Yale Researchers Find All of the Gene Targets for a Protein
Using new DNA chip technology, Yale researchers have identified virtually all of the gene targets of some key proteins, known as transcription factors.
Transcription factors tell a cell whether it will be, for example, a muscle cell or a nerve cell. They determine the fate of a cell by “turning on” a particular assortment of genes within the cell and they can control cell proliferation.
The transcription factors studied by the Yale team control cell proliferation in yeast. Previously, only a few targets had been identified. The new technology developed by the Yale team allow them to find all of the targets simultaneously using DNA chip technology. DNA chips are glass microscope slides that are spotted with very small amounts of DNA. All of the genes, which are composed of DNA, that are found in the yeast genome are placed in their own individual spot on a single slide. By using these yeast DNA chips, researchers are able to identify all of the genes that a transcription factor will bind.
“Our method takes advantage of genomics and all of the targets in one simple experiment,” said Michael Snyder, professor and chairman of the Department of Molecular, Cellular and Developmental Biology and professor in the Department of Molecular Biophysics and Biochemistry at Yale. “Then you have a good idea of how a transcription factor turns cells into what they normally do. The transcription factors we tested govern the cell cycle. They tell cells it’s time to enter a new cell cycle, when it’s time to make a new cell.”
In the study published in this week’s issue of the journal, Nature, Yale researchers in collaboration with researchers at Stanford University identified almost 250 genes that were bound by these key transcription factors. Many of these genes are known to play a role in the start of a new cell cycle or in the making of a new cell. But many genes with unknown functions were also identified.
The principal authors of this study were Vishwanath Iyer, currently a professor at the Institute of Molecular and Cellular Biology at the University of Texas in Austin, and Christine Horak, a graduate student in Snyder’s laboratory in the Department of Molecular, Cellular and Developmental Biology. Co-authors include Charles Scafe, a postdoctoral fellow in genetics at Stanford; David Botstein, a professor of genetics at Stanford, and Patrick Brown, a Howard Hughes investigator and professor in the Department of Biochemistry at Stanford.
Snyder said the method of analyzing the transcription factors can be used for any organism and for any species - including humans.
“The transcription factors we looked at in yeast have counterparts in humans,” he said. About two-thirds of the yeast genes exhibit similarity to human genes. Applying the method developed for analyzing transcription factors in humans will prove to be powerful. It’s a step towards understanding, for example, why a brain cell is a brain cell and how a muscle cell becomes a muscle cell.
Snyder’s laboratory has pioneered many new chip technologies. His laboratory has recently invented new protein chip technologies for analyzing hundreds to thousands of proteins simultaneously.
Protein chips are disposable arrays of microwells in silicone sheets placed on top of microscopic slides. The high density and small size of the wells allows for high throughput (a measure of rate of production) batch processing and simultaneous analysis of many individual samples. Only small amounts of protein are required.
In a study published in the November issue of Nature Genetics, Yale researchers overexpressed nearly all of the yeast protein kinase and analyzed them using 17 different substrates and protein chips. Protein kinases are key regulatory molecules that control many biological processes. They discovered many novel activities of the protein kinases that were not known previously.
“Our study identified a number of novel features of the protein and demonstrates that protein chip technology is useful for high throughput screening of protein biochemical activity,” Snyder said. “Our method takes advantage of genomics and all of the targets in one simple experiment.”
Co-authors of the protein chip study in addition to Snyder were Heng Zhu, principal author and a postdoctoral fellow in the molecular, cellular and developmental biology; James Klemic, a postdoctoral associate in electrical engineering and applied physics; Paul Bertone, a graduate student in molecular biophysics and biochemistry; Mark Gerstein, assistant professor of molecular biophysics and biochemistry, and Mark Reed, the Harold Hodgkinson professor of engineering and applied science, chairman of the Department of Electrical Engineering, and professor of applied physics.