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Published September 6, 2012 | Supplemental Material + Published
Journal Article Open

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 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.

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.

Attached Files

Published - nature11247-s5.txt

Published - nature11247.pdf

Supplemental Material - nature11247-s1.pdf

Supplemental Material - nature11247-s10.xls

Supplemental Material - nature11247-s11.mov

Supplemental Material - nature11247-s12.mov

Supplemental Material - nature11247-s2.pdf

Supplemental Material - nature11247-s3.xls

Supplemental Material - nature11247-s4.xlsx

Supplemental Material - nature11247-s6.txt

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Supplemental Material - nature11247-s8.xls

Supplemental Material - nature11247-s9.xls


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