Scientists Visualize Gene Regulation In Living Cells

A research team led by scientists at the National Cancer Institute (NCI), part of the National Institutes of Health (NIH), has applied advanced imaging methods and computer simulations to be able to glance at the regulation of a cancer-related gene in a living cell. They found that the efficiency with which the components of the cell's gene reading machinery come together has an impact on gene expression, the process by which a gene translates its information into a new protein. The findings, published in the May 23, 2008 issue of Molecular Cell, shed new light on the means by which living cells regulate gene activity.

"Each new discovery in the realm of gene regulation gives us a fuller appreciation of how a cell controls the expression of its own genetic program," said NCI Director John E. Niederhuber, M.D. "These findings remind us that the puzzle is not yet complete, that there are nuances to how genes are translated that we do not yet completely understand."

A key question regarding how the cell controls gene expression relates to interactions between genes and certain gene reading proteins, and between genes and transcription factors, which regulate gene transcription from DNA to RNA. The process requires the assembly of numerous transcription complexes, particularly one called RNA polymerase, at the site of a gene's promoter (the stretch of DNA before the start of a gene to which transcription factors bind) at the right time.

From earlier work done primarily by NCI researchers, the interactions among transcription factors, and between them and their target DNA, is known to be highly dynamic. What has remained unclear is whether this dynamic nature itself serves some role in regulating gene activity.

To understand the regulatory implications of this dynamism, a team of scientists probed the relationships between a large gene-reading complex known as RNA pol I and genes that encode ribosomal RNAs (rRNAs), which are key components of the cell's protein manufacturing machinery. The rRNA genes are excellent models for studying the dynamics of regulation because their transcription factors are well known, and their interactions with RNA pol I can be visualized using quantitative live-cell fluorescent microscopy, a sophisticated technique for analyzing the activities of proteins and genes in living cells in real-time.

The group's data suggest that there is indeed a regulatory role for these dynamic relationships. RNA pol I is not a single protein but rather a complex of subunits that assemble into the full polymerase when needed. According to the researchers' observations, as the cell increases rRNA production, some of the subunits associate more stably with the gene and assemble active and complete RNA pol I complexes more efficiently. As a result, the cell's production of rRNA increases.

The scientists then interfered with the interactions between the RNA pol I subunits and another transcription factor, thereby mimicking the conditions of a cell that was able to produce rRNA at a high rate. As a result, the efficiency of RNA pol I assembly and the pace of rRNA output both decreased dramatically.

The findings suggest that the efficiency with which the RNA pol I complex assembles all its subunits -- which is controlled by a dynamic interplay of polymerase and non-polymerase transcription factors -- plays a significant role in determining when a given gene is turned on. While the group looked only at RNA polymerase I, other research suggests that the phenomena they observed may represent a general mechanism for regulating gene transcription.