Transcript Identification Through Long-Read Sequencing

doi:10.1007/978-1-0716-1307-8_29

. 2021:2284:531-541.

doi: 10.1007/978-1-0716-1307-8_29.

Transcript Identification Through Long-Read Sequencing

Masahide Seki¹, Miho Oka^{1

2}, Liu Xu¹, Ayako Suzuki¹, Yutaka Suzuki³

Affiliations

¹ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.
² Ono Pharmaceutical Co., Ltd., Osaka, Osaka, Japan.
³ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan. ysuzuki@edu.k.u-tokyo.ac.jp.

PMID: 33835462
DOI: 10.1007/978-1-0716-1307-8_29

Transcript Identification Through Long-Read Sequencing

Masahide Seki et al. Methods Mol Biol. 2021.

. 2021:2284:531-541.

doi: 10.1007/978-1-0716-1307-8_29.

Authors

Masahide Seki¹, Miho Oka^{1

2}, Liu Xu¹, Ayako Suzuki¹, Yutaka Suzuki³

Affiliations

¹ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.
² Ono Pharmaceutical Co., Ltd., Osaka, Osaka, Japan.
³ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan. ysuzuki@edu.k.u-tokyo.ac.jp.

PMID: 33835462
DOI: 10.1007/978-1-0716-1307-8_29

Abstract

RNA-seq using long-read sequencing, such as nanopore and SMRT (Single Molecule, Real-Time) sequencing, enabled the identification of the full-length structure of RNA molecules. Several tools for long-read RNA-seq were developed recently. In this section, we introduce an analytical pipeline of long-read RNA-seq for isoform identification and the estimation of expression levels using minimap2, TranscriptClean, and TALON. We applied this pipeline to the public direct RNA-seq data of the HAP1 and HEK293 cell lines to identify transcript isoforms which can be detected only using long-read RNA-seq data.

Keywords: Alternative splicing; Direct RNA sequencing; Expression estimation; Long-read sequencing; Transcript isoform.

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References

1. Stark R, Grzelak M, Hadfield J (2019) RNA sequencing: the teenage years. Nat Rev Genet 20:631–656. https://doi.org/10.1038/s41576-019-0150-2 - DOI - PubMed
1. Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31:1009–1014. https://doi.org/10.1038/nbt.2705 - DOI - PubMed - PMC
1. Oikonomopoulos S, Wang YC, Djambazian H et al (2016) Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 6:31602. https://doi.org/10.1038/srep31602 - DOI - PubMed - PMC
1. Gupta I, Collier PG, Haase B et al (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol 36:1197–1202. https://doi.org/10.1038/nbt.4259 - DOI
1. Byrne A, Beaudin AE, Olsen HE et al (2017) Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun 8:16027. https://doi.org/10.1038/ncomms16027 - DOI - PubMed - PMC

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[1] Stark R, Grzelak M, Hadfield J (2019) RNA sequencing: the teenage years. Nat Rev Genet 20:631–656. https://doi.org/10.1038/s41576-019-0150-2 - DOI - PubMed

[2] Stark R, Grzelak M, Hadfield J (2019) RNA sequencing: the teenage years. Nat Rev Genet 20:631–656. https://doi.org/10.1038/s41576-019-0150-2 - DOI - PubMed

[3] Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31:1009–1014. https://doi.org/10.1038/nbt.2705 - DOI - PubMed - PMC

[4] Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31:1009–1014. https://doi.org/10.1038/nbt.2705 - DOI - PubMed - PMC

[5] Oikonomopoulos S, Wang YC, Djambazian H et al (2016) Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 6:31602. https://doi.org/10.1038/srep31602 - DOI - PubMed - PMC

[6] Oikonomopoulos S, Wang YC, Djambazian H et al (2016) Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 6:31602. https://doi.org/10.1038/srep31602 - DOI - PubMed - PMC

[7] Gupta I, Collier PG, Haase B et al (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol 36:1197–1202. https://doi.org/10.1038/nbt.4259 - DOI

[8] Gupta I, Collier PG, Haase B et al (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol 36:1197–1202. https://doi.org/10.1038/nbt.4259 - DOI

[9] Byrne A, Beaudin AE, Olsen HE et al (2017) Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun 8:16027. https://doi.org/10.1038/ncomms16027 - DOI - PubMed - PMC

[10] Byrne A, Beaudin AE, Olsen HE et al (2017) Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun 8:16027. https://doi.org/10.1038/ncomms16027 - DOI - PubMed - PMC

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Transcript Identification Through Long-Read Sequencing

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