ABOVE: An example of the reporter system designed by Lara Mahal and colleagues to reveal miRNA regulation of a given gene, where decreased fluorescence signifies downregulation of gene expression while increased fluorescence signifies upregulation. Lara Mahal
MicroRNAs—snippets of nucleic acids a couple dozen base pairs in length—are so small that they went unnoticed for decades despite wielding enormous influence in our cells. It’s now known that they suppress the expression of thousands of genes through a process called RNA interference, in which they bind to messenger RNAs (mRNAs) and prevent their translation. But a study published November 9 in ACS Central Science finds that microRNAs (miRNAs) can also amplify gene expression.
“It changes the landscape of microRNA,” Lara Mahal, a chemist at the University of Alberta in Canada tells The Scientist. “There isn’t one mode of microRNA regulation: There are two.”
See “The Noncoding Regulators of the Brain”
This isn’t the first time that miRNAs were found to enhance gene expression. A paper published in Science in 2007 pointed to cases of miRNA-mediated upregulation in cells that had stopped dividing. Still, since then, upregulation was thought to be rare and limited to idle cells, explains Mahal. So when she and colleagues aimed to better characterize the miRNAs involved in glycosylation (the process by which sugary molecules are stuck onto proteins), they weren’t expecting to find any ramping up gene expression.
They probed the miRNA profile of two glycosylation proteins: ST6GAL1, which is ubiquitously expressed, and ST6GAL2, which operates in just a few cell types. Work from their lab had previously found that ST6GAL1 is overactive in pancreatic cancer, peppering cancerous cells’ membranes with a sugar called 2,6-sialic acid. An abundance of sugars on their surface enables tumor cells to evade the immune system, metastasize, and invade other tissues.
To determine how miRNAs adjust enzyme expression, they developed a sensor consisting of a gene’s regulatory region (where miRNA binding occurs) and a sequence that codes for a fluorescent protein. They expressed the sensor, along with a human miRNA library, in dividing cells. If miRNAs inhibit a protein’s translation, the cells’ color dims, while if they turn up gene expression, the cells glow brighter.
They discovered that while the miRNAs that interact with ST6GAL2 downregulate its expression, those that interact with ST6GAL1 boost its expression and therefore increase levels of 2,6-sialic acid attachment. “We were floored. We thought it was a mistake,” says Mahal.
We were floored. We thought it was a mistake.
—Lara Mahal, University of Alberta
However, the team soon replicated their findings in four cancer cell lines taken from the lungs, ovaries, pancreas, and colon. Furthermore, mutating potential miRNA binding sites caused the upregulation to disappear, suggesting that the miRNAs directly control the gene’s expression.
Mahal believes that miRNA-mediated upregulation may have gone largely unnoticed because most groups tend to focus on transcripts that are far more abundant. When there are lots of copies of a protein being made, its effects can be straightforwardly fine-tuned by metering translation. But for genes already expressed at low levels, like the ones that regulate glycosylation, downregulation doesn’t make as much biological sense, she says.
“It’s an exciting study,” says Pinar Uysal Onganer, a cancer biologist at the University of Westminster in the UK who was not involved in the work. Similar high-throughput studies are essential for validating miRNA interactions, enabling researchers to make better predictions of their effects, she says.
The accuracy of those predictions is especially crucial if miRNAs are to be used therapeutically, says Mahal, a possibility that researchers have been exploring in recent years given their influence over protein production. Indeed, several miRNAs are currently in clinical trials for the treatment of several diseases, including Huntington’s disease and hepatitis C. “If you’re going to use something as a therapeutic, especially something that has such strong effects, I think it’s important to understand what it can really do,” she says.