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A map of the cis-regulatory sequences in the mouse genome

A map of the cis-regulatory sequences in the mouse genome A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Springer Journals

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References (31)

  • E. Nora, B. Lajoie, Edda Schulz, L. Giorgetti, I. Okamoto, N. Servant, T. Piolot, N. Berkum, Johannes Meisig, J. Sedat, J. Gribnau, E. Barillot, N. Blüthgen, J. Dekker, E. Heard (2012)

    Spatial partitioning of the regulatory landscape of the X-inactivation centre

    Nature, 485

  • I. Jordan, Ahsan Huda (2011)

    Faculty Opinions recommendation of Mapping and analysis of chromatin state dynamics in nine human cell types.

  • D. Parkhomchuk, T. Borodina, V. Amstislavskiy, Maria Banaru, Linda Hallén, S. Krobitsch, H. Lehrach, A. Soldatov (2009)

    Transcriptome analysis by strand-specific sequencing of complementary DNA

    Nucleic Acids Research, 37

  • I. Chepelev, Gang Wei, Darawalee Wangsa, Qingsong Tang, K. Zhao (2012)

    Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

    Cell Research, 22

  • Guoliang Li, Xiaoan Ruan, Raymond Auerbach, K. Sandhu, Meizhen Zheng, Ping Wang, H. Poh, Yufen Goh, Joanne Lim, Jingyao Zhang, Hui Sim, Su Peh, F. Mulawadi, C. Ong, Y. Orlov, Shuzhen Hong, Zhizhuo Zhang, S. Landt, D. Raha, G. Euskirchen, Chia-Lin Wei, W. Ge, Huaien Wang, Carrie Davis, Katherine Fisher-Aylor, A. Mortazavi, M. Gerstein, T. Gingeras, B. Wold, Y. Sun, M. Fullwood, E. Cheung, E. Liu, W. Sung, M. Snyder, Y. Ruan (2012)

    Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

    Cell, 148

  • Chin-Tong Ong, V. Corces (2011)

    Enhancer function: new insights into the regulation of tissue-specific gene expression

    Nature Reviews Genetics, 12

  • Tae Kim, Z. Abdullaev, Andrew Smith, K. Ching, D. Loukinov, Roland Green, Michael Zhang, Victor Lobanenkov, B. Ren (2007)

    Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

    Cell, 128

  • Nathaniel Heintzman, R. Stuart, G. Hon, Yutao Fu, Christina Ching, R. Hawkins, Leah Barrera, Sara Calcar, Chunxu Qu, K. Ching, Wei Wang, Z. Weng, Roland Green, G. Crawford, B. Ren (2007)

    Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

    Nature Genetics, 39

  • M. Creyghton, A. Cheng, G. Welstead, T. Kooistra, B. Carey, Eveline Steine, J. Hanna, Michael Lodato, G. Frampton, P. Sharp, L. Boyer, R. Young, R. Jaenisch (2010)

    Histone H3K27ac separates active from poised enhancers and predicts developmental state

    Proceedings of the National Academy of Sciences, 107

  • Sushmita Roy, J. Ernst, P. Kharchenko, P. Kheradpour, N. Negre, M. Eaton, J. Landolin, Christopher, A. Bristow, Lijia Ma, Michael Lin, Stefan Washietl, Bradley Arshinoff, F. Ay, Patrick Meyer, N. Robine, N. Washington, Luisa Di, Stefano, Eugene Berezikov, Christopher Brown, Rogerio Candeias, W. Joseph, Carlson, A. Carr, Irwin Jungreis, D. Marbach, Rachel Sealfon, Michael, Y. Tolstorukov, S. Will, A. Alekseyenko, C. Artieri, W. Benjamin, Booth, Angela Brooks, Q. Dai, Carrie Davis, M. Duff, Xin Feng, A. Gorchakov, Tingting Gu, J. Henikoff, P. Kapranov, Renhua Li, Heather Macalpine, J. Malone, Aki Minoda, Jared Nordman, K. Okamura, M. Perry, S. Powell, N. Riddle, Akiko Sakai, A. Samsonova, Jeremy Sandler, Y. Schwartz, Noa Sher, Rebecca Spokony, D. Sturgill, Marijke, V. Baren, K. Wan, Li Yang, Charles Yu, E. Feingold, P. Good, Mark, Guyer, R. Lowdon, K. Ahmad, J. Andrews, Bonnie Berger, E. Steven, Brenner, M. Brent, L. Cherbas, S. Elgin, R. Thomas, Gingeras, R. Grossman, R. Hoskins, T. Kaufman, W. Kent, M. Kuroda, T. Orr-Weaver, N. Perrimon, V. Pirrotta, W. James, Posakony, Bing Ren, S. Russell, P. Cherbas, B. Graveley, Suzanna, Lewis, G. Micklem, B. Oliver, P. Park, S. Celniker, Steven, Henikoff, G. Karpen, E. Lai, D. MacAlpine, D. Lincoln, Stein, Kevin White, Manolis Kellis (2011)

