For their vital tasks, all RNA molecules in our cells require proteins as binding partners. Scientists have developed the first method with which they can analyze the composition of the entire RNA-protein network of the cell. The new method has now been published in the scientific journal Cell.

RNA molecules perform vital tasks in every cell: Messenger RNA (mRNA) helps to translate the genetic information stored in the DNA into proteins. However, many other RNA molecules exist, which are not being translated into protein. In fact, only five percent 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 being 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 the lead author.

Until now, such analyses could only be carried out for one class of RNAs, namely mRNAs. mRNAs are the templates that instruct protein sequence. Protein interactions with all other so-called non-coding RNA types, some of which have only been known for a few years, could not be detected using the existing method. "Non-coding RNAs by far outnumber mRNA molecules, and they fulfill various regulatory purposes" explains the author.

They have now succeeded in developing a method termed XRNAX to analyze the interactions of all RNA classes with cellular proteins. Using XRNAX, the scientists can also make quantitative statements: They can not only see what protein binds RNA but also to what extent. In this way, they were able to observe how RNA binding changes when cells are exposed to a toxin. In addition, with the new method the research team identified hundreds of proteins that previously were not known to bind RNA.

Authors show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, they observed drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-related changes in the total proteome. In addition, the authors combined XRNAX with crosslinking immunoprecipitation sequencing (CLIP-seq) to validate the interaction of ncRNA with lamin B1 and EXOSC2. 

"With XRNAX we are able to measure all interactions between protein and RNA, which is something nobody could measure before." explains another author. "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."

https://www.cell.com/cell/fulltext/S0092-8674(18)31463-6?