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Molecular Machinery That Controls Genes

Yuichiro Takagi
Department of Structural Biology
Stanford University School of Medicine
March 2002

I have been studying the molecular machinery called "Mediator". Mediator is one of the key players involved in reading the genetic information stored in DNA. Since cells can become cancerous or diseased if they incorrectly read genetic information, studies of how Mediator works will lead to a deeper understanding of the mechanisms of many diseases.

The mapping of the human genome is an unprecedented achievement. After all, what genes are made out of is the blueprint of every living organism including human beings. What is important now, however, is to understand how cells use the information found in DNA, which determines almost every aspect of biological activity including development. It is such an important step that problems in reading genetic data may lead to various diseases. Indeed, the malfunction of certain genes has already been linked to the formation of cancers such as leukemia.
I have been studying how cells read DNA information by looking at the molecular machinery involved in this process. This process is called transcription. My principal approach lies in biochemistry, an approach in which the cross-section of life is assembled in a test tube. It is like cooking in which all the necessary ingredients are mixed and cooked at a certain temperature for a defined period of time, and one can see how much of a final product has been made or how the presence or absence of a particular ingredient affects the outcome. By mimicking the activity that goes on inside cells and looking at the actions of the different ingredients, one might be able to peek at what is going on inside real cells.
In my experiments, DNA and the proteins obtained from the cells were the ingredients in order to mimic transcription in a test tube. Some proteins are directly involved in reading DNA information. Others play roles in controlling them. One of the key controlling players is a factor called Mediator. It was named Mediator because its apparent role is to channel the signals sent by the cell to tell the DNA reading machinery to start transcription. In other words, Mediator appears to be the component between the cell and the reading machinery. How Mediator works remains a mystery. That has been a focus of my research. My method has a slight twist. Rather than just looking at the normal form or "wild type" of Mediator, I have been studying the mutant form of Mediator. This mutant form of Mediator is interesting in that it behaves just like the wild type. However, once the temperature gets slightly higher, it does not work at all, just as if it no longer existed.
I have found that once mutant Mediator becomes defective in its function upon shifting to higher temperature, no transcription takes place. This was surprising because the test tube contained all the components sufficient to start transcription, and Mediator is not a part of the DNA reading machinery. Yet, it is essential for transcription. Why?
I now believe that other unidentified players exist in the test tube that prevents transcription from happening if Mediator is not working properly. Mediator seems to remove negative effects and set the stage for transcription to occur. My finding has led to a fascinating speculation that Mediator may play a critical role in a decision-making:
Transcription will not be turned on until Mediator works to suppress negative effects. Mediator might be a traffic controller in reading genetic information.