Study provides new insights into emerging theory of gene regulation

With the full sequence of the human genome now in hand, scientists are turning renewed attention to the molecular processes that regulate the genes encoded by DNA. Estimates are that only a tenth of all genes are expressed at any given time. What controls when and where genes are activated?

Increasingly, researchers believe that the mechanisms that govern gene activity themselves resemble a complicated non-DNA code – an intricate pattern of activity among the molecules that package and control access to the DNA. They suspect that the coordinated interplay of a number of specific enzymes is required to turn on a particular gene.

Now, in a new study using the techniques of structural biology, investigators at The Wistar Institute have shown in detail how two enzymes work together to activate a specific gene by loosening, at that gene’s location, the compact coils of DNA and packaging proteins called chromatin. The findings bolster the emerging theory that something like a code is responsible for orchestrating genetic activity. A report on the research appears in the August issue of Molecular Cell, published August 28.

“This is the first time we’ve understood the precise mechanism of how two specific modifications to the DNA packaging proteins interact synergistically to promote the expression of a particular gene,” says Ronen Marmorstein, Ph.D., a professor in the Gene Expression and Regulation Program at Wistar and senior author on the study.

Most of the time, the great majority of genes are silenced, locked away within the packaging proteins of chromatin. For a given gene to be activated when needed, the chromatin must be opened at that gene’s location on the DNA, and that location only, to make the gene physically accessible for transcription. Histone proteins play a key role in this process.

Histones are relatively small proteins around which DNA is coiled to create structures called nucleosomes. Compact strings of nucleosomes, then, form into chromatin, a substructure of chromosomes. When the DNA is tightly wrapped around the histones, the genes cannot be accessed and their expression is repressed. When the coils of DNA around the histones are loosened, the genes become available for expression, and it is the enzymatic activity governing this process in a specific case that Marmorstein’s laboratory was able to illuminate.

Working in yeast, Marmorstein and his colleagues showed that when a kinase enzyme adds a phosphoryl group to a histone molecule at a particular location, it helps a histone acetyltransferase enzyme to add an acetyl group at a second location on the same histone molecule. The acetylation of the histone then is thought to prompt a loosening of the DNA coils around the histone to permit transcription of the gene on that length of DNA.

“Five to ten years ago, most biologists thought that the proteins that package DNA served only to maintain physical order,” Marmorstein notes. “It’s becoming clear, however, that these non-DNA elements of chromosomal structure dramatically influence gene expression. Proteins are coming on and off the DNA at specific times and locations to trigger the activation of genes.”

The so-called “histone code” theory of gene regulation, advanced by C. David Allis, Ph.D., at the University of Virginia, and others, suggests that complex, interdependent modifications to the histones are responsible for controlling gene activity. The new data from the Wistar research team supports this view.

The two lead authors on the Molecular Cell study are Adrienne Clements, Ph.D., at Wistar, and Arienne N. Poux, at Wistar and the University of Pennsylvania. Wan-Sheng Lo, Ph.D., at Wistar, and Lorraine Pillus, at the University of San California, San Diego, are co-authors. Shelley L. Berger, Ph.D., the Hilary Koprowski Professor in the Gene Expression and Regulation Program at Wistar, was a collaborator and co-author on the study.

An earlier study by Berger and Wistar associate professor Ramin Shiekhattar, Ph.D., published in the August 10, 2001, issue of Science, reported the link between the two chromatin-modifying events, but details concerning the mechanism of action remained to be determined in the current research project.

Primary funding for the research was provided by the National Institutes of Health. Additional support came from the Commonwealth of Pennsylvania and the Leukemia & Lymphoma Society.

The Wistar Institute is an independent nonprofit biomedical research institution dedicated to discovering the causes and cures for major diseases, including cancer, cardiovascular disease, autoimmune disorders, and infectious diseases. Founded in 1892 as the first institution of its kind in the nation, The Wistar Institute today is a National Cancer Institute-designated Cancer Center – one of only eight focused on basic research. Discoveries at Wistar have led to the development of vaccines for such diseases as rabies and rubella, the identification of genes associated with breast, lung, and prostate cancer, and the development of monoclonal antibodies and other significant research technologies and tools.