Long-read RNA Sequencing: A Transformative Technology for Exploring Transcriptome Complexity in Human Diseases

Overview

Journal Mol Ther

Publisher Cell Press

Specialties Molecular Biology
Pharmacology

Date 2024 Nov 20

PMID 39563027

Authors

Isabelle Heifetz Ament

Nicole DeBruyne

Feng Wang

Lan Lin

Affiliations

Soon will be listed here.

Abstract

Long-read RNA sequencing (RNA-seq) is emerging as a powerful and versatile technology for studying human transcriptomes. By enabling the end-to-end sequencing of full-length transcripts, long-read RNA-seq opens up avenues for investigating various RNA species and features that cannot be reliably interrogated by standard short-read RNA-seq methods. In this review, we present an overview of long-read RNA-seq, delineating its strengths over short-read RNA-seq, as well as summarizing recent advances in experimental and computational approaches to boost the power of long-read-based transcriptomics. We describe a wide range of applications of long-read RNA-seq, and highlight its expanding role as a foundational technology for exploring transcriptome variations in human diseases.

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References

Zheng Y, Ji P, Chen S, Hou L, Zhao F . Reconstruction of full-length circular RNAs enables isoform-level quantification. Genome Med. 2019; 11(1):2. PMC: 6339429. DOI: 10.1186/s13073-019-0614-1. View

Berrens R, Yang A, Laumer C, Lun A, Bieberich F, Law C . Locus-specific expression of transposable elements in single cells with CELLO-seq. Nat Biotechnol. 2021; 40(4):546-554. PMC: 7614850. DOI: 10.1038/s41587-021-01093-1. View

Shahid S, Slotkin R . The current revolution in transposable element biology enabled by long reads. Curr Opin Plant Biol. 2020; 54:49-56. DOI: 10.1016/j.pbi.2019.12.012. View

Pan Y, Kadash-Edmondson K, Wang R, Phillips J, Liu S, Ribas A . RNA Dysregulation: An Expanding Source of Cancer Immunotherapy Targets. Trends Pharmacol Sci. 2021; 42(4):268-282. PMC: 8761020. DOI: 10.1016/j.tips.2021.01.006. View

Su Y, Yu Z, Jin S, Ai Z, Yuan R, Chen X . Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nat Commun. 2024; 15(1):3972. PMC: 11087464. DOI: 10.1038/s41467-024-48117-3. View

Acera Mateos P, J Sethi A, Ravindran A, Srivastava A, Woodward K, Mahmud S . Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications. Nat Commun. 2024; 15(1):3899. PMC: 11082244. DOI: 10.1038/s41467-024-47953-7. View

Reggiardo R, Maroli S, Peddu V, Davidson A, Hill A, LaMontagne E . Profiling of repetitive RNA sequences in the blood plasma of patients with cancer. Nat Biomed Eng. 2023; 7(12):1627-1635. PMC: 10727983. DOI: 10.1038/s41551-023-01081-7. View

Schwenk V, Leal Silva R, Scharf F, Knaust K, Wendlandt M, Hausser T . Transcript capture and ultradeep long-read RNA sequencing (CAPLRseq) to diagnose HNPCC/Lynch syndrome. J Med Genet. 2023; 60(8):747-759. PMC: 10423559. DOI: 10.1136/jmg-2022-108931. View

Byron S, Van Keuren-Jensen K, Engelthaler D, Carpten J, Craig D . Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016; 17(5):257-71. PMC: 7097555. DOI: 10.1038/nrg.2016.10. View

10.

Byrne A, Cole C, Volden R, Vollmers C . Realizing the potential of full-length transcriptome sequencing. Philos Trans R Soc Lond B Biol Sci. 2019; 374(1786):20190097. PMC: 6792442. DOI: 10.1098/rstb.2019.0097. View

11.

Jia Y, Xie Z, Li H . Intergenically Spliced Chimeric RNAs in Cancer. Trends Cancer. 2017; 2(9):475-484. PMC: 5305119. DOI: 10.1016/j.trecan.2016.07.006. View

12.

Sedaghat-Hamedani F, Rebs S, Kayvanpour E, Zhu C, Amr A, Muller M . Genotype Complements the Phenotype: Identification of the Pathogenicity of an LMNA Splice Variant by Nanopore Long-Read Sequencing in a Large DCM Family. Int J Mol Sci. 2022; 23(20). PMC: 9602549. DOI: 10.3390/ijms232012230. View

13.

Au K, Sebastiano V, Afshar P, Durruthy J, Lee L, Williams B . Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A. 2013; 110(50):E4821-30. PMC: 3864310. DOI: 10.1073/pnas.1320101110. View

14.

Pan Q, Shai O, Lee L, Frey B, Blencowe B . Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008; 40(12):1413-5. DOI: 10.1038/ng.259. View

15.

Dainis A, Tseng E, Clark T, Hon T, Wheeler M, Ashley E . Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3. Circ Genom Precis Med. 2019; 12(5):e002464. DOI: 10.1161/CIRCGEN.119.002464. View

16.

Zhang J, Hou L, Zuo Z, Ji P, Zhang X, Xue Y . Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat Biotechnol. 2021; 39(7):836-845. DOI: 10.1038/s41587-021-00842-6. View

17.

Park E, Pan Z, Zhang Z, Lin L, Xing Y . The Expanding Landscape of Alternative Splicing Variation in Human Populations. Am J Hum Genet. 2018; 102(1):11-26. PMC: 5777382. DOI: 10.1016/j.ajhg.2017.11.002. View

18.

Logsdon G, Vollger M, Eichler E . Long-read human genome sequencing and its applications. Nat Rev Genet. 2020; 21(10):597-614. PMC: 7877196. DOI: 10.1038/s41576-020-0236-x. View

19.

Bizuayehu T, Labun K, Jakubec M, Jefimov K, Niazi A, Valen E . Long-read single-molecule RNA structure sequencing using nanopore. Nucleic Acids Res. 2022; 50(20):e120. PMC: 9723614. DOI: 10.1093/nar/gkac775. View

20.

Edge P, Bafna V, Bansal V . HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. 2016; 27(5):801-812. PMC: 5411775. DOI: 10.1101/gr.213462.116. View