Expanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2021
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| Online Access: | https://hdl.handle.net/1721.1/128921 |
| _version_ | 1810973452727746560 |
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| author | Moore, Jill E. Purcaro, Michael J. Pratt, Henry E. Epstein, Charles B. Shoresh, Noam Adrian, Jessika Kawli, Trupti Davis, Carrie A. Dobin, Alexander Kaul, Rajinder Halow, Jessica Van Nostrand, Eric L. Freese, Peter Dale Gorkin, David U. Shen, Yin He, Yupeng Mackiewicz, Mark Pauli-Behn, Florencia Williams, Brian A. Mortazavi, Ali Keller, Cheryl A. Zhang, Xiao-Ou Elhajjajy, Shaimae I. Huey, Jack Dickel, Diane E. Snetkova, Valentina Wei, Xintao Wang, Xiaofeng Rivera-Mulia, Juan Carlos Rozowsky, Joel Zhang, Jing Chhetri, Surya B. Zhang, Jialing Victorsen, Alec White, Kevin P. Visel, Axel Yeo, Gene W. Burge, Christopher B Lécuyer, Eric Gilbert, David M. Dekker, Job Rinn, John Mendenhall, Eric M. Ecker, Joseph R. Kellis, Manolis Klein, Robert J. Noble, William S. Kundaje, Anshul Guigó, Roderic Farnham, Peggy J. Cherry, J. Michael Myers, Richard M. Ren, Bing Graveley, Brenton R. Gerstein, Mark B. Pennacchio, Len A. Snyder, Michael P. Bernstein, Bradley E. Wold, Barbara Hardison, Ross C. Gingeras, Thomas R. Stamatoyannopoulos, John A. Weng, Zhiping |
| author2 | Massachusetts Institute of Technology. Computational and Systems Biology Program |
| author_facet | Massachusetts Institute of Technology. Computational and Systems Biology Program Moore, Jill E. Purcaro, Michael J. Pratt, Henry E. Epstein, Charles B. Shoresh, Noam Adrian, Jessika Kawli, Trupti Davis, Carrie A. Dobin, Alexander Kaul, Rajinder Halow, Jessica Van Nostrand, Eric L. Freese, Peter Dale Gorkin, David U. Shen, Yin He, Yupeng Mackiewicz, Mark Pauli-Behn, Florencia Williams, Brian A. Mortazavi, Ali Keller, Cheryl A. Zhang, Xiao-Ou Elhajjajy, Shaimae I. Huey, Jack Dickel, Diane E. Snetkova, Valentina Wei, Xintao Wang, Xiaofeng Rivera-Mulia, Juan Carlos Rozowsky, Joel Zhang, Jing Chhetri, Surya B. Zhang, Jialing Victorsen, Alec White, Kevin P. Visel, Axel Yeo, Gene W. Burge, Christopher B Lécuyer, Eric Gilbert, David M. Dekker, Job Rinn, John Mendenhall, Eric M. Ecker, Joseph R. Kellis, Manolis Klein, Robert J. Noble, William S. Kundaje, Anshul Guigó, Roderic Farnham, Peggy J. Cherry, J. Michael Myers, Richard M. Ren, Bing Graveley, Brenton R. Gerstein, Mark B. Pennacchio, Len A. Snyder, Michael P. Bernstein, Bradley E. Wold, Barbara Hardison, Ross C. Gingeras, Thomas R. Stamatoyannopoulos, John A. Weng, Zhiping |
| author_sort | Moore, Jill E. |
| collection | MIT |
| description | The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes. |
| first_indexed | 2024-09-23T08:07:49Z |
| format | Article |
| id | mit-1721.1/128921 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T08:07:49Z |
