DNA Microarrays

Gene expression analysis can also be done using a powerful technique called serial analysis of gene expression (SAGE). Like microarrays, SAGE starts by isolating RNA from the tissue of interest. This RNA is then processed through a long series of steps resulting in the isolation of a set of very short sequences, called tags, from each transcript in the cell. These tags are converted into corresponding segments of DNA. These pieces of DNA, which are 14 base pairs long, are then linked together into long chains, and their sequence of bases is determined. Tens of thousands of these SAGE tags are sequenced from each tissue that is being studied. The tags corresponding to a given gene from one tissue are counted and compared to those from the same gene in another tissue.

For example, a colon cancer tumor sample might generate 50,000 SAGE tags, thirty-three of which correspond to a specific gene. A second library made from normal colon cells might have fifty thousand tags, eleven of which correspond to the same gene. This would indicate that the gene is expressed at a level that is three times as great in tumor cells than it is in normal cells.

SAGE data is significantly more difficult and expensive to produce than microarray data, but it offers the advantage of providing very precise and quantitative measurements of expression levels. SAGE has the further advantage that it can detect genes that have not been previously characterized. Such unknown genes cannot be detected by microarrays, because researchers must first know their sequence before they can place them on the array. SAGE therefore can be used as a gene discovery tool.

SAGE has been used most extensively in cancer research. Investigators in the Cancer Genome and Anatomy Project have created more than one hundred SAGE libraries from normal and cancerous tissue. Analysis of these libraries has revealed a great deal about the way that gene expression changes in cancerous tissue, which in turn has provided insight into new diagnostic and treatment options.

SAGE has also been used as a tool to help calculate the total number of genes in the human body, as well as to describe the ways in which genes are regulated and processed at different times. Microarrays and SAGE analysis are only two of the many ways that scientists have examined gene expression. As these techniques become more refined, and as new techniques are developed, they will provide a powerful tool to investigate how the incredible diversity and complexity of our tissues can arise, even though every cell in our bodies contains exactly the same set of genes.