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Hairpin Serving As Gene Control

No. 29 | 10/05/2013 | by Sel

Scientists from the German Cancer Research Center (DKFZ) discovered a previously unknown switch controlling how much of a protein a cell produces. The hairpin-shaped structure lies in the messenger RNA – the copy of a gene serving as a template for protein synthesis. As soon the hairpin is forming, various cellular components bind to and degrade the messenger RNA. This is to prevent producing too much of a harmful protein. The researchers headed by Georg Stoecklin published their results in the journal “Cell”.


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

With more than 3,000 employees, the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) is Germany’s largest biomedical research institute. DKFZ scientists identify cancer risk factors, investigate how cancer progresses and develop new cancer prevention strategies. They are also developing new methods to diagnose tumors more precisely and treat cancer patients more successfully. The DKFZ's Cancer Information Service (KID) provides patients, interested citizens and experts with individual answers to questions relating to cancer.

To transfer promising approaches from cancer research to the clinic and thus improve the prognosis of cancer patients, the DKFZ cooperates with excellent research institutions and university hospitals throughout Germany:

  • National Center for Tumor Diseases (NCT, 6 sites)
  • German Cancer Consortium (DKTK, 8 sites)
  • Hopp Children's Cancer Center (KiTZ) Heidelberg
  • Helmholtz Institute for Translational Oncology (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ
  • DKFZ-Hector Cancer Institute at the University Medical Center Mannheim
  • National Cancer Prevention Center (jointly with German Cancer Aid)
The DKFZ is 90 percent financed by the Federal Ministry of Education and Research and 10 percent by the state of Baden-Württemberg. The DKFZ is a member of the Helmholtz Association of German Research Centers.


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