Enhanced detection of RNA modifications in Escherichia coli utilizing direct RNA sequencing.

ABSTRACT: RNA modifications play crucial roles in prokaryotic cellular processes. In this study, we found that the recent advances in direct RNA sequencing have improved yield, accuracy, and signal-to-noise ratio in bacterial samples. By evaluating four current RNA modification calling models in Escherichia coli transcriptome using native and in vitro transcribed (IVT) RNA, we found the models identified most known rRNA modifications but produced false positives. To address this, we developed nanoSundial, a comparative method leveraging raw current signals from native and IVT samples to de novo identify multiple RNA modifications. We optimized nanoSundial on well-studied E. coli rRNA modification sites and validated its effectiveness with tRNAs. It identified 190 stably modified mRNA regions, which

SUBMITTER: Guo Z 

PROVIDER: S-EPMC12539251 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature