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An integrated encyclopedia of DNA elements in the human genome

Marinov, Georgi K. and Wold, Barbara and Williams, Brian A. and Antoshechkin, Igor and Fejes Toth, Kata and King, Brandon and Schaeffer, Lorain and Trout, Diane and Vielmetter, Jost and Gasper, Clarke and Pepke, Shirley and Amrhein, Henry and Anaya, Michael and McCue, Kenneth and Fisher-Aylor, Katherine I. and DeSalvo, Gilberto and Balasubramanian, Sreeram (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836. PMCID PMC4243026. https://resolver.caltech.edu/CaltechAUTHORS:20130513-153517455

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Abstract

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 has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nature11247DOIArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243026/PubMed CentralArticle
http://rdcu.be/cseoPublisherFree ReadCube access
ORCID:
AuthorORCID
Marinov, Georgi K.0000-0003-1822-7273
Wold, Barbara0000-0003-3235-8130
Antoshechkin, Igor0000-0002-9934-3040
Fejes Toth, Kata0000-0001-6558-2636
Anaya, Michael0000-0002-6944-3614
Additional Information:© 2012 Macmillan Publishers Limited. This paper is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence, and the online version of the paper is freely available to all readers. The authors declare no competing financial interests. Received 24 November 2011; accepted 29 May 2012. We thank additional members of our laboratories and institutions who have contributed to the experimental and analytical components of this project. We thank D. Leja for assistance with production of the figures. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 (W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder); U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541, U01HG004561,RC2HG005679 and R01HG003988 (L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.
Funders:
Funding AgencyGrant Number
NIHU54HG004570
NIHU01HG004695
NIHU54HG004563
NIHU54HG004557
NHGRINIH
NIHU41HG004568
NIHU54HG004576
NIHU54HG004558
NIHU54HG004592
NIHR01HG003143
NIHRC2HG005591
NIHR01HG003700
NIHR01HG004456-03
NIHU01HG004571
NIHU01HG004561
NIHRC2HG005679
NIHU54HG004570
NIHU54HG004563
NIHU41HG004568
NIHU54HG004592
NIHR01HG003143
NIHRC2HG005591
NIHR01HG003541
NIHU01HG004561
NIHRC2HG005679
NIHR01HG003988
NIHZIAHG200323
NIHZIAHG200341
National Human Genome Research InstituteUNSPECIFIED
American Recovery and Reinvestment Act (ARRA)UNSPECIFIED
Subject Keywords:Genetics; Genomics; Molecular biology
Issue or Number:7414
PubMed Central ID:PMC4243026
Record Number:CaltechAUTHORS:20130513-153517455
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130513-153517455
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:38472
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:14 May 2013 14:59
Last Modified:15 Apr 2020 16:55

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