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A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

Author

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  • Charlotte Soneson

    (University of Zurich
    SIB Swiss Institute of Bioinformatics
    Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics)

  • Yao Yao

    (University of Zurich
    SIB Swiss Institute of Bioinformatics)

  • Anna Bratus-Neuenschwander

    (ETHZ/University of Zurich)

  • Andrea Patrignani

    (ETHZ/University of Zurich)

  • Mark D. Robinson

    (University of Zurich
    SIB Swiss Institute of Bioinformatics)

  • Shobbir Hussain

    (University of Bath)

Abstract

A platform for highly parallel direct sequencing of native RNA strands was recently described by Oxford Nanopore Technologies, but despite initial efforts it remains crucial to further investigate the technology for quantification of complex transcriptomes. Here we undertake native RNA sequencing of polyA + RNA from two human cell lines, analysing ~5.2 million aligned native RNA reads. To enable informative comparisons, we also perform relevant ONT direct cDNA- and Illumina-sequencing. We find that while native RNA sequencing does enable some of the anticipated advantages, key unexpected aspects currently hamper its performance, most notably the quite frequent inability to obtain full-length transcripts from single reads, as well as difficulties to unambiguously infer their true transcript of origin. While characterising issues that need to be addressed when investigating more complex transcriptomes, our study highlights that with some defined improvements, native RNA sequencing could be an important addition to the mammalian transcriptomics toolbox.

Suggested Citation

  • Charlotte Soneson & Yao Yao & Anna Bratus-Neuenschwander & Andrea Patrignani & Mark D. Robinson & Shobbir Hussain, 2019. "A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11272-z
    DOI: 10.1038/s41467-019-11272-z
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    Cited by:

    1. Alexandra Sneddon & Agin Ravindran & Somasundhari Shanmuganandam & Madhu Kanchi & Nadine Hein & Simon Jiang & Nikolay Shirokikh & Eduardo Eyras, 2024. "Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Kirill Grigorev & Theodore M. Nelson & Eliah G. Overbey & Nadia Houerbi & JangKeun Kim & Deena Najjar & Namita Damle & Evan E. Afshin & Krista A. Ryon & Jean Thierry-Mieg & Danielle Thierry-Mieg & Ari, 2024. "Direct RNA sequencing of astronaut blood reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Ruth E. Drury & Susana Camara & Irina Chelysheva & Sagida Bibi & Katherine Sanders & Salle Felle & Katherine Emary & Daniel Phillips & Merryn Voysey & Daniela M. Ferreira & Paul Klenerman & Sarah C. G, 2024. "Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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