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Deep genomics

e to do every different cell type to get a complete picture of the organism, and that's a daunting prospect."

ChIP experiments

"In the Nature experiment," Elgin continues, "we started by looking at two different types of fruit fly cells, called S2 and BG3, that we could grow in tissue culture. By culturing the cells, we ensured we would have an abundant supply of cells whose chromatin structure we could be reasonably certain was always the same."

The cells were then run through a highly automated process to map the epigenetic marks on the DNA. For this study, the tool of choice was the chromatin immunoprecipitation or chIP array.

"In a typical experiment," says Elgin, "we expose the chromatin to formaldehyde, which binds the packaging proteins to the DNA. Then we shear the DNA into little fragments.

"And then this is the key step we put in an antibody to a particular protein modification, a chemical that binds to that protein.

"You have to be sure that your antibodies are good," Elgin says. "We went to a lot of trouble on that issue. The antibodies must recognize one protein and only that protein. That's absolutely crucial.

"Now we use that antibody to fish out all the fragments that have that modified protein and we put them in one pot, discarding all the rest of the fragments. Next we purify the selected DNA, throwing away the proteins, and we identify the fragments of selected DNA by putting them on a microarray (see illustration)."

The microarrays are read at Vincenzo Pirrotta's lab at Rutgers, and the data are sent to Peter Parks' lab at the Center for Biomedical Informatics at Harvard Medical School where computers map the marks onto the known fruit fly genome.

"You could not do this kind of biology without computers," Elgin says. "No way. The computer is an essential tool if you're going to be a biologist. Times have changed!

"We then do the same experiment ov

Contact: Diana Lutz
Washington University in St. Louis

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