Direct Sequencing of RNA and RNA Modification Identification Using Nanopore

Methods Mol Biol. 2022:2477:71-77. doi: 10.1007/978-1-0716-2257-5_5.

Abstract

Direct RNA sequencing (dRNA-seq) simultaneously enables the detection of RNA modifications and characterization of full-length transcripts. In principle, full-length native RNA molecule is translocated through the nanopore by a motor protein while a sensor measures ionic current shifts. Then, the current shifts are interpreted by an algorithm that turn out to RNA sequence. Currently, the standard protocol of dRNA-seq provided by Oxford Nanopore Technologies (ONT) allows to directly ligate and sequence only polyadenylated RNA (poly(A) RNA). Here, we describe a method of dRNA-seq that can be applied for both poly(A) RNA and non-poly(A) tailed-RNA.

Keywords: Direct RNA sequencing; Epitranscriptome; Long-read; Methylation; Modification; Nanopore; Native; RNA; Sequencing Technology; Transcriptome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Nucleotide Sequencing / methods
  • Nanopore Sequencing*
  • Nanopores*
  • RNA / genetics
  • RNA, Messenger / genetics
  • Sequence Analysis, RNA / methods
  • Transcriptome

Substances

  • RNA, Messenger
  • RNA