    Identification of functional elements and regulatory circuits by Drosophila modENCODE

    Lawrence Berkeley National Laboratory

  • M. Gerstein, Z. Lu, Eric Nostrand, Chao Cheng, Bradley Arshinoff, Tao Liu, Kevin Yip, R. Robilotto, A. Rechtsteiner, Kohta Ikegami, P. Alves, A. Chateigner, M. Perry, M. Morris, Raymond Auerbach, Xin Feng, Jing Leng, A. Vielle, W. Niu, K. Rhrissorrakrai, A. Agarwal, Roger Alexander, G. Barber, Cathleen Brdlik, J. Brennan, J. Brouillet, Adrian Carr, Ming-Sin Cheung, H. Clawson, S. Contrino, Luke Dannenberg, A. Dernburg, A. Desai, L. Dick, A. Dosé, Jiang Du, Thea Egelhofer, Sevinç Ercan, G. Euskirchen, B. Ewing, E. Feingold, R. Gassmann, P. Good, P. Green, F. Gullier, M. Gutwein, M. Guyer, L. Habegger, Ting Han, J. Henikoff, Stefan Henz, A. Hinrichs, H. Holster, T. Hyman, A. Iniguez, J. Janette, M. Jensen, Masaomi Kato, W. Kent, E. Kephart, Vishal Khivansara, Ekta Khurana, John Kim, P. Kolasinska-Zwierz, E. Lai, I. Latorre, A. Leahey, S. Lewis, P. Lloyd, L. Lochovsky, R. Lowdon, Yaniv Lubling, R. Lyne, M. MacCoss, Sebastian Mackowiak, Marco Mangone, S. McKay, D. Mecenas, Gennifer Merrihew, David Miller, A. Muroyama, J. Murray, S. Ooi, Hoang Pham, T. Phippen, E. Preston, N. Rajewsky, Gunnar Rätsch, Heidi Rosenbaum, J. Rozowsky, Kim Rutherford, P. Ruzanov, M. Sarov, Rajkumar Sasidharan, A. Sboner, P. Scheid, E. Segal, Hyunjin Shin, C. Shou, F. Slack, C. Slightam, Richard Smith, W. Spencer, E. Stinson, S. Taing, T. Takasaki, D. Vafeados, K. Voronina, Guilin Wang, N. Washington, Christina Whittle, Beijing Wu, Koon-Kiu Yan, G. Zeller, Z. Zha, Mei Zhong, Xingliang Zhou, J. Ahringer, S. Strome, K. Gunsalus, G. Micklem, X. Liu, V. Reinke, Stuart Kim, L. Hillier, S. Henikoff, F. Piano, M. Snyder, L. Stein, J. Lieb, R. Waterston (2010)

    Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

    Science, 330

  • A. Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin Schones, Zhibin Wang, Gang Wei, I. Chepelev, K. Zhao (2007)

    High-Resolution Profiling of Histone Methylations in the Human Genome

    Cell, 129

  • Erez Lieberman-Aiden, Nynke Berkum, Louise Williams, Maxim Imakaev, T. Ragoczy, A. Telling, I. Amit, B. Lajoie, P. Sabo, M. Dorschner, R. Sandstrom, B. Bernstein, M. Bender, M. Groudine, A. Gnirke, J. Stamatoyannopoulos, L. Mirny, E. Lander, J. Dekker (2009)

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

    Science, 326

  • E. Splinter, H. Heath, J. Kooren, Robert-Jan Palstra, P. Klous, F. Grosveld, N. Galjart, W. Laat (2006)

    CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus.

