RNA Snippets Pack Power

TWO INDEPENDENT REPORTS help clarify how microRNA (miRNA) molecules regulate gene expression in cells. Collectively, the studies show that cells use miRNAs to fine-tune protein synthesis and that each miRNA molecule can control the production of a surprisingly large number of proteins.

Every eukaryotic genome encodes hundreds of miRNAs, which are short RNA sequences 22- to 24-nucleotides long. These tiny snippets of RNA molecules work in two ways: They inhibit gene expression by blocking the translation of messenger RNAs (mRNAs) into proteins by binding to short complementary sequences in the untranslated region of target mRNAs, and they inhibit protein synthesis by increasing the degradation of target mRNAs.

A team led by David Bartel, a member of the Whitehead Institute for Biomedical Research and biology professor at MIT, has now shown that the mRNA destabilization route is particularly important. Although miRNAs depress production of target proteins only slightly, this minor inhibition gives cells an important way to fine-tune protein synthesis, they report (Nature, DOI: 10.1038/nature07242).

In a separate study, systems biology professor Nikolaus Rajewsky of the Max Delbrück Center for Molecular Medicine, in Berlin, and Matthias Selbach, director of the center's intracellular signaling and mass spectrometry team, used a modified version of the isotope-labeling technique known as SILAC to show that each miRNA in the cell modulates the production of a surprisingly large number of cellular proteins (Nature, DOI: 10.1038/nature07228). "A single miRNA appears to tune expression of almost all cellular proteins in a seemingly reversible manner," Selbach says.

Traditional SILAC (stable isotope labeling of amino acids in cell culture) allows researchers to quantitatively measure protein synthesis in cells but is limited to analyzing only proteins with high turnover rates. Rajewsky and Selbach's team altered this method to examine proteins without high turnover rates. To measure the specific effects of a single miRNA on overall protein synthesis, the group inserted a gene that overproduces a miRNA into cells growing in culture. The modified cells and a control group of cells that contain normal levels of the miRNA were then transferred to media containing amino acids labeled with medium-heavy and heavy isotopes, respectively. By using two isotopes, the researchers were able to measure protein production over time in both groups of cells using mass spectrometry. The ratio of medium-heavy to heavy isotopes identifies which proteins' levels have decreased—and by how much—in the presence of the additional miRNA.

Together, says Anindya Dutta, professor of biochemistry and molecular genetics at the University of Virginia Medical School, these findings indicate that researchers, with the help of quantitative proteomic measurements, likely would discover many new miRNA targets.