Genes to proteins

An individual’s genome contains a set of genes: DNA sequences that code for the individual protein molecules that are essential to build a healthy functioning cell. That genome also contains sequences of DNA that aid in regulating how the genes are “expressed, ”that is, what happens when a particular gene is turned on so that it results in the transcription of the genetic code, and the subsequent production of its protein. Functional genomics aims to understand how genes are regulated and how an entire suite of gene products, RNA and proteins, act in concert to achieve function.

“If we can understand how a cell works at the level of all its proteins, we will be in a much, much better position to understand how to address the problems that arise from malfunctions in cells, resulting, for example, from inherited disease or infection,” according to Los Alamos researcher Norman Doggett.

“We need this to achieve the next advances in medicine and biology,” he said.

Functional genomics will help to determine or assign function to each gene or gene product of the genome. “It’s understanding the purpose of every gene in the genome.”

Up to this point, researchers have decoded the characters that make up the genes —researchers for example know there are about 30,000 to 35,000 genes in the genome. “But that still doesn’t tell us what those genes do,” said Doggett.

One approach, global gene expression analysis, uses a fluorescently tagged DNA copy of a cell ’s messenger RNA, or ribonucleic acid, to bind to a collection of genes that are spotted on a glass slide.

Using specially treated microscope slides, researchers can place about 40,000 DNA spots corresponding to different genes into an area that is smaller than a postage stamp. The fluorescently labeled DNA copy of messenger RNA binds to its matching genes to let researchers know which genes are active in a given cell type.

In this global gene expression study, scientists can determine which genes are transcribed into RNA and which in turn are translated into protein.

“We want to know for each gene which tissue or cell type it is expressed in — in which tissue or cell type it is turned on, thereby making an active protein.” said Doggett.

Los Alamos has created a database and supporting computational software to address global gene expression data that researchers around the world are using.

Another method of functional genomics that researchers are actively engaged in is being pioneered at Los Alamos: phage display. Phage is a virus that infects bacterial cells; bacteria phage is used as a tool for producing antibodies. Antibodies are important tools for functional genomics analysis because they help researchers understand the function of proteins in a cell. Researchers also use the phage-display approach to isolate and identify proteins.

Yet another approach, called mass spectrometry, uses a mass spectrometer that allows researchers to take an unknown protein and determine enough of its amino acid composition to identify what protein it is and what gene it came from. This approach is particularly useful for determining how cells respond to external stimuli such as low dose radiation or exposure to pathogenic agents.

“If I want to study how a cell responds to the influenza virus, this is a very important approach...we will see how a cell responds at the protein level,” said Doggett.

Researchers using this approach also can see how proteins bind to other proteins, what are their biochemical pathways, which again is important in determining how genes function. In addition to work being done at Los Alamos, the Department of Energy recently announced a new initiative that builds upon existing genome esearch. The “Genomes to Life” initiative will develop genome-scale high-throughput and computational approaches for how genes function.