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Science 22 December 2000: Vol. 290. no. 5500, pp. 2306 - 2309 DOI: 10.1126/science.290.5500.2306
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Reports
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. Young12
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.
To whom correspondence should be addressed. E-mail:
young{at}wi.mit.edu
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Nucleic Acids Res.
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Nucleic Acids Res.
35, 1085-1097
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