Novel Method for Measuring tRNA Abundance and Modification Developed

Researchers at the Centre for Genomic Regulation in Barcelona have developed a new method that can measure both the abundance and modification of tRNA molecules in a single step. The method is called Nano-tRNAseq and it overcomes the limitations of currently used techniques such as next-generation sequencing or mass spectrometry, which are either unable to detect modifications, or they cannot identify at which location of the tRNA they are occurring at.  

tRNAs are “information-rich” molecules with huge potential for the diagnosis and prognosis of diseases, but so far haven’t been exploited for such purpose due to the lack of methods that can capture this information in a quantitative and cost-efficient manner. For example, some types of cancers are difficult to diagnose because their symptoms are non-specific and can be confused with other conditions. At the same time, certain tRNA modification profiles are only known to exist in specific cancer types and can serve as highly specific biomarkers. 

Nano-tRNAseq is based on nanopore sequencing, a technology that can directly sequence individual RNA molecules by passing them through a small pore. As a proof of concept, the researchers used Nano-tRNAseq to accurately measure tRNA abundances and modifications in samples taken from yeast cells exposed to different environmental conditions. 

“For the first time, we can study both tRNA abundance and tRNA modification profiles simultaneously. As a bonus, the method is rapid, cost-effective, high-throughput, and has single-molecule resolution. Previously, we relied on two separate methods that, together, are less informative, and it would take weeks and cost thousands of euros to obtain results. Nano-tRNAseq is a fraction of the cost, and we can have results within a couple of days, and in the near future, within a few hours,” says Morghan Lucas, first author of the study published in Nature Biotechnology.  

The researchers note there are still some limitations to the new method, such as the inability to predict which tRNA modification is dysregulated in a given sample unless the precise modifications found in that tRNA have been previously identified using other experimental methods. “While tRNA modification profiles of lower eukaryotic species, such as yeast, are well characterized, this is not the case for humans. By using Nano-tRNAseq in parallel with other methods, we can describe the modification profiles of the complete set of human tRNAs and, in the future, use Nano-tRNAseq to identify which changes in tRNAs are associated with a given human disease,” adds Lucas.