ENCODE

ENCODE
ENCODE
Content Description whole-genome data Contact Research center Laboratory Authors University of California Santa Cruz Center for Biomolecular Science and Engineering Brian J Raney [1]

Primary Citation PMID 21037257 Release date 2010 Access Website encodeproject.org Tools Miscellaneous [2]

The Encyclopedia of DNA Elements (ENCODE) is a public research consortium launched by the US National Human Genome Research Institute (NHGRI) in September 2003.[1][3][4][5] The goal is to find all functional elements in the human genome, one of the most critical projects by NHGRI after it completed the successful Human Genome Project. All data generated in the course of the project will be released rapidly into public databases. On 5 September 2012, initial results of the project were released in a coordinated set of 30 papers published in the journals Nature, Genome Biology, and Genome Research.[6][7] These publications combine to show that at least 80% of the human genome is biologically active, rather than being mainly junk DNA as once believed.[8]

Pilot phase
The project was initiated with a $12 million pilot phase. The aim of this was to evaluate a variety of different methods for use in later stages. Essentially this involved using a number of existing techniques to analyse a portion of the genome equal to about 1% (30mb). The results of these analyses will then be evaluated based on their ability to identify regions of DNA which are known or suspected to contain functional elements. 50% of the sample area selected for study under this phase was manually selected whilst the other 50% was selected at random.[9] The manually selected regions have been selected based on the presence of well studied genes and the availability of comparative data. Methods currently being evaluated include chromatin immunoprecipitation (ChIP) and quantitative PCR. The ENCODE pilot project rapidly released all of its data into public databases.[10] The pilot phase was successfully finished and the results were published in June 2007 in Nature[4] and a special issue of Genome Research.[11]

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Production phase
In September 2007, NHGRI began funding the production phase of the ENCODE project. In this phase, the goal is to analyze the entire genome and to conduct "additional pilot-scale studies".[12] Like the pilot project, the production effort is organized as an open consortium. In October 2007, NHGRI awarded grants totaling more than $80 million over four years.[13] The production phase also includes a Data Coordination Center, a Data Analysis Center, and a Technology Development Effort.[14]

As of 2010, over 1,000 genome-wide data sets were produced by the ENCODE project. In conjunction, these data sets show which regions are transcribed into RNA, which regions are likely to control the genes that are used in a particular type of cell, and which regions are associated with a wide variety of proteins. The primary assays used in ENCODE are ChIP-seq, DNaseI Hypersensitivity, and RNA-seq, and assays of DNA methylation. In September 2012, the project released a much more extensive set of results, in 30 papers published simultaneously in several journals, including six in Nature and a special issue of the journal Genome Research.[15] The most striking finding was that the fraction of human DNA that is biologically active is considerably higher than even the most optimistic previous estimates. In an overview paper, the ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.[16] Much of this was found to be involved in controlling the expression levels of coding DNA, which makes up less than 1% of the genome.

Image of ENCODE data in the UCSC Genome Browser. This shows several tracks containing information on gene regulation. The gene on the left is transcribed in a wide variety of cells. The gene on the right is only transcribed in a few types of cells, including embryonic stem cells.

modENCODE project
The Model Organism ENCyclopedia Of DNA Elements (modENCODE) project is a continuation of the original ENCODE project targeting the identification of functional elements in selected model organism genomes, specifically, Drosophila melanogaster and Caenorhabditis elegans.[17] The extension to model organisms permits biological validation of the computational and experimental findings of the ENCODE project, something that is difficult or impossible to do in humans.[17] Funding for the modENCODE project was announced by the National Institutes of Health (NIH) in 2007 and included several different research institutions in the US.[18][19] In late 2010, the modENCODE consortium unveiled its first set of results with publications on annotation and integrative analysis of the worm and fly genomes in Science.[20][21] Data from these publications is available from modencode.org [22].

FactorBook
An analysis of transcription factor binding data generated by the ENCODE project is available in the web-accessible repository FactorBook.

References
[1] Raney, Brian J; Cline, Melissa S; Rosenbloom, Kate R; Dreszer, Timothy R; Learned, Katrina; Barber, Galt P; Meyer, Laurence R; Sloan, Cricket A; Malladi, Venkat S; Roskin, Krishna M; Suh, Bernard B; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Kirkup, Vanessa; Fujita, Pauline A; Rhead, Brooke; Smith, Kayla E; Pohl, Andy; Kuhn, Robert M; Karolchik, Donna; Haussler, David; and Kent, W James (January 2011). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Research 39 (Database issue): D871-5. doi:10.1093/nar/gkq1017. PMC3013645. PMID21037257. [2] http:/ / encodeproject. org/

