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Science 290 (5500): 2306-2309

Copyright © 2000 by the American Association for the Advancement of Science

Genome-Wide Location and Function of DNA Binding Proteins

Bing Ren,1* François Robert,1* John J. Wyrick,12* Oscar Aparicio,24 Ezra G. Jennings,12 Itamar Simon,1 Julia Zeitlinger,1 Jörg Schreiber,1 Nancy Hannett,1 Elenita Kanin,1 Thomas L. Volkert,1 Christopher J. Wilson,5 Stephen P. Bell,23 Richard A. Young12dagger

Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.

1 Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
2 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
3 Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
4 Program in Molecular Biology University of Southern California, Los Angeles, CA 90089-1340, USA.
5 Corning, Inc., Corning, NY 14834, USA.
*   These authors contributed equally to this work.

dagger    To whom correspondence should be addressed. E-mail: young{at}wi.mit.edu

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