RNA methylation detection at single-molecule resolution uncovers isoform-specific modifications during mouse brain development

Abstract

We describe a new computational tool that enables, for the first time, the identification of RNA modifications in individual nanopore read signals at single-nucleotide resolution and in any sample. Using extensive benchmarking with data from synthetic and natural RNA, we demonstrate a higher accuracy than other methods at detecting m6A and m5C transcriptomic sites and quantifying their stoichiometry levels. Application to mouse embryonic samples uncovers isoform-specific modifications during brain development that are altered in a mouse model of autism. Our strategy can be expanded to other modifications to unveil the full span of the epitranscriptome in normal and disease conditions.