Study
Design
Location
Analysis
Gene
Expression Data
Additional
Insights
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Our long term goal is to understand how DNA-binding
proteins control global gene expression, chromosomal
replication and cellular proliferation in vivo. We have
developed a genome-wide location profiling method for
DNA-bound proteins and have used it to monitor dynamic
binding of Gal4 and Ste12, two gene-specific transcription
activators of yeast cells. Genome-wide location analysis
should be a powerful tool for further dissecting gene
regulatory networks, annotating gene functions and exploring
how genomes are replicated.

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Crosslink protein to DNA
in vivo with formaldehyde
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Break open cells and
shear DNA
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Immunoprecipitate
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Reverse-crosslinks,
blunt DNA and ligate
to unidirectional linkers
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LM-PCR
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Hybridize to array
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Schematic summary of the Genome-wide location
profiling method.
The genome-wide location analysis method we have developed
allows protein-DNA interactions to be monitored across the
entire yeast genome. The method combines a modified
Chromatin Immunoprecipitation (ChIP) procedure, which has
been previously used to study in vivo protein-DNA
interactions at one or a small number of specific DNA sites
(Aparicio,
1999; Orlando
et al., 2000), with DNA microarray analysis.
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