    Genes & development, 20 17

  • A. Visel, Simon Minovitsky, I. Dubchak, L. Pennacchio (2006)

    VISTA Enhancer Browser—a database of tissue-specific human enhancers

    Nucleic Acids Research, 35

  • K. Pruitt, T. Tatusova, D. Maglott (2005)

    Ncbi reference sequence (refseq): a curated non - redundant sequence database of genomes

    Nucleic Acids Research

  • A. Visel, M. Blow, Zirong Li, Tao Zhang, J. Akiyama, Amy Holt, I. Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, B. Ren, E. Rubin, L. Pennacchio (2009)

    ChIP-seq accurately predicts tissue-specific activity of enhancers

    Nature, 457

  • E. Birney, J. Stamatoyannopoulos, A. Dutta, R. Guigó, T. Gingeras, E. Margulies, Z. Weng, M. Snyder, E. Dermitzakis, R. Thurman, Michael Kuehn, Christopher Taylor, Shane Neph, Christoph Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. Greenbaum, R. Andrews, Paul Flicek, Patrick Boyle, Hua Cao, N. Carter, Gayle Clelland, S. Davis, Nathan Day, P. Dhami, Shane Dillon, M. Dorschner, H. Fiegler, P. Giresi, J. Goldy, M. Hawrylycz, Andrew Haydock, R. Humbert, K. James, Brett Johnson, Ericka Johnson, Tristan Frum, Elizabeth Rosenzweig, N. Karnani, K. Lee, Gregory Lefebvre, P. Navas, Fidencio Neri, Stephen Parker, P. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, Man Yu, F. Collins, J. Dekker, J. Lieb, T. Tullius, G. Crawford, S. Sunyaev, W. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, Srinka Ghosh, A. Sandelin, I. Hofacker, R. Baertsch, Damian Keefe, S. Dike, Jill Cheng, H. Hirsch, E. Sekinger, Julien Lagarde, J. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Stefan Washietl, J. Korbel, O. Emanuelsson, J. Pedersen, N. Holroyd, Ruth Taylor, D. Swarbreck, N. Matthews, M. Dickson, D. Thomas, M. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. Srinivasan, W. Sung, H. Ooi, K. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. Tress, A. Valencia, S. Choo, C. Choo, C. Ucla, C. Manzano, Carine Wyss, E. Cheung, T. Clark, James Brown, M. Ganesh, Sandeep Patel, H. Tammana, Jacqueline Chrast, C. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, Jiaqian Wu, Z. Lian, Jin Lian, P. Newburger, Xueqing Zhang, P. Bickel, J. Mattick, Piero Carninci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. Myers, J. Rogers, P. Stadler, T. Lowe, Chia-Lin Wei, Y. Ruan, K. Struhl, M. Gerstein, S. Antonarakis, Yutao Fu, E. Green, Ulas Karaöz, A. Siepel, James Taylor, L. Liefer, K. Wetterstrand, P. Good, E. Feingold, M. Guyer, G. Cooper, G. Asimenos, Colin Dewey, Minmei Hou, S. Nikolaev, J. Montoya-Burgos, A. Löytynoja, S. Whelan, F. Pardi, Tim Massingham, Haiyan Huang, Na Zhang, I. Holmes, Jim Mullikin, A. Ureta-Vidal, B. Paten, Michael Seringhaus, D. Church, K. Rosenbloom, W. Kent, Eric Stone, S. Batzoglou, N. Goldman, R. Hardison, D. Haussler, Webb Miller, A. Sidow, N. Trinklein, Zhengdong Zhang, Leah Barrera, R. Stuart, D. King, A. Ameur, Stefan Enroth, M. Bieda, Jonghwan Kim, A. Bhinge, N. Jiang, Jun Liu, Fei Yao, V. Vega, C. Lee, Patrick Ng, A. Yang, Z. Moqtaderi, Zhou Zhu, Xiaoqin Xu, S. Squazzo, M. Oberley, David Inman, Michael Singer, T. Richmond, Kyle Munn, Á. Rada-Iglesias, O. Wallerman, J. Komorowski, J. Fowler, Phillippe Couttet, Alexander Bruce, O. Dovey, P. Ellis, C. Langford, D. Nix, G. Euskirchen, S. Hartman, A. Urban, P. Kraus, Sara Calcar, Nathaniel Heintzman, Tae Kim, Kun Wang, Chunxu Qu, G. Hon, R. Luna, C. Glass, M. Rosenfeld, S. Aldred, S. Cooper, Anason Halees, J. Lin, H. Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar Haidar, Yon-Jong Yu, V. Iyer, Roland Green, C. Wadelius, P. Farnham, B. Ren, R. Harte, A. Hinrichs, Heather Trumbower, H. Clawson, J. Hillman-Jackson, A. Zweig, Kayla Smith, Archana Thakkapallayil, G. Barber, R. Kuhn, D. Karolchik, L. Armengol, C. Bird, P. Bakker, Andrew Kern, N. López-Bigas, Joel Martin, B. Stranger, A. Woodroffe, Eugene Davydov, A. Dimas, E. Eyras, Ingileif Hallgrímsdóttir, J. Huppert, M. Zody, G. Abecasis, X. Estivill, G. Bouffard, Xiaobin Guan, N. Hansen, J. Idol, V. Maduro, Baishali Maskeri, Jennifer Mcdowell, Morgan Park, Pamela Thomas, Alice Young, R. Blakesley, D. Muzny, E. Sodergren, D. Wheeler, K. Worley, Huaiyang Jiang, G. Weinstock, R. Gibbs, T. Graves, R. Fulton, E. Mardis, R. Wilson, M. Clamp, James Cuff, S. Gnerre, D. Jaffe, Jean Chang, K. Lindblad-Toh, E. Lander, M. Koriabine, M. Nefedov, K. Osoegawa, Y. Yoshinaga, B. Zhu, P. Jong (2007)

