Researcher:
Richard Young, member, Whitehead Institute for Biomedical Research, Cambridge, Mass.
Project:
Mapping transcription factor binding across the yeast genome.
Problem:
Chromatin immunoprecipitation (ChIP) is the standard technique for mapping protein-DNA interactions. Originally it was a targeted assay: You had to query specific genomic regions. Young wanted to probe the entire genome.
Solution:
Young combined ChIP with homemade microarrays ("chips") of 6,361 yeast intergenic fragments to obtain a genome-wide perspective on Gal4 and Ste12 binding - proteins involved in galactose metabolism and mating pheromone responses, respectively. In ChIP cells are fixed with formaldehyde to crosslink proteins to DNA. The DNA is then harvested, fragmented, and subjected to immunoprecipitation with an antibody against a protein (or DNA modifications such as methylcytosine) of interest. The cross-link is then reversed to release the DNA. In classical ChIP, the resulting DNA is queried via PCR to see if a particular fragment ...
