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A comparative encyclopedia of DNA elements in the mouse genome
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory progra...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Nature Publishing Group UK
2014
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106/ https://www.ncbi.nlm.nih.gov/pubmed/25409824 http://dx.doi.org/10.1038/nature13992 |
| _version_ | 1782348978629640192 |
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| author | Yue, Feng Cheng, Yong Breschi, Alessandra Vierstra, Jeff Wu, Weisheng Ryba, Tyrone Sandstrom, Richard Ma, Zhihai Davis, Carrie Pope, Benjamin D. Shen, Yin Pervouchine, Dmitri D. Djebali, Sarah Thurman, Robert E. Kaul, Rajinder Rynes, Eric Kirilusha, Anthony Marinov, Georgi K. Williams, Brian A. Trout, Diane Amrhein, Henry Fisher-Aylor, Katherine Antoshechkin, Igor DeSalvo, Gilberto See, Lei-Hoon Fastuca, Meagan Drenkow, Jorg Zaleski, Chris Dobin, Alex Prieto, Pablo Lagarde, Julien Bussotti, Giovanni Tanzer, Andrea Denas, Olgert Li, Kanwei Bender, M. A. Zhang, Miaohua Byron, Rachel Groudine, Mark T. McCleary, David Pham, Long Ye, Zhen Kuan, Samantha Edsall, Lee Wu, Yi-Chieh Rasmussen, Matthew D. Bansal, Mukul S. Kellis, Manolis Keller, Cheryl A. Morrissey, Christapher S. Mishra, Tejaswini Jain, Deepti Dogan, Nergiz Harris, Robert S. Cayting, Philip Kawli, Trupti Boyle, Alan P. Euskirchen, Ghia Kundaje, Anshul Lin, Shin Lin, Yiing Jansen, Camden Malladi, Venkat S. Cline, Melissa S. Erickson, Drew T. Kirkup, Vanessa M. Learned, Katrina Sloan, Cricket A. Rosenbloom, Kate R. Lacerda de Sousa, Beatriz Beal, Kathryn Pignatelli, Miguel Flicek, Paul Lian, Jin Kahveci, Tamer Lee, Dongwon James Kent, W. Ramalho Santos, Miguel Herrero, Javier Notredame, Cedric Johnson, Audra Vong, Shinny Lee, Kristen Bates, Daniel Neri, Fidencio Diegel, Morgan Canfield, Theresa Sabo, Peter J. Wilken, Matthew S. Reh, Thomas A. Giste, Erika Shafer, Anthony Kutyavin, Tanya Haugen, Eric Dunn, Douglas Reynolds, Alex P. Neph, Shane Humbert, Richard Scott Hansen, R. De Bruijn, Marella Selleri, Licia Rudensky, Alexander Josefowicz, Steven Samstein, Robert Eichler, Evan E. Orkin, Stuart H. Levasseur, Dana Papayannopoulou, Thalia Chang, Kai-Hsin Skoultchi, Arthur Gosh, Srikanta Disteche, Christine Treuting, Piper Wang, Yanli Weiss, Mitchell J. Blobel, Gerd A. Cao, Xiaoyi Zhong, Sheng Wang, Ting Good, Peter J. Lowdon, Rebecca F. Adams, Leslie B. Zhou, Xiao-Qiao Pazin, Michael J. Feingold, Elise A. Wold, Barbara Taylor, James Mortazavi, Ali Weissman, Sherman M. Stamatoyannopoulos, John A. Snyder, Michael P. Guigo, Roderic Gingeras, Thomas R. Gilbert, David M. Hardison, Ross C. Beer, Michael A. Ren, Bing |
| author_facet | Yue, Feng Cheng, Yong Breschi, Alessandra Vierstra, Jeff Wu, Weisheng Ryba, Tyrone Sandstrom, Richard Ma, Zhihai Davis, Carrie Pope, Benjamin D. Shen, Yin Pervouchine, Dmitri D. Djebali, Sarah Thurman, Robert E. Kaul, Rajinder Rynes, Eric Kirilusha, Anthony Marinov, Georgi K. Williams, Brian A. Trout, Diane Amrhein, Henry Fisher-Aylor, Katherine Antoshechkin, Igor DeSalvo, Gilberto See, Lei-Hoon Fastuca, Meagan Drenkow, Jorg Zaleski, Chris Dobin, Alex Prieto, Pablo Lagarde, Julien Bussotti, Giovanni Tanzer, Andrea Denas, Olgert Li, Kanwei Bender, M. A. Zhang, Miaohua Byron, Rachel Groudine, Mark T. McCleary, David Pham, Long Ye, Zhen Kuan, Samantha Edsall, Lee Wu, Yi-Chieh Rasmussen, Matthew D. Bansal, Mukul S. Kellis, Manolis Keller, Cheryl A. Morrissey, Christapher S. Mishra, Tejaswini Jain, Deepti Dogan, Nergiz Harris, Robert S. Cayting, Philip Kawli, Trupti Boyle, Alan P. Euskirchen, Ghia Kundaje, Anshul Lin, Shin Lin, Yiing Jansen, Camden