Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing

BMC Genomics

Research

Virginie Calderon¹  Ludovic Malet¹  Seda Barutcu¹  Gabrielle Deschamps-Francoeur¹  Eunjeong Kwon¹  Juan-Carlos A. Padilla²  Eric Lécuyer³ 

[1] Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, H2W 1R7, Montréal, QC, Canada;Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, H2W 1R7, Montréal, QC, Canada;Division of Experimental Medicine, McGill University, H4A 3J1, Montréal, QC, Canada;Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, H2W 1R7, Montréal, QC, Canada;Division of Experimental Medicine, McGill University, H4A 3J1, Montréal, QC, Canada;Département de Biochimie et de Médecine Moléculaire, Université de Montréal, H3T 1J4, Montréal, QC, Canada;

关键词: Extracellular vesicles;    Long-Read RNA Sequencing;    Nanopore sequencing;    Polyadenylated transcriptome;    Poly-A;    mRNA;    lncRNA;    Transcriptomics;    Transcript Isoforms;    RNA-seq;   

DOI  :  10.1186/s12864-023-09552-6

 received in 2023-04-21, accepted in 2023-08-03,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundWhile numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-targeted RNA populations. It has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and the extent to which full-length mRNAs are present within EVs remains to be clarified.ResultsUsing long-read nanopore RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 443 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 10.58% of all EV reads, and 18.67% of all cellular (WC) reads, corresponded to known full-length transcripts, with mRNAs representing the largest biotype for each group (EV = 58.13%, WC = 43.93%). We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples.ConclusionThis work provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs, while also underscoring the potential usefulness of nanopore sequencing to interrogate secreted RNA transcriptomes.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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