A series of discoveries that dramatically alter the understanding of how cells turn genes on are announced in July issues of the international science journals Nature and Cell. The research, which reviewers at Cell have described as "provocative and highly significant," reveals molecules previously unknown to be involved in gene expression plus unexpected dynamics among these molecules, which work together as a team to activate genes.
"Gene-activation is a factor in diseases involving cancers, viruses, and hormones, and we now are starting to get a much more detailed understanding of how this important process works," says Jerry L. Workman, associate professor of molecular and cell biology at Penn State and the leader of the research group that made the discoveries.
Workman's research reveals new players on the team of molecules that turn on a gene--a precise section of DNA containing one of the cell's operating instructions--by making a copy of its code, which the cell then uses as a template for making whatever protein the gene is designed to produce. "Each cell turns on only the particular genes it needs for whatever function it needs to perform," Workman explains.
Scientists already knew some of the players on the gene-copying team, which Workman's research has now shown to be much larger and more complicated. They knew that inactive genes are locked inside densely knotted structures called nucleosomes. They also knew that the nucleosome knots are held together by powerful histone proteins, whose grip has to be broken before a gene can loosen up enough to be turned on by another kind of molecule, the transcription enzyme RNA polymerase. "RNA polymerase turns a gene on by attaching to it and moving along its length, making an RNA copy of its DNA code," Workman explains. Recently Workman's lab also characterized a powerful enzyme called SWI/SNF that overpowers the histone proteins, untangling the gene and making it accessible to the RNA polymerase enzyme. Plus, they showed recently that another molecule, a transcription activator, helps RNA polymerase attach exactly at the right spot on the DNA to start copying a specific gene.
Now, Workman's lab has identified even more molecular players plus the roles they play and some of the complex interactions among them. "Rhea Utley, a graduate student in our group, discovered that the transcription activators directly link to a very large protein group called a histone acetyltransferase complex (HAT), which contains an enzyme called Gcn5 that remodels nucleosomes by attaching a chemical group called an acetate," Workman says. "Dave Steger, a postdoc in the group, found that this acetylation reaction is involved very intimately in the regulation of gene transcription," explains Workman, who speculates that it somehow helps the RNA polymerase enzyme to copy the gene.
Workman's group also discovered two large HAT complexes containing between ten and twenty proteins each, which they describe in the Cell and Nature papers. "Once an activator is able to bind to a gene, it can grab one of these HAT complexes and bring it to the gene so that the Gcn5 enzyme can unlock the nucleosomes by adding acetate groups onto the histones," Workman explains.
"Patrick Grant, a postdoc in our group, found that HAT complexes not only contain histone acetylation proteins but also TAF proteins, which are known to bind to another very large system of proteins known as TFIID, which is important for telling the RNA polymerase where to start copying a gene," Workman says. "We've also shown that this binding process requires a molecule called Acetyl CoA, which is a little protein that has an acetate group attached to it," he says, explaining that the Gcn5 enzyme takes the acetate group off the Acetyl CoA molecule and adds it to the histones.
One reason the Workman group was able to make so many discoveries at once is that it is the first lab to isolate and purify the individual HAT complexes, and then the individual proteins within each complex, and to make enough of the purified proteins to do experiments designed to find out how each one works. The purifications were done by current and former postdocs in the Workman lab, including Patrick Grant, Jacques Cote, Anton Eberharter, and Sam John. "Some of the experiments we've done show that transcription activators and HAT complexes bind to each other," Workman explains. Some of his other experiments showed that this binding causes the HAT complexes to acetylate only those nucleosomes that are bound by the transcription activator.
"This research changes and complicates quite a bit our picture of how gene regulation at the level of transcription actually is orchestrated," Workman comments. "It demonstrates that the process controlling gene expression is very dynamic, very interactive, and very complicated."
Supporters of this research include the Howard Hughes Medical Institute, United States National Institutes of Health, National Center for Research Resources, National Institute of General Medical Sciences, American Cancer Society, Howard Hughes Medical Institute, National Science Foundation Science and Technology Center, Leukemia Society, Austrian Science Foundation, Cancer Research Institute, and Canadian Medical Research Council. In addition to Workman, researchers at Penn State include Assistant Professor Joseph C. Reese; graduate student Rhea T. Utley, postdoctoral fellows Anton Eberharter, Patrick A. Grant, Keiko Ikeda, Sam John, and David J. Steger; and research associate Marilyn G. Pray-Grant. Researchers at the University of Washington include research associate David Schieltz and professor John R. Yates, III, and at Laval University include professor Jacques Cote. Workman is a former Leukemia Society Scholar and is currently a Howard Hughes Medical Institute Investigator.
The above story is based on materials provided by Penn State. Note: Materials may be edited for content and length.
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