Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2

Direct RNA sequencing for the epitranscriptomic modification pseudouridine (Ψ), an isomer of uridine (U), was conducted with a protein nanopore sensor using a helicase brake to slowly feed the RNA into the sensor. Synthetic RNAs with 100% Ψ or U in 20 different known human sequence contexts identified differences during sequencing in the base-calling, ionic current, and dwell time in the nanopore sensor; however, the signals were found to have a dependency on the context that would result in biases when sequencing unknown samples. A solution to the challenge was the identification that the passage of Ψ through the helicase brake produced a long-range dwell time impact with less context bias that was used for modification identification. The data analysis approach was employed to analyze publicly available direct RNA sequencing data for SARS-CoV-2 RNA taken from cell culture to locate five conserved Ψ sites in the genome. Two sites were found to be substrates for pseudouridine synthase 1 and 7 in an in vitro assay, providing validation of the analysis. Utilization of the helicase as an additional sensor in direct RNA nanopore sequencing provides greater confidence in calling RNA modifications.