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The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing

Nature Methods volume 20, pages 20–24 (2023)Cite this article

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Long-read sequencing has become a widely employed technology that enables a comprehensive view of RNA transcripts. Here, we discuss the importance of long-read sequencing in interpreting the variables along RNA molecules, such as polyadenylation sites, transcription start sites, splice sites and other RNA modifications. In addition, we highlight the history of short-read and long-read technologies and their advantages and disadvantages, as well as future directions in the field.

The long chains that compose DNA, RNA and protein molecules are a fundamental molecular property forming the basis of life. DNA chains can reach extreme lengths, with human chromosome 1 harboring almost 250 × 106 bp. RNA molecules are usually much shorter, with very few molecules reaching >100,000 nucleotides. By virtue of intron removal, the correspondence of three ribonucleotides to one amino acid, and the existence of untranslated regions (UTRs), the translated protein chains are again usually shorter than RNA molecules.

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Fig. 1: RNA variables and their non-random combinations.
Fig. 2: Long-read sequencing applications.
Fig. 3: An overview and timeline of various SRS and LRS technologies.

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Acknowledgements

H.U.T. is supported by NIGMS grant 1R01GM135247-01, Brain Initiative grant 1RF1MH121267-01, NIDA grant U01 DA053625-01 and the Feil Family Foundation. C.F. is supported by NSF GRFP No. NSF 2139291. N.B. is supported by NIDA T32 grant 5T32DA039080-0. S.P. is supported by NIGMS grant 1R01GM135247-03S1. Opinions, findings, conclusions or recommendations herein are those of the authors and do not necessarily reflect the views of NSF or NIH.

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  1. These authors contributed equally: Careen Foord, Justine Hsu, Julien Jarroux.

Authors and Affiliations

  1. Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA

    Careen Foord, Justine Hsu, Julien Jarroux, Wen Hu, Natan Belchikov, Shaun Pollard, Yi He, Anoushka Joglekar & Hagen U. Tilgner

  2. Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA

    Careen Foord, Justine Hsu, Julien Jarroux, Wen Hu, Natan Belchikov, Shaun Pollard, Yi He, Anoushka Joglekar & Hagen U. Tilgner

  3. Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine, New York, NY, USA

    Natan Belchikov

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C.F., J.H., J.J. and H.U.T. wrote the manuscript. W.H., N.B., S.P., Y.I. and A.J. revised the manuscript.

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Correspondence to Hagen U. Tilgner.

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Foord, C., Hsu, J., Jarroux, J. et al. The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing. Nat Methods 20, 20–24 (2023). https://doi.org/10.1038/s41592-022-01715-9

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