Once the Human Genome Project delivers a list of all of our genes, the next trick will be figuring out just what those genes do. Making the job a little easier, though, is a new DNA microarray technique developed by scientists at the Whitehead Institute at the Massachusetts Institute of Technology and Corning, Inc. Reporting in today's issue of Science, Richard Young and his colleagues unveil a method that identifies in about a week which cellular circuits are controlled by which master switches in the genomea task that ordinarily takes years. "We are very excited by these results because they suggest that our technique can be used to create a 'user's manual' for the cell's master controls, a booklet that matches the master switches to the circuits they control in the genome," Young says.
The master switches are in fact proteins, called gene activators, that bind to specific regions of DNA, or genes, and in doing so, initiate series of steps that control everything from cell growth and development to seeding disease. Young's group built their method around DNA microarrays because these devices make it possible to take a kind of snapshot of a cell, and see which genes are turned on and which are turned off. For biologists, knowing which genes are active as a cell performs some function is incredibly useful information, much like being able to match the individual notes in a chord with the sound they produce. But it doesn't reveal which master switchor handplayed the notes, and the human genome contains about 1,000 master switches. To date, scientists know the activity of only a quarter of them, such as the p53 protein, which plays a role in cancer.
The first step in the new technique is fixing the master switch proteins in living cells to their DNA binding sites using chemical crosslinking methodssort of like gluing the hands to the keys they are striking. The scientists then open the cells, creating a soup of protein-DNA complexes. They use antibodies with magnetic beads to draw out interesting fragments of DNA, with the master switch protein still attached. Next they isolate the DNA fragments, label them with fluorescent dye and hybridize them to a DNA array containing genomic DNA from yeast, which identifies what they are. As a test of the method, Young and his colleagues demonstrated that it can successfully pick out the cellular circuits controlled by two known master switches. "Our goal is to use this technique to find the circuits controlled by the 200 or so master switches in yeast," Young adds, "and then develop analogous techniques in humans."