February 6, 2004— A method for determining the function of large numbers of genes is being developed and piloted by Howard Hughes Medical Institute (HHMI) researchers at Harvard Medical School. In a trial of the technique, the researchers characterized the role in growth and viability of nearly all the genes in the genome of the fruit fly Drosophila.

　　Although the fruit fly genome was chosen for the first study, the researchers are confident that their technique can be applied to any organism, including humans. “A major challenge now that many genome sequences have been determined, is to extract meaningful functional information from those projects,” said HHMI researcher Norbert Perrimon, who directed the study. “While there are a number of analytical approaches that can measure the level of gene expression or the interaction between proteins, ours is really the first high-throughput, full-genome screening method that allows a systematic interrogation of the function of every gene.”

　　The research team, which included Perrimon and colleagues at Harvard Medical School, the University of Heidelberg and the Max Planck Institute for molecular Genetics in Germany, described its technique in the February 6, 2004, issue of the journal Science.

　　The screening technique developed by Perrimon and his colleagues builds on methods developed in one of the hottest areas of biology, RNA interference (RNAi) research. In RNAi, double-stranded RNA (dsRNA) that matches the messenger RNA produced by a given gene degrades that messenger RNA — in effect wiping out the function of that gene in a cell. RNAi is widely used as a research tool to selectively erase the cellular contributions of individual genes to study their function.

　　In their mass screening technique, Perrimon and his colleagues first created a library of 21,000 dsRNA that corresponded to each of the more than 16,000 genes in the Drosophila genome. They then applied each of these dsRNA molecules to cultures of Drosophila cells and assayed how knocking down the function of a targeted gene affected cell numbers in the cultures. This basic measure, said Perrimon, revealed genes that are not only involved in general cell growth, but also in the cell cycle, cell survival and other such functions.

　　The researchers then selected 438 GENEs for further characterization. The degradation of these genes produced profound affects on cell number. “Out of this subset, we found many that produced proteins involved in general metabolic processes such as the ribosomes that are components of the protein synthesis machinery,” said Perrimon. “But we also found genes that are more specific to cell survival.”

　　According to Perrimon, only 20 percent of the genes that were identified had corresponding mutations — an important characteristic for studying gene function. “The classic approach to studying gene function is to identify mutations in genes and select those that produce interesting phenotypes that yield insight into function,” said Perrimon. “But this approach has never really given us access to the full repertoire of genes. With this high-throughput technology, however, we can study the function of a complete set of genes. We can systematically identify all the genes involving one process.”