22 Dec 2000

In today's issue of Science, researchers at the Whitehead Institute and Corning Inc. describe a new microarray technique that can decipher the function of master switches in a cell by identifying the set of genes they control across the entire genome. These master switches are DNA-binding proteins called gene activators. In humans, there are about a 1,000 such activators controlling important functions in life, including cell growth and development. Some of the best known of these switches-the p53 protein, for example-are those that play a role in cancer.

DNA arrays are useful for capturing a snapshot of genes that are being expressed at a given moment, but pinpointing the master switch genes amid the welter of expressed genes has been a daunting challenge. In this study, the researchers created a technique to overcome this problem. The technique involves first fixing DNA-binding proteins in living cells to their binding sites using chemical crosslinking methods, and then utilizing antibodies coupled with magnetic beads to fish out DNA fragments cross-linked to proteins of interest. The purified DNA-protein complexes are then broken apart to yield DNA fragments that bind to proteins of interest. The researchers then label these fragments with fluorescent dye and hybridize them to a DNA array containing genomic DNA from yeast to reveal their identity.

"Our goal is to use this technique to find the circuits controlled by the 200 or so master switches in yeast and then develop analogous techniques in humans," says study leader Richard Young. The study reports that the technique can correctly identify the circuits controlled by two known master switches in yeast. "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," says Young. Scientists know the identity of nearly 600 master switches and know the function of at least 250 of them; their hope always has been to find the set of all genes they control so that they could crack open the genetic basis of health and disease. The new technique provides a way to obtain the data in a global fashion and leapfrog over years of painstaking molecular and biochemical analysis that was previously required to get at this information.—June Kinoshita