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Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing
Juan-Carlos A Padilla1,2, Seda Barutcu1, Ludovic Malet1
1Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada.
BMC Genomics
|September 22, 2023
Summary
Extracellular vesicles (EVs) contain diverse full-length RNA transcripts, including mRNAs and long non-coding RNAs. Nanopore sequencing reveals these EV RNA profiles, offering new insights into their composition.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Previous studies on extracellular vesicle (EV) transcriptomes often used RNA fragmentation, limiting analysis of RNA integrity and isoform diversity.
- It was hypothesized that EV-associated mRNAs are primarily fragmentation products, with limited understanding of full-length mRNA presence.
Purpose of the Study:
- To characterize the full-length polyadenylated (poly-A) transcriptome of EVs using long-read nanopore RNA sequencing.
- To investigate the presence and diversity of full-length RNA isoforms within EVs.
Main Methods:
- Long-read nanopore RNA sequencing of EVs from K562 cells.
- Analysis of RNA biotypes, including mRNAs, long non-coding RNAs, and pseudogenes.
- Comparison of full-length transcript isoform ratios between EVs and whole cells (WC).
Main Results:
- Detected 443 enriched and 280 depleted RNAs in EVs.
- Identified full-length transcripts, with mRNAs being the predominant biotype in both EVs (58.13%) and WC (43.93%).
- Observed diverse full-length transcript isoforms in EVs, reflecting but often differing in ratio from cellular samples.
Conclusions:
- This study provides novel insights into the compositional diversity of poly-A transcript isoforms within EVs.
- Highlights the utility of nanopore sequencing for interrogating the full-length RNA content of secreted vesicles.
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