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Comparative analysis of regulatory information and circuits across distant species

Author

Listed:
  • Alan P. Boyle

    (Stanford University School of Medicine)

  • Carlos L. Araya

    (Stanford University School of Medicine)

  • Cathleen Brdlik

    (Stanford University School of Medicine)

  • Philip Cayting

    (Stanford University School of Medicine)

  • Chao Cheng

    (Program of Computational Biology and Bioinformatics, Yale University)

  • Yong Cheng

    (Stanford University School of Medicine)

  • Kathryn Gardner

    (Yale University School of Medicine)

  • LaDeana W. Hillier

    (University of Washington)

  • Judith Janette

    (Yale University School of Medicine)

  • Lixia Jiang

    (Stanford University School of Medicine)

  • Dionna Kasper

    (Yale University School of Medicine)

  • Trupti Kawli

    (Stanford University School of Medicine)

  • Pouya Kheradpour

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology)

  • Anshul Kundaje

    (Stanford University
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology)

  • Jingyi Jessica Li

    (University of California
    University of California)

  • Lijia Ma

    (University of Washington)

  • Wei Niu

    (Yale University School of Medicine)

  • E. Jay Rehm

    (Institute for Genomics and Systems Biology, University of Chicago)

  • Joel Rozowsky

    (Program of Computational Biology and Bioinformatics, Yale University)

  • Matthew Slattery

    (Institute for Genomics and Systems Biology, University of Chicago)

  • Rebecca Spokony

    (Institute for Genomics and Systems Biology, University of Chicago)

  • Robert Terrell

    (University of Washington)

  • Dionne Vafeados

    (University of Washington)

  • Daifeng Wang

    (Program of Computational Biology and Bioinformatics, Yale University)

  • Peter Weisdepp

    (University of Washington)

  • Yi-Chieh Wu

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology)

  • Dan Xie

    (Stanford University School of Medicine)

  • Koon-Kiu Yan

    (Program of Computational Biology and Bioinformatics, Yale University)

  • Elise A. Feingold

    (National Human Genome Research Institute, National Institutes of Health)

  • Peter J. Good

    (National Human Genome Research Institute, National Institutes of Health)

  • Michael J. Pazin

    (National Human Genome Research Institute, National Institutes of Health)

  • Haiyan Huang

    (University of California)

  • Peter J. Bickel

    (University of California)

  • Steven E. Brenner

    (University of California
    University of California)

  • Valerie Reinke

    (Yale University School of Medicine)

  • Robert H. Waterston

    (University of Washington)

  • Mark Gerstein

    (Program of Computational Biology and Bioinformatics, Yale University)

  • Kevin P. White

    (Institute for Genomics and Systems Biology, University of Chicago)

  • Manolis Kellis

    (Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology)

  • Michael Snyder

    (Stanford University School of Medicine)

Abstract

A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.

Suggested Citation

  • Alan P. Boyle & Carlos L. Araya & Cathleen Brdlik & Philip Cayting & Chao Cheng & Yong Cheng & Kathryn Gardner & LaDeana W. Hillier & Judith Janette & Lixia Jiang & Dionna Kasper & Trupti Kawli & Pouy, 2014. "Comparative analysis of regulatory information and circuits across distant species," Nature, Nature, vol. 512(7515), pages 453-456, August.
    • Handle: RePEc:nat:nature:v:512:y:2014:i:7515:d:10.1038_nature13668
    DOI: 10.1038/nature13668
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    Citations

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    Cited by:

    1. Yan-Ping Zhang & Wen-Hong Zhang & Pan Zhang & Qi Li & Yue Sun & Jia-Wen Wang & Shaobing O. Zhang & Tao Cai & Cheng Zhan & Meng-Qiu Dong, 2022. "Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Yuyan Cheng & Yuqin Yin & Alice Zhang & Alexander M. Bernstein & Riki Kawaguchi & Kun Gao & Kyra Potter & Hui-Ya Gilbert & Yan Ao & Jing Ou & Catherine J. Fricano-Kugler & Jeffrey L. Goldberg & Zhigan, 2022. "Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    3. Kellianne D. Alexander & Shankar Ramachandran & Kasturi Biswas & Christopher M. Lambert & Julia Russell & Devyn B. Oliver & William Armstrong & Monika Rettler & Samuel Liu & Maria Doitsidou & Claire B, 2023. "The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    4. Yuyun Zhang & Zijuan Li & Jinyi Liu & Yu’e Zhang & Luhuan Ye & Yuan Peng & Haoyu Wang & Huishan Diao & Yu Ma & Meiyue Wang & Yilin Xie & Tengfei Tang & Yili Zhuang & Wan Teng & Yiping Tong & Wenli Zha, 2022. "Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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