Genome-wide Location and Function of DNA-binding Proteins

This site supports Ren et al., Science 290:2306-2309 (2000).

Study Design


Location Analysis


Gene Expression Data


Additional Insights



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.

Chromatin Immunoprecipitation Schematic

Crosslink protein to DNA
in vivo with formaldehyde

Break open cells and
shear DNA


blunt DNA and ligate
to unidirectional linkers


Hybridize to array


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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