Rapid, gel-free and cost-effective isolation of all known classes of silencing small RNAs
Silencing small (s)RNAs are key to gene expression control, yet accessing ‘sRNAomes’ is labor-intensive. A publication in Nucleic Acids Research by the Voinnet group describes a highly simplified and universal method developed to that aim, likely to become transformative for research and diagnostic.
Intense efforts have been geared at isolating and characterizing silencing sRNAs from various tissues across kingdoms, including via deep-sequencing. High-quality sRNA purification via polyacrylamide gel-purification – the gold-standard method – is tedious and time-consuming, however. Due to their size (20-35-nt), sRNAs are also often contaminated with rRNA, tRNA or other RNA breakdown fragments.
sRNAs come in all sorts of forms and functions, yet one of their unifying properties is to tightly associate with ARGONAUTE(AGO)-family proteins. As part of RNA-induced silencing complexes (RISCs), AGO-bound sRNAs are the universal effectors of RNA silencing.
The developed gel-free, 15-min benchtop extraction procedure is coined TraPR for “Trans-kingdom, rapid, affordable Purification of RISCs”. TraPR entails a vastly simplified anion exchange chromatography method exploiting the highly conserved biochemistry of AGO-sRNA complexes. TraPR purifies all known sRNA classes irrespectively of organisms/tissues, and scales to minute amounts of input material. TraPR sequencing libraries outperform those from gold-standard in-gel separation or AGO immunoprecipitation, including from difficult-to-handle mammalian plasma, and regardless of RNA contamination or degradation.
Thanks to ETH-transfer, TraPR represents an academic but also IP success. The technology was exclusively licensed to Lexogen from which several TrAPR-based kits are now available. Since the TraPR’s rights are retained within the ETH domain, ETH colleagues can also contact O. Voinnet for competitive, non-commercial access.
Link to the paper in external page Nucleic Acids Research