The untapped potential of RNA structures

The human genome has just over 20,000 protein-coding genes. However, it produces at least ten times as many different non-coding RNA molecules, which can often take more than one shape. At least some of this RNA structure is functional in physiology or pathophysiology.

In an invited review for Nature Reviews GeneticsDanny Incarnato, a molecular geneticist from the University of Groningen (Netherlands), and his colleague Robert C. Spitale from the University of California, Irvine (USA) describe ways to develop the hitherto largely untapped potential of RNA structures .

RNA is perhaps best known as the intermediary between genome and protein synthesis: messenger RNA molecules copy the genetic code of a gene in the cell’s nucleus and transport it to the cytoplasm, where ribosomes translate the code into protein. However, RNA is also a key regulator of almost every cellular process, and the structures adopted by RNA molecules are often thought to be essential to their functions.

Mode

Danny Incarnato, Assistant Professor of Molecular Genetics, has long been interested in the role of RNA structures in the cell and has been working on methods to elucidate the different structures in living cells. So when he was asked to write a review of RNA structures, he accepted without hesitation. “And I was delighted to invite my friend and colleague Robert Spitale, one of the pioneers of the ‘RNA revolution,’ to join me.”

In recent years, knowledge of RNA molecules in the cell has increased dramatically. The ENCODE project revealed the vast number of non-coding RNAs in cells. in human cells, more than ten times higher than the number of coding genes. “Not everything has a function,” Incarnato points out. “But many do, and in terms of their variety, we’ve barely scratched the surface.”

Drug research

Different types of non-coding RNAs have been known for a long time, and it was also clear that their structure could play an important role. One example is riboswitches: RNAs that can respond to changes in the external environment by changing shape, which in turn can affect specific gene activity.

“We also knew that RNA molecules can function as enzymes,” says Incarnato. “And, of course, ribosomes are RNA structures.” Thus, RNA molecules can act as sensors, catalysts, switches or scaffolds and affect RNA translation, but they can also affect RNA degradation and alternative splicing.

Therefore, it is not surprising that RNAs have rapidly gained momentum in drug research. However, our knowledge of the structure is still very limited. “So far, we have looked almost exclusively at single structures. But RNA molecules are very dynamic, and molecules with the same sequence can take on different shapes,” explains Incarnato. “Because of the way these structures were determined, they are often averages of all possible configurations of a single molecule.”

RNA viruses

Incarnato has pioneered methods to reveal the structural heterogeneity of RNA molecules. “We can combine this with high-throughput RNA sequencing to investigate structural heterogeneity.” In some cases, different structures are simply an “evolutionary by-product”, while in other cases they are functional. Incarnato says, “In this way, RNA molecules can regulate almost anything within a cell and therefore play a role in both physiology and pathophysiology.

Although developments in this field are rapid, they are not proceeding in a very orderly manner. Incarnato: “There is applied pharmaceutical research going on alongside a lot of basic research.” Interfering with RNAs could be an important way to fight diseases, including those caused by RNA viruses such as SARS-CoV2.

“However, we have no idea about off-target effects. For small molecules that interfere with specific enzymes, such as kinases, profiling panels are available to assess off-target profiles. However, we do not know how many RNAs have similar shapes. We really need a clear map of structure of RNA.”

Software

Another problem is that in many cases, it is impossible to know which of the different structural versions of a given RNA molecule is responsible for its function or malfunction. “And on top of that, RNAs can interact and create complex regulatory networks. We also need a deeper understanding of how this works in cells.”

There is still much work to be done. In addition, software is important. computer programs are required to translate biochemical analyzes of RNAs into their different structures. Incarnato says, “In our field, you have to know as much about coding as you do about high-throughput sequencing. We’re all at home in both liquid labs and bioinformatics.”