GeneChip

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

Immunoprecipitate

Reverse-crosslinks,
blunt DNA and ligate
to unidirectional linkers

LM-PCR

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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