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Fig. 1 | Genome Biology

Fig. 1

From: DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing

Fig. 1

Characterization of A-to-I RNA editing events on nanopore reads. a Construction of Schizosaccharomyces pombe strains with de novo RNA editing machinery. Top, introduction of human hADAR2 gene into S. pombe chromosome II through homologous recombination. Bottom, the negative strain without hADAR2 coding sequence. mnt1, transcription promoter. hADAR2, coding sequence. ADH1, transcription terminator. LEU1, insertion locus on chromosome II. b Confirmation of RNA editing events in positive FY-ADAR2 and negative FY-HFF1 strains by Illumina datasets, shown with counts of single nucleotide variations (SNVs) on x-axis and SNV types on y-axis. ADAR2-1 and ADAR2-2 are two replicates of FY-ADAR2 strain. HFF1-1 and HFF1-2 are two replicates of FY-HFF1 strain. c The edited adenine sites had a significant upward p-value shift at the editing sites as well as nearby bases. Violin plots show the p-values (-log10 transformed) of context bases from − 5 to + 5 around the edited bases (position 0). Top, P values of editing domains. Bottom, P values of random “A” domains. d Examples of ADAR2-specific errors (ASEs) around editing positions. Bases from − 4 to + 4 surrounding the editing sites are shown, with the correct reference bases displayed on the top. The gray bars denote reads coverage. The colored bars denote the ratios of different bases for the error sites. Red, thymine. Blue, cytosine. Orange, guanine. Green, adenine. e Frequencies of different types of ADAR2-specific errors, shown with bases from − 5 to + 5 around editing sites. f Electrical signal separation of different read types. Red lines denote A-type reads from FY-ADAR2 samples. Blue lines denote I-type reads from FY-ADAR2 samples. Green lines denote negative control reads from FY-HFF1 samples

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