So many mods in so little time greater than 45 RNA modifications profiled by direct RNA-Seq

Abstract

Epitranscriptomic marks on nucleic acids produce disruptions in ion flow when they are fed through biological nanopores. In principle, this effect enables the identification of any modification that generates a differentiable signal distortion; however, distinguishing the signals produced by the more than 170 distinct chemical modifications present on RNA molecules is a non-trivial technical challenge. We leveraged the diverse chemical repertoire of tRNAs, the most abundantly modified class of RNA, to evaluate the signals produced at known modification sites across a broad range of viral, prokaryotic, and eukaryotic species. We evaluated signals from more than 45 distinct RNA modifications using both first- and second-generation nanopore RNA sequencing chemistry, and further report a proof-of-concept approach for detecting low-abundance mitochondrial and viral tRNA reads using the higher library throughputs enabled by the new RNA004 chemistry. This work provides a roadmap to guide future efforts towards de novo detection of RNA modifications across the tree of life using nanopore sequencing.

Biography

Laura White is an RNA Bioinformatics Fellow at the University of Colorado School of Medicine, where she leads nanopore method development and analysis efforts within the CU RNA Bioscience Initiative. She completed her PhD in Jay Hesselberth’s laboratory in 2021, wherein she leveraged nanopore sequencing to detect repaired RNA molecules. Her current research is focused on tRNA biology as well as novel methods development for direct RNA sequencing and RNA modification detection.