| publishDate | 2021 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1289212024-06-25T23:56:25Z Expanded encyclopaedias of DNA elements in the human and mouse genomes Moore, Jill E. Purcaro, Michael J. Pratt, Henry E. Epstein, Charles B. Shoresh, Noam Adrian, Jessika Kawli, Trupti Davis, Carrie A. Dobin, Alexander Kaul, Rajinder Halow, Jessica Van Nostrand, Eric L. Freese, Peter Dale Gorkin, David U. Shen, Yin He, Yupeng Mackiewicz, Mark Pauli-Behn, Florencia Williams, Brian A. Mortazavi, Ali Keller, Cheryl A. Zhang, Xiao-Ou Elhajjajy, Shaimae I. Huey, Jack Dickel, Diane E. Snetkova, Valentina Wei, Xintao Wang, Xiaofeng Rivera-Mulia, Juan Carlos Rozowsky, Joel Zhang, Jing Chhetri, Surya B. Zhang, Jialing Victorsen, Alec White, Kevin P. Visel, Axel Yeo, Gene W. Burge, Christopher B Lécuyer, Eric Gilbert, David M. Dekker, Job Rinn, John Mendenhall, Eric M. Ecker, Joseph R. Kellis, Manolis Klein, Robert J. Noble, William S. Kundaje, Anshul Guigó, Roderic Farnham, Peggy J. Cherry, J. Michael Myers, Richard M. Ren, Bing Graveley, Brenton R. Gerstein, Mark B. Pennacchio, Len A. Snyder, Michael P. Bernstein, Bradley E. Wold, Barbara Hardison, Ross C. Gingeras, Thomas R. Stamatoyannopoulos, John A. Weng, Zhiping Massachusetts Institute of Technology. Computational and Systems Biology Program Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes. NIH (Grants U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442) 2021-01-04T14:36:57Z 2021-01-04T14:36:57Z 2020-07 2017-08 2020-12-15T16:39:31Z Article http://purl.org/eprint/type/JournalArticle 0028-0836 1476-4687 https://hdl.handle.net/1721.1/128921 Moore, Jill E. et al. "Expanded encyclopaedias of DNA elements in the human and mouse genomes." Nature 583, 7818 (August 2020): 699–710 © 2020 The Author(s) en http://dx.doi.org/10.1038/s41586-020-2493-4 Nature Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Moore, Jill E. Purcaro, Michael J. Pratt, Henry E. Epstein, Charles B. Shoresh, Noam Adrian, Jessika Kawli, Trupti Davis, Carrie A. Dobin, Alexander Kaul, Rajinder Halow, Jessica Van Nostrand, Eric L. Freese, Peter Dale Gorkin, David U. Shen, Yin He, Yupeng Mackiewicz, Mark Pauli-Behn, Florencia Williams, Brian A. Mortazavi, Ali Keller, Cheryl A. Zhang, Xiao-Ou Elhajjajy, Shaimae I. Huey, Jack Dickel, Diane E. Snetkova, Valentina Wei, Xintao Wang, Xiaofeng Rivera-Mulia, Juan Carlos Rozowsky, Joel Zhang, Jing Chhetri, Surya B. Zhang, Jialing Victorsen, Alec White, Kevin P. Visel, Axel Yeo, Gene W. Burge, Christopher B Lécuyer, Eric Gilbert, David M. Dekker, Job Rinn, John Mendenhall, Eric M. Ecker, Joseph R. Kellis, Manolis Klein, Robert J. Noble, William S. Kundaje, Anshul Guigó, Roderic Farnham, Peggy J. Cherry, J. Michael Myers, Richard M. Ren, Bing Graveley, Brenton R. Gerstein, Mark B. Pennacchio, Len A. Snyder, Michael P. Bernstein, Bradley E. Wold, Barbara Hardison, Ross C. Gingeras, Thomas R. Stamatoyannopoulos, John A. Weng, Zhiping Expanded encyclopaedias of DNA elements in the human and mouse genomes |
| title | Expanded encyclopaedias of DNA elements in the human and mouse genomes |
| title_full | Expanded encyclopaedias of DNA elements in the human and mouse genomes |
| title_fullStr | Expanded encyclopaedias of DNA elements in the human and mouse genomes |
| title_full_unstemmed | Expanded encyclopaedias of DNA elements in the human and mouse genomes |
| title_short | Expanded encyclopaedias of DNA elements in the human and mouse genomes |
| title_sort | expanded encyclopaedias of dna elements in the human and mouse genomes |
| url | https://hdl.handle.net/1721.1/128921 |
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