Researchers at the Universities of Bonn and Bayreuth in Germany have developed a much more specific optical switch that makes it possible to control the lifespan of regulatory RNA molecules precisely. This novel approach could easily allow for regulating micro RNAs and short hairpin RNAs in a spatiotemporally precise manner. Findings from this new study were published recently in Nature Communications through an article titled “Optoribogenetic control of regulatory RNA molecules.”

Within every cell resides a mechanism that ensures mRNA transcriptions are “shredded” after a short time. This ensures that protein is only produced as long as it is needed. Several decades ago, researchers came up with the idea of using this shredder for their purposes—by specifically attaching a marker to specific mRNAs. This ensures that the transcriptions are not used as building instructions at all but are destroyed immediately—a process also known as RNA silencing. The cell then lacks the corresponding protein. This makes it possible to determine the protein’s function quickly.

In the current study, the researchers took a similar approach—however, allowing for a far more differentiated control over the lifespan of the mRNA copies. “We use a bacterial molecule to control the shredding of mRNA transcriptions with the help of light,” explained senior study investigator Günter Mayer, PhD, who heads the Chemical Biology & Medicinal Chemistry Research Group at the LIMES Institute of the University of Bonn.

The bacterial molecule PAL acts as a kind of switch. It changes its shape under the influence of blue light. In the process, a pocket is exposed that can bind to individual molecules. “We searched a huge library of artificially produced short RNA molecules called aptamers,” said Mayer. “Eventually we came across an aptamer that’s a good match for the pocket in the PAL molecule.”

When illuminated the PAL molecule binds to the aptamer (blue loop at the top left). The label made of regulatory RNA can therefore no longer bind to the mRNA. This way it will not be degraded. [Sebastian Pilsl/AG Mayer/Uni Bonn]
We generated chimeric regulatory RNAs that interact reversibly and light-dependently with the light-oxygen-voltage photoreceptor PAL,” the authors wrote. “By harnessing this interaction, the function of micro RNAs and short hairpin RNAs in mammalian cells can be regulated in a spatiotemporally precise manner. The underlying strategy is generic and can be adapted to near-arbitrary target sequences. Owing to full genetic encodability, it establishes optoribogenetic control of cell state and physiology.”

The researchers coupled this aptamer to one of the molecular markers that can attach to mRNAs and release them for degradation. “When we irradiate the cell with blue light, PAL binds to the marker via the aptamer and thus puts it out of action,” noted lead study investigator Sebastian Pilsl, a PhD candidate at the University of Bonn. “The mRNA is then not destroyed but translated into the corresponding protein.” As soon as the researchers switch off the blue light, PAL rereleases the label. Now it can attach itself to the mRNA, which is then shredded.

This technology should enable researchers to investigate exactly where and when a protein is needed in a cell, simply by immersing an area of the cell in blue light at a certain time and then looking at the consequences. In the current study, they applied this to proteins that play an important role in the regulation of the cell cycle and cell division. The combination of aptamer and degradation marker is introduced into the cell by genetic engineering. This means that it generates the light-dependent degradation signal itself—it does not have to be supplied from outside.

“This method can therefore be used to switch off practically every mRNA molecule in the cell in a controlled manner,” concluded co-senior study investigator Andreas Möglich, PhD, a professor at the University of Bayreuth.

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