE Project Consortium*. S The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional approaches, such as cDNA-cloning efforts elements in the human genome sequence. The pilot phase of the Project is focused on (4, 5) and chip-based transcriptome analyses a specified 30 megabases (È1%) of the human genome sequence and is organized as (6, 7), have revealed the existence of many an international consortium of computational and laboratory-based scientists transcribed sequences of unknown function. working to develop and apply high-throughput approaches for detecting all sequence As a reflection of this complexity, about 5% elements that confer biological function. The results of this pilot phase will guide of the human genome is evolutionarily future efforts to analyze the entire human genome. conserved with respect to rodent genomic sequences, and therefore is inferred to be With the complete human genome sequence namics; undoubtedly, additional, yet-to-be- functionally important (8, 9). Yet only about now in hand (1–3), we face the enormous defined types of functional sequences will one-third of the sequence under such selec- challenge of interpreting it and learning how also need to be included. tion is predicted to encode proteins (1, 2). to use that information to understand the To illustrate the magnitude of the chal- Our collective knowledge about putative biology of human health and disease. The lenge involved, it only needs to be pointed out functional, noncoding elements, which repre- ENCyclopedia Of DNA Elements (ENCODE) that an inventory of the best-defined func- sent the majority of the remaining functional Project is predicated on the belief that a tional components in the human genome— sequences in the human genome, is remark- comprehensive catalog of the structural and the protein-coding sequences—is still incom- ably underdeveloped at the present time.
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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
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National Human Genome Research Institute EA Feingold, PJ G
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Multiple Genes Encode Nuclear Factor 1-Like Proteins That Bind To
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