Hairpin Serving As Gene Control

A couple of years ago, Dr. Georg Stoecklin, Junior Research Group leader at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), discovered the short segment on the messenger RNA of tumor necrosis factor (TNF). “Certain cells of the immune system, particularly macrophages, produce TNF when pathogens invade the body. TNF attracts other immune cells, makes blood vessels more permeable and triggers an inflammation – the body’s response,” Stoecklin describes the effects of TNF. “It is absolutely vital that the macrophages do not produce too much of TNF, because this may cause septic shock!” Taking a closer look at the gene for TNF, the researchers came across a segment “highly conserved” in all mammals. “This is a hint for a very important region” said Stoecklin, who became more interested in this region.

“We found this region being present in over fifty other genes,” says Kathrin Leppek, first author of the article. These included genes important in the immune system as well as genes playing a role during embryonic development. “Both during immune response and development, a number of genes are active for only a short time. The cell has to ensure it can rapidly turn off these genes,” says Leppek. “To this end, it is necessary to degrade gene transcripts, the messenger RNA.” During her PhD thesis she found out that the short segment in the mRNA folds into a hairpin-like structure: a short stem formed by base-pairing nucleotides and a small loop at the top end. “Cellular proteins normally recognize and bind to a conspicuous structure like this,” Stoecklin explains the next step, “so we started searching for RNA-binding proteins.” Using a new purification method developed by the group, the scientists were lucky: The Roquin protein binds to the hairpin. Although this protein was already known, its exact working mechanism had not been described previously. The scientists found out that Roquin – bound to the RNA – binds an RNA degrading enzyme called ribonuclease, which degrades the messenger RNA. When preventing the formation of the hairpin structure by interfering with the gene, the scientists were able to stop the RNA decay. “Thus, we were able to demonstrate that the hairpin guarantees the only brief activity of the messenger RNA with the protein it encodes being produced only for a short time.”

This process may be a useful target in rheumatism and other chronic inflammations as well as in cachexia, a state of extreme wasting in cancer patients. In all of these conditions too much TNF is produced over a prolonged period of time. “It would be interesting to interfere in these cases by promoting the binding of Roquin to the hairpin and thus accelerating degradation of TNF messenger RNA,” Stoecklin speculates. Unfortunately, disrupting an interaction is much easier than stabilizing it. “Nevertheless, it is worth working on,” says Stoecklin, indicating his group’s future research goals.

Kathrin Leppek, Johanna Schott, Sonja Reitter, Fabian Poetz, Ming C. Hammond and Georg Stoecklin. Roquin Promotes Constitutive mRNA Decay via a Conserved Class of Stem-Loop Recognition Motifs, Cell (2013), DOI: 10.1016/j.cell.2013.04.016