Genome Biology (Jul 2023)

L-GIREMI uncovers RNA editing sites in long-read RNA-seq

  • Zhiheng Liu,
  • Giovanni Quinones-Valdez,
  • Ting Fu,
  • Elaine Huang,
  • Mudra Choudhury,
  • Fairlie Reese,
  • Ali Mortazavi,
  • Xinshu Xiao

DOI
https://doi.org/10.1186/s13059-023-03012-w
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 18

Abstract

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Abstract Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.

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