Malladi, Venkat S. Cline, Melissa S. Erickson, Drew T. Kirkup, Vanessa M. Learned, Katrina Sloan, Cricket A. Rosenbloom, Kate R. Lacerda de Sousa, Beatriz Beal, Kathryn Pignatelli, Miguel Flicek, Paul Lian, Jin Kahveci, Tamer Lee, Dongwon James Kent, W. Ramalho Santos, Miguel Herrero, Javier Notredame, Cedric Johnson, Audra Vong, Shinny Lee, Kristen Bates, Daniel Neri, Fidencio Diegel, Morgan Canfield, Theresa Sabo, Peter J. Wilken, Matthew S. Reh, Thomas A. Giste, Erika Shafer, Anthony Kutyavin, Tanya Haugen, Eric Dunn, Douglas Reynolds, Alex P. Neph, Shane Humbert, Richard Scott Hansen, R. De Bruijn, Marella Selleri, Licia Rudensky, Alexander Josefowicz, Steven Samstein, Robert Eichler, Evan E. Orkin, Stuart H. Levasseur, Dana Papayannopoulou, Thalia Chang, Kai-Hsin Skoultchi, Arthur Gosh, Srikanta Disteche, Christine Treuting, Piper Wang, Yanli Weiss, Mitchell J. Blobel, Gerd A. Cao, Xiaoyi Zhong, Sheng Wang, Ting Good, Peter J. Lowdon, Rebecca F. Adams, Leslie B. Zhou, Xiao-Qiao Pazin, Michael J. Feingold, Elise A. Wold, Barbara Taylor, James Mortazavi, Ali Weissman, Sherman M. Stamatoyannopoulos, John A. Snyder, Michael P. Guigo, Roderic Gingeras, Thomas R. Gilbert, David M. Hardison, Ross C. Beer, Michael A. Ren, Bing |
| author_sort | Yue, Feng |
| collection | PubMed |
| description | The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature13992) contains supplementary material, which is available to authorized users. |
| format | Online Article Text |
| id | pubmed-4266106 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2014 |
| publisher | Nature Publishing Group UK |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-42661062015-05-20 A comparative encyclopedia of DNA elements in the mouse genome Yue, Feng Cheng, Yong Breschi, Alessandra Vierstra, Jeff Wu, Weisheng Ryba, Tyrone Sandstrom, Richard Ma, Zhihai Davis, Carrie Pope, Benjamin D. Shen, Yin Pervouchine, Dmitri D. Djebali, Sarah Thurman, Robert E. Kaul, Rajinder Rynes, Eric Kirilusha, Anthony Marinov, Georgi K. Williams, Brian A. Trout, Diane Amrhein, Henry Fisher-Aylor, Katherine Antoshechkin, Igor DeSalvo, Gilberto See, Lei-Hoon Fastuca, Meagan Drenkow, Jorg Zaleski, Chris Dobin, Alex Prieto, Pablo Lagarde, Julien Bussotti, Giovanni Tanzer, Andrea Denas, Olgert Li, Kanwei Bender, M. A. Zhang, Miaohua Byron, Rachel Groudine, Mark T. McCleary, David Pham, Long Ye, Zhen Kuan, Samantha Edsall, Lee Wu, Yi-Chieh Rasmussen, Matthew D. Bansal, Mukul S. Kellis, Manolis Keller, Cheryl A. Morrissey, Christapher S. Mishra, Tejaswini Jain, Deepti Dogan, Nergiz Harris, Robert S. Cayting, Philip Kawli, Trupti Boyle, Alan P. Euskirchen, Ghia Kundaje, Anshul Lin, Shin Lin, Yiing Jansen, Camden Malladi, Venkat S. Cline, Melissa S. Erickson, Drew T. Kirkup, Vanessa M. Learned, Katrina Sloan, Cricket A. Rosenbloom, Kate R. Lacerda de Sousa, Beatriz Beal, Kathryn Pignatelli, Miguel Flicek, Paul Lian, Jin Kahveci, Tamer Lee, Dongwon James Kent, W. Ramalho Santos, Miguel Herrero, Javier Notredame, Cedric Johnson, Audra Vong, Shinny Lee, Kristen Bates, Daniel Neri, Fidencio Diegel, Morgan Canfield, Theresa Sabo, Peter J. Wilken, Matthew S. Reh, Thomas A. Giste, Erika Shafer, Anthony Kutyavin, Tanya Haugen, Eric Dunn, Douglas Reynolds, Alex P. Neph, Shane Humbert, Richard Scott Hansen, R. De Bruijn, Marella Selleri, Licia Rudensky, Alexander Josefowicz, Steven Samstein, Robert Eichler, Evan E. Orkin, Stuart H. Levasseur, Dana Papayannopoulou, Thalia Chang, Kai-Hsin Skoultchi, Arthur Gosh, Srikanta Disteche, Christine Treuting, Piper Wang, Yanli Weiss, Mitchell J. Blobel, Gerd A. Cao, Xiaoyi Zhong, Sheng Wang, Ting Good, Peter J. Lowdon, Rebecca F. Adams, Leslie B. Zhou, Xiao-Qiao