Transcriptional regulatory code of a eukaryotic genome

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. Jennings, Julia Zeitlinger, Dmitry K. Pokholok, Manolis Kellis, P. Alex Rolfe, Ken T. Takusagawa, Eric S. Lander, David K. Gifford, Ernest Fraenkel () and Richard A. Young ()
Additional contact information
Christopher T. Harbison: Whitehead Institute for Biomedical Research, Nine Cambridge Center
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
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
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
David K. Gifford: MIT Computer Science and Artificial Intelligence Laboratory
Ernest Fraenkel: Whitehead Institute for Biomedical Research, Nine Cambridge Center
Richard A. Young: Whitehead Institute for Biomedical Research, Nine Cambridge Center

Nature, 2004, vol. 431, issue 7004, 99-104

Abstract: 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.

Date: 2004
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DOI: 10.1038/nature02800

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