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[3] Becker, Peter B., ed. (2011). "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLoS Biology 9 (4): e1001046. doi:10.1371/journal.pbio.1001046. PMC3079585. PMID21526222. [4] Birney, E.; Stamatoyannopoulos, J. A.; Dutta, A.; Guig, R.; Gingeras, T. R.; Margulies, E. H.; Weng, Z.; Snyder, M. et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799816. Bibcode2007Natur.447..799B. doi:10.1038/nature05874. PMC2212820. PMID17571346. [5] Guig, R.; Flicek, P.; Abril, J. F.; Reymond, A.; Lagarde, J.; Denoeud, F.; Antonarakis, S.; Ashburner, M. et al. (2006). "EGASP: The human ENCODE Genome Annotation Assessment Project". Genome Biology 7: S2. doi:10.1186/gb-2006-7-s1-s2. PMC1810551. PMID16925836. [6] "ENCODE project at UCSC" (http:/ / genome. ucsc. edu/ ENCODE/ ). ENCODE Consortium. . Retrieved 2012-09-05. [7] Walsh, Fergus (2012-09-05). "Detailed map of genome function" (http:/ / www. webcitation. org/ 6ASmAMpP9). BBC News. Archived from the original (http:/ / www. bbc. co. uk/ news/ health-19202141) on 2012-09-06. . Retrieved 2012-09-06. [8] Maher B (2012). "ENCODE: The human encyclopaedia" (http:/ / www. nature. com/ news/ encode-the-human-encyclopaedia-1. 11312). Nature 489 (7414). . [9] "ENCODE Pilot Project: Target Selection" (http:/ / www. genome. gov/ 10506161). The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. . Retrieved 2011-08-05. [10] "ENCODE Project at UCSC" (http:/ / genome. ucsc. edu/ ENCODE/ ). University of California at Santa Cruz. . Retrieved 2011-08-05. [11] Weinstock, G. M. (2007). "ENCODE: More genomic empowerment". Genome Research 17 (6): 667668. doi:10.1101/gr.6534207. PMID17567987. [12] "Genome.gov | ENCODE and modENCODE Projects" (http:/ / www. genome. gov/ 10005107). The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. . Retrieved 2011-08-05. [13] "National Human Genome Research Institute - Organization" (http:/ / www. nih. gov/ about/ almanac/ organization/ NHGRI. htm). The NIH Almanac. United States National Institutes of Health. . Retrieved 2011-08-05. [14] "Genome.gov | ENCODE Participants and Projects" (http:/ / www. genome. gov/ 26525220). The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. . Retrieved 2011-08-05. [15] Joseph R. Ecker, Wendy A. Bickmore, Ins Barroso, Jonathan K. Pritchard, Yoav Gilad, Eran Segal (2012). "Genomics: ENCODE explained" (http:/ / www. nature. com/ nature/ journal/ v489/ n7414/ full/ 489052a. html). Nature 489: 52-55. . [16] The ENCODE Project Consortium (2012). "An integrated encyclopedia of DNA elements in the human genome" (http:/ / www. nature. com/ nature/ journal/ v489/ n7414/ full/ nature11247. html). Nature 489: 57-74. doi:10.1038/nature11247. . [17] "The modENCODE Project: Model Organism ENCyclopedia Of DNA Elements (modENCODE)" (http:/ / www. genome. gov/ 26524507). NHGRI website. . Retrieved 2008-11-13. [18] "modENCODE Participants and Projects" (http:/ / www. genome. gov/ 26524648). NHGRI website. . Retrieved 2008-11-13. [19] "Berkeley Lab Life Sciences Awarded NIH Grants for Fruit Fly, Nematode Studies" (http:/ / www. lbl. gov/ Science-Articles/ Archive/ LSD-modENCODE. html). Lawrence Berkeley National Laboratory website. 2007-05-14. . Retrieved 2008-11-13. [20] Gerstein, M. B.; Lu, Z. J.; Van Nostrand, E. L.; Cheng, C.; Arshinoff, B. I.; Liu, T.; Yip, K. Y.; Robilotto, R. et al. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science 330 (6012): 17751787. Bibcode2010Sci...330.1775G. doi:10.1126/science.1196914. PMID21177976. [21] Roy, S.; Ernst, J.; Kharchenko, P. V.; Kheradpour, P.; Negre, N.; Eaton, M. L.; Landolin, J. M.; Bristow, C. A. et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science 330 (6012): 17871797. Bibcode2010Sci...330.1787R. doi:10.1126/science.1198374. PMID21177974. [22] http:/ / modencode. org

External links
Official website (http://encodeproject.org/) ENCODE project (http://www.genome.gov/10005107) at the National Human Genome Research Institute ENCODE/GENCODE project (http://www.sanger.ac.uk/PostGenomics/encode/) at the Wellcome Trust Sanger Institute ENCODE-sponsored introductory tutorial (http://www.openhelix.com/ENCODE) FactorBook (http://www.factorbook.org/) ENCODE threads Explorer (http://www.nature.com/encode/#/threads) at the Nature (journal)

Article Sources and Contributors

Article Sources and Contributors

ENCODE Source: http://en.wikipedia.org/w/index.php?oldid=511026328 Contributors: Avocado, Black Falcon, Boghog, Cheng, Cmungall, Duncan.Hull, FTasc, GalaxyGingerasLab, Headbomb, Hopefuldonor, Jebus989, Jim1138, Jimkent, Looie496, Mbgmbg, Meisterflexer, Mild Bill Hiccup, Narayanese, Nina, Odmrob, PDH, Peak, Physicistjedi, Plindenbaum, Robin klein, Seikameoka, SteveChervitzTrutane, Thorwald, Wavelength, Wclathe, Westerness, Yug, 14 anonymous edits

Image Sources, Licenses and Contributors

File:EncodeSample.png Source: http://en.wikipedia.org/w/index.php?title=File:EncodeSample.png License: Public Domain Contributors: Jimkent

License
Creative Commons Attribution-Share Alike 3.0 Unported //creativecommons.org/licenses/by-sa/3.0/