    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

    Nature, 447

  • Jesse Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun Liu, B. Ren (2012)

    Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions

    Nature, 485

  • Mouse Consortium (2002)

    Initial sequencing and comparative analysis of the mouse genome

    Nature, 420

  • K. Pruitt, T. Tatusova, D. Maglott (2004)

    NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

    Nucleic Acids Research, 33

  • R. Hawkins, G. Hon, Leonard Lee, Queminh Ngo, R. Lister, Mattia Pelizzola, Lee Edsall, Samantha Kuan, Ying Luu, Sarit Klugman, Jessica Antosiewicz-Bourget, Z. Ye, Celso Espinoza, Saurabh Agarwahl, Liping Shen, Victor Ruotti, Wei Wang, R. Stewart, J. Thomson, J. Ecker, B. Ren (2010)

    Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

    Cell stem cell, 6 5

  • A. Siepel, G. Bejerano, J. Pedersen, A. Hinrichs, Minmei Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. Hillier, S. Richards, G. Weinstock, R. Wilson, R. Gibbs, W. Kent, W. Miller, D. Haussler (2005)

    Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

    Genome research, 15 8

  • M. Kagey, J. Newman, S. Bilodeau, Y. Zhan, David Orlando, Nynke Berkum, Christopher Ebmeier, J. Goossens, P. Rahl, S. Levine, D. Taatjes, J. Dekker, R. Young (2010)

    Mediator and Cohesin Connect Gene Expression and Chromatin Architecture

    Nature, 467

  • A. Visel, E. Rubin, L. Pennacchio (2009)

    Genomic Views of Distant-Acting Enhancers

    Nature, 461

  • X. Chen, H. Xu, P. Yuan, Fang Fang, M. Huss, V. Vega, Eleanor Wong, Y. Orlov, Weiwei Zhang, Jianming Jiang, Y. Loh, Hock Yeo, Z. Yeo, V. Narang, K. Govindarajan, Bernard Leong, A. Shahab, Y. Ruan, G. Bourque, W. Sung, N. Clarke, Chia-Lin Wei, H. Ng (2008)

    Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

    Cell, 133

  • Nathaniel Heintzman, G. Hon, R. Hawkins, P. Kheradpour, A. Stark, L. Harp, Z. Ye, Leonard Lee, R. Stuart, Christina Ching, K. Ching, Jessica Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland Green, Victor Lobanenkov, R. Stewart, J. Thomson, G. Crawford, Manolis Kellis, B. Ren (2009)

    Histone modifications at human enhancers reflect global cell-type-specific gene expression

    Nature, 459

  • J Ernst (2011)

    Mapping and analysis of chromatin state dynamics in nine human cell types

    Nature, 473

  • Á. Rada-Iglesias, R. Bajpai, T. Swigut, S. Brugmann, Ryan Flynn, J. Wysocka (2011)

    A unique chromatin signature uncovers early developmental enhancers in humans

    Nature, 470

  • Dominic Schmidt, M. Wilson, B. Ballester, Petra Schwalie, Gordon Brown, Aileen Marshall, C. Kutter, S. Watt, C. Martinez-Jimenez, Sarah Mackay, I. Talianidis, Paul Flicek, D. Odom (2010)

    Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

    Science, 328

  • Tae Kim, Leah Barrera, Ming Zheng, Chunxu Qu, Michael Singer, T. Richmond, Ying Wu, Roland Green, B. Ren (2005)

    A high-resolution map of active promoters in the human genome

    Nature, 436

Publisher
Springer Journals
Copyright
Copyright © 2012 by Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
Subject
Science, Humanities and Social Sciences, multidisciplinary; Science, Humanities and Social Sciences, multidisciplinary; Science, multidisciplinary
ISSN
0028-0836
eISSN
1476-4687
DOI
10.1038/nature11243
Publisher site
See Article on Publisher Site

Abstract

A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences.

Journal

NatureSpringer Journals

Published: Jul 1, 2012

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