Pazin, Michael J. Feingold, Elise A. Wold, Barbara Taylor, James Mortazavi, Ali Weissman, Sherman M. Stamatoyannopoulos, John A. Snyder, Michael P. Guigo, Roderic Gingeras, Thomas R. Gilbert, David M. Hardison, Ross C. Beer, Michael A. Ren, Bing Nature Article The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature13992) contains supplementary material, which is available to authorized users. Nature Publishing Group UK 2014-11-19 2014 /pmc/articles/PMC4266106/ /pubmed/25409824 http://dx.doi.org/10.1038/nature13992 Text en © The Author(s) 2014 https://creativecommons.org/licenses/by-nc-sa/3.0/This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ (https://creativecommons.org/licenses/by-nc-sa/3.0/) . |
| spellingShingle | Article Yue, Feng Cheng, Yong Breschi, Alessandra Vierstra, Jeff Wu, Weisheng Ryba, Tyrone Sandstrom, Richard Ma, Zhihai Davis, Carrie Pope, Benjamin D. Shen, Yin Pervouchine, Dmitri D. Djebali, Sarah Thurman, Robert E. Kaul, Rajinder Rynes, Eric Kirilusha, Anthony Marinov, Georgi K. Williams, Brian A. Trout, Diane Amrhein, Henry Fisher-Aylor, Katherine Antoshechkin, Igor DeSalvo, Gilberto See, Lei-Hoon Fastuca, Meagan Drenkow, Jorg Zaleski, Chris Dobin, Alex Prieto, Pablo Lagarde, Julien Bussotti, Giovanni Tanzer, Andrea Denas, Olgert Li, Kanwei Bender, M. A. Zhang, Miaohua Byron, Rachel Groudine, Mark T. McCleary, David Pham, Long Ye, Zhen Kuan, Samantha Edsall, Lee Wu, Yi-Chieh Rasmussen, Matthew D. Bansal, Mukul S. Kellis, Manolis Keller, Cheryl A. Morrissey, Christapher S. Mishra, Tejaswini Jain, Deepti Dogan, Nergiz Harris, Robert S. Cayting, Philip Kawli, Trupti Boyle, Alan P. Euskirchen, Ghia Kundaje, Anshul Lin, Shin Lin, Yiing Jansen, Camden Malladi, Venkat S. Cline, Melissa S. Erickson, Drew T. Kirkup, Vanessa M. Learned, Katrina Sloan, Cricket A. Rosenbloom, Kate R. Lacerda de Sousa, Beatriz Beal, Kathryn Pignatelli, Miguel Flicek, Paul Lian, Jin Kahveci, Tamer Lee, Dongwon James Kent, W. Ramalho Santos, Miguel Herrero, Javier Notredame, Cedric Johnson, Audra Vong, Shinny Lee, Kristen Bates, Daniel Neri, Fidencio Diegel, Morgan Canfield, Theresa Sabo, Peter J. Wilken, Matthew S. Reh, Thomas A. Giste, Erika Shafer, Anthony Kutyavin, Tanya Haugen, Eric Dunn, Douglas Reynolds, Alex P. Neph, Shane Humbert, Richard Scott Hansen, R. De Bruijn, Marella Selleri, Licia Rudensky, Alexander Josefowicz, Steven Samstein, Robert Eichler, Evan E. Orkin, Stuart H. Levasseur, Dana Papayannopoulou, Thalia Chang, Kai-Hsin Skoultchi, Arthur Gosh, Srikanta Disteche, Christine Treuting, Piper Wang, Yanli Weiss, Mitchell J. Blobel, Gerd A. Cao, Xiaoyi Zhong, Sheng Wang, Ting Good, Peter J. Lowdon, Rebecca F. Adams, Leslie B. Zhou, Xiao-Qiao Pazin, Michael J. Feingold, Elise A. Wold, Barbara Taylor, James Mortazavi, Ali Weissman, Sherman M. Stamatoyannopoulos, John A. Snyder, Michael P. Guigo, Roderic Gingeras, Thomas R. Gilbert, David M. Hardison, Ross C. Beer, Michael A. Ren, Bing A comparative encyclopedia of DNA elements in the mouse genome |
| title | A comparative encyclopedia of DNA elements in the mouse genome |
| title_full | A comparative encyclopedia of DNA elements in the mouse genome |
| title_fullStr | A comparative encyclopedia of DNA elements in the mouse genome |
| title_full_unstemmed | A comparative encyclopedia of DNA elements in the mouse genome |
| title_short | A comparative encyclopedia of DNA elements in the mouse genome |
| title_sort | comparative encyclopedia of dna elements in the mouse genome |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106/ https://www.ncbi.nlm.nih.gov/pubmed/25409824 http://dx.doi.org/10.1038/nature13992 |
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