Researchers at the University of Vienna have developed a new method to better understand how a specific RNA-binding protein, called tristetraprolin (TTP), interacts with RNA inside cells. RNA-binding proteins (RBPs) play important roles in controlling how genes are expressed by attaching to RNA molecules. However, many RBPs can bind to different types of RNA, including pre-mRNA, which is the early form of RNA that still contains non-coding parts called introns, and mature mRNA, which is the processed form used to make proteins.

Until now, it has been difficult for scientists to tell whether RBPs prefer to bind the more common mature mRNA or the less abundant pre-mRNA. The new protocol helps solve this problem by identifying and measuring which parts of the RNA, introns or exons, are attached to TTP. This allows researchers to see if TTP favors binding to pre-mRNA or mRNA.

The method uses RNA sequencing data and special analysis steps to distinguish between intronic sequences (found in pre-mRNA) and exonic sequences (found in mature mRNA) that are bound to the protein. Although this protocol was developed for TTP, it can be adapted to study other RNA-binding proteins as well. This advancement opens new doors for understanding how RBPs regulate gene expression at different stages and may lead to insights in disease mechanisms where RNA processing is disrupted.