Chemical Probe-Based Nanopore Sequencing to Selectively Assess the RNA Modifications

Nanopore direct RNA sequencing (dRNA-Seq) reads reveal RNA modifications through consistent error profiles specific to a modified nucleobase. However, a null data set is required to identify actual RNA modification-associated errors for distinguishing it from confounding highly intrinsic sequencing errors. Here, we reveal that inosine creates a signature mismatch error in dRNA-Seq reads and obviates the need for a null data set by harnessing the selective reactivity of acrylonitrile for validating the presence of actual inosine modifications. Selective reactivity of acrylonitrile toward inosine altered multiple dRNA-Seq parameters like signal intensity and trace value. We also deduced the stoichiometry of inosine modification through deviation in signal intensity and trace value using this chemical biology approach. Furthermore, we devised Nano ICE-Seq, a protocol to overcome the low coverage issue associated with direct RNA sequencing. Taken together, our chemical probe-based approach may facilitate the knockout-free detection of disease-associated RNA modifications in clinical scenarios.

Automated summary

Nanopore direct RNA sequencing (dRNA-Seq) can reveal RNA modifications, and in this study, we demonstrated that inosine creates a signature mismatch error in dRNA-Seq reads, allowing validation of actual inosine modifications using the selective reactivity of acrylonitrile. We also developed Nano ICE-Seq, a protocol to address the low coverage issue associated with direct RNA sequencing. This chemical probe-based approach may facilitate the knockout-free detection of disease-associated RNA modifications in clinical scenarios.