Direct sequencing of modified nucleotides in viral, host, and therapeutic RNAs

Understanding and exploiting messenger RNA requires techniques to assay beyond the raw sequence, such as the modifications occurring to mRNA and defining its life stages. A step change is needed towards "big data" to enable mapping of multiple modifications to individual transcripts and isoforms at the whole-transcriptome level.

The realisation that mRNA nucleotide modifications are dynamically written, erased, and recognised by specific proteins has driven a paradigm shift in RNA biology. There are over 160 modifications thus far identified on RNA1 with fundamental roles in all stages of the RNA life cycle, gene expression, and disease2,3. The emerging field of Epitranscriptomics seeks to characterise these enigmatic modifications. Many viruses encode their own or capture host modification writers to evade or exploit host mechanisms, whilst therapeutic RNA must do the same in order to fine-tune the activities of the molecule in the host. Greater understanding of modification deposition and biological impact expands the toolkit from which we can combat viral infections, or fine-tune mRNA therapeutics.