Scientists use DNA Chips to Dissect Cells’ Genome Circuitry

CAMBRIDGE, Mass. — Using a hot new microchip technology, scientists at the Whitehead Institute for Biomedical Research have identified how key components of the cell’s gene-reading machinery coordinate the expression of genes throughout the genome of a living organism. This first generation genome-control map, deduced in yeast, represents a major step forward in dissecting the circuitry by which genomes—the genetic instructions that make up organisms—are turned on and off during normal and abnormal growth and development. Because the gene-reading apparatus in yeast and human cells are highly similar, these findings will help researchers lay the foundation for producing a similar genome-control map in humans.

The genome-control map is similar to an electrical wiring diagram. It describes the connections and switches that control the hundreds or even thousands of genes active in a cell at any one time. Such information is fundamental to understanding basic disease processes and for developing new drugs. The results are published in the November 25 issue of Cell by a team led by Dr. Richard Young of the Whitehead Institute. The project also represents a new level of sophistication in the use of web technology to convey complex research results.

Scientists’ understanding of gene regulation has been limited by the study of a few dozen genes, but living organisms contain thousands of genes that are controlled in an organized fashion so as to determine whether a cell becomes a liver cell or a brain or muscle cell. “Until recently, the circuitry controlling genome regulation was a black box—we didn’t know exactly how it was wired to interpret the genetic blueprint in cells. What we were able to do in this study is find the set of parts that are responsible for regulating each gene, and the set of genes regulated by each part,” says Dr. Young.

In identifying the circuitry, first author Dr. Frank Holstege, Dr. Young, and their colleagues used California-based company Affymetrix’s GeneChip® probe arrays. DNA arrays are used by biotech companies and genome laboratories to analyze the activity of thousands of genes simultaneously. Called “expression profiling,” this technology produces signature patterns of genome expression that help researchers identify cell states—determine the stage of cancer or tell if it is metastatic—and aids drug discovery by allowing researchers to see how the pattern of genome expression changes when exposed to a battery of drugs. The technology also is useful in diagnosis, toxicology, and basic research into the mechanisms of genes.

“Although DNA arrays have been used in expression profiling of healthy and diseased cells, this is the first time that the technology has been used to identify the fundamental genome-control circuitry of a cell,” says Dr. Young.

The Whitehead team dissected the genome-wide expression of genes by introducing mutations into various components of the yeast’s gene-reading apparatus and noting the effects of these defects on gene expression. From this information, researchers derived a circuitry that describes the set of components responsible for regulating each gene and the set of genes that are controlled by each transcription factor. The researchers then deduced the target of the molecular pathways by comparing the genome expression signature produced by altering the environment of the cell and the signatures produced by mutations in each component of the transcription apparatus.

“In this and in other ways, the genome control map is fundamental for interpreting the biological meaning of data from genome expression monitoring. Such information will lay the foundation for understanding how the cell responds to the environment by remodeling gene expression throughout the genome,” says Dr. Holstege. The Whitehead researchers plan to obtain a complete description of the regulatory components of yeast genes by next summer. In yeast, there are 250 activator proteins that turn genes on or off and about 100 components that comprise the gene-reading machinery.

“As more academic and pharmaceutical scientists use array-based technology, understanding the circuitry that produces specific gene-expression profiles is becoming very important. Expression profiling allows researchers to understand the mechanisms involved in diseases, the pathways of drug action, and potential side effects. Genome control maps of the type we have produced will allow us to fully understand these expression profiles and should improve our understanding of diseases and facilitate drug development,” says Dr. Young.

The study was funded by a Genome Consortium, comprised of Affymetrix Inc., Bristol-Myers Squibb Company, and Millennium Pharmaceuticals; the National Institutes of Health; and by fellowship support from European Molecular Biology Organization, the Human Frontier Science Program, and the Howard Hughes Medical Institute, the National Science Foundation; and by a Burroughs-Wellcome Fund Career Award in Biomedical Sciences.

Citation

Holstege, F. C., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., ... & Young, R. A. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell, 95(5), 717-728.