Evaluation and application of RNA-Seq by MinION. (20th November 2018)

• Record Type: Journal Article
• Authors: Seki, Masahide; Katsumata, Eri; Suzuki, Ayako; Sereewattanawoot, Sarun; Sakamoto, Yoshitaka; Mizushima-Sugano, Junko; Sugano, Sumio; Kohno, Takashi; Frith, Martin C; Tsuchihara, Katsuya; Suzuki, Yutaka
• Editors: Hattori, Masahira
• Is Part Of: DNA research. Volume 26:Number 1(2019)
• Page Start: 55
• Page End: 65
• Publication Date: 2018-11-20
• Subjects: nanopore sequencing -- transcriptome -- transcript isoform -- allelic expression; Genes -- Periodicals; Genomes -- Periodicals; Genes -- Research -- Periodicals; Genomics -- Periodicals; DNA -- Research -- Periodicals; 572.86072
• DOI: 10.1093/dnares/dsy038
• Languages: English
• ISSNs: 1340-2838

Abstract

Abstract: The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION. We applied MinION RNA-Seq for various applications, which would not always be easy using the usual RNA-Seq by Illumina. First, we examined and found that even though the sequencing accuracy was still limited to 92.3%, practically useful RNA-Seq analysis is possible. Particularly, taking advantage of the long-read nature of MinION, we demonstrate the identification of splicing patterns and their combinations as a form of full-length cDNAs without losing precise information concerning their expression levels. Transcripts of fusion genes in cancer cells can also be identified and characterized. Furthermore, the full-length cDNA information can be used for phasing of the SNPs detected by WES on the transcripts, providing essential information to identify allele-specific transcriptional events. We constructed a catalogue of full-length cDNAs in seven major organs for two particular individuals and identified allele-specific transcription and splicing. Finally, we demonstrate that single-cell sequencing is also possible. RNA-Seq on the MinION platform should provide a novel approach that is complementary to the current RNA-Seq.