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Transcriptional regulatory code of a eukaryotic genome

Author

Listed:
  • Christopher T. Harbison

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center
    Massachusetts Institute of Technology)

  • D. Benjamin Gordon

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Tong Ihn Lee

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Nicola J. Rinaldi

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center
    Massachusetts Institute of Technology)

  • Kenzie D. Macisaac

    (MIT Computer Science and Artificial Intelligence Laboratory)

  • Timothy W. Danford

    (MIT Computer Science and Artificial Intelligence Laboratory)

  • Nancy M. Hannett

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Jean-Bosco Tagne

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • David B. Reynolds

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Jane Yoo

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Ezra G. Jennings

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Julia Zeitlinger

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Dmitry K. Pokholok

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center)

  • Manolis Kellis

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center
    MIT Computer Science and Artificial Intelligence Laboratory
    Broad Institute)

  • P. Alex Rolfe

    (MIT Computer Science and Artificial Intelligence Laboratory)

  • Ken T. Takusagawa

    (MIT Computer Science and Artificial Intelligence Laboratory)

  • Eric S. Lander

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center
    Massachusetts Institute of Technology
    Broad Institute)

  • David K. Gifford

    (MIT Computer Science and Artificial Intelligence Laboratory
    Broad Institute)

  • Ernest Fraenkel

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center
    MIT Computer Science and Artificial Intelligence Laboratory)

  • Richard A. Young

    (Whitehead Institute for Biomedical Research, Nine Cambridge Center
    Massachusetts Institute of Technology
    Broad Institute)

Abstract

DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression1. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation2,3,4,5,6, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed an initial map of yeast's transcriptional regulatory code by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators.

Suggested Citation

  • Christopher T. Harbison & D. Benjamin Gordon & Tong Ihn Lee & Nicola J. Rinaldi & Kenzie D. Macisaac & Timothy W. Danford & Nancy M. Hannett & Jean-Bosco Tagne & David B. Reynolds & Jane Yoo & Ezra G., 2004. "Transcriptional regulatory code of a eukaryotic genome," Nature, Nature, vol. 431(7004), pages 99-104, September.
    • Handle: RePEc:nat:nature:v:431:y:2004:i:7004:d:10.1038_nature02800
    DOI: 10.1038/nature02800
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