New ways to look at protein-RNA networks

A network of interacting RNAs and proteins is active in each of our cells.
A network of interacting RNAs and proteins is active in each of our cells. IMAGE: Adobe Stock

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Researchers develop new method to analyse the entire protein-RNA network of the cell

To carry out their vital tasks, all RNA molecules in our cells require proteins as binding partners. Scientists at the German Cancer Research Center (DKFZ) and EMBL have developed a method that enables researchers to analyse the composition of the entire protein-RNA network of the cell. The new method has now been published in the journal Cell.

RNA molecules perform vital tasks in every cell: messenger RNA (mRNA) carries genetic information from the DNA to be translated into proteins. However, many other RNA molecules exist which are not translated into proteins. In fact, only 5% of RNA in a human cell is mRNA.

For many of their functions, RNA molecules have to interact with proteins. Sometimes, different types of RNA come together with specific proteins to form highly complex molecular machines – the best example is the ribosome where protein synthesis takes place.

“A gigantic network of interacting RNAs and proteins is active in each of our cells, but we still know extremely little about the exact composition of this network. We want to understand which proteins bind to RNAs, and how this differs between cell types, or in conditions when cells are stressed. We have now developed a method that enables us to investigate this for the first time,” says Jeroen Krijgsveld from the DKFZ.

Until now, such analyses could only be carried out for mRNAs. Protein interactions with all other RNA types – known as non-coding RNAs – could not be detected using the existing method. “Non-coding RNAs by far outnumber mRNA molecules, and they fulfill various regulatory purposes,” explains Krijgsveld.

Together with colleagues from EMBL, Krijgsveld has succeeded in developing a method called XRNAX to analyse the interactions of all RNA types with cellular proteins. Using XRNAX, the scientists can also make quantitative statements: they can see not only which proteins bind RNA but also to what extent. In this way, they are able to observe how RNA binding changes when cells are exposed to a toxin. With the new method the research team also identified hundreds of proteins that previously were not known to bind RNA.

“With XRNAX we are able to measure all interactions between protein and RNA, which is something nobody could measure before,” explains Jakob Trendel, a PhD student at EMBL who developed XRNAX. “Many protein-RNA interactions are suspected to be the underlying cause for diseases including cancer, amyotrophic lateral sclerosis, or viral infections like HIV. Now we have a way to look at them.”

This article was originally published by the DKFZ