A new approach to revealing the complexity of RNAs that genomes really encode

They passed RNA through pores developed by Oxford Nanopore Technology to reveal directly the sequence of 1000s of RNA molecules.

In order to know what genomes encode and which genes are active in certain cells, scientists not only sequence DNA, but a related molecule called RNA. When a gene is switched on, the code it contains is copied into a messenger RNA molecule. Sequencing RNA usually involves converting it back into DNA and fragmenting it into shorter pieces to accommodate current sequencing technologies. Interpreting such data is difficult and the computational reconstruction of the original RNA molecules is an unsolved problem. By sequencing RNA directly, the Dundee team were able to circumvent many of these problems.

The Dundee team led by Professors Gordon Simpson and Geoff Barton first used this approach with the model plant Arabidopsis, but they have already applied this technology to neglected crops targeted by the African Orphan Crops Consortium. In this way they are transforming our understanding of what their genomes encode and so helping to make informed improvements in these crops by conventional breeding.

The second major advance of the study was that they devised a computational approach to detect modifications in RNA. Chemical modifications to RNA bases have been known for some time, but it is only recently that we have realized they comprise a neglected, but crucial, layer of gene control. The Dundee team are the first to map RNA modifications in all of a cells messenger RNAs in this way. By combining the insight into full length RNA molecules and modifications in the same experiment, the Dundee team were able to reveal that the major impact of RNA modification in the model plant Arabidopsis was on where RNA copies stop. They could implicate a special adaptation of a protein in plants involved in this process. Interestingly, the only species apart from plants that have this same adaptation is a group of parasites that cause diseases such as malaria and toxoplasmosis in animals and humans. Consequently, these findings may not only reveal how plants control their genes but also open a new target for drug design.

Professor Simpson said “It is relatively early days for this technology, but we could show it can provide new insight to help us understand what genomes encode and how they are controlled. Our team worked really well together to provide innovative solutions and applications of this approach”.

Professor Ewan Birney, Director of the European Bioinformatics Institute in Cambridge writing on social media commented “It is great to see these papers which start to use the genome scale, near base pair resolution of RNA modification in biology using direct RNA from Oxford Nanopore Technology.  This is a whole new layer of information management in the cell which is now observable.”

The research was carried out in the School of Life Sciences at the University of Dundee and was funded by the BBSRC and GCRF with a European Commission Marie-Sklodowska Curie Fellowship to Kasia Knop. Mass Spectrometry facilities used in the study were funded by the Wellcome Trust.