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Integrative profiling of Epstein-Barr virus transcriptome using a multiplatform approach.

Ádám Fülöp1, Gábor Torma1, Norbert Moldován1

  • 1Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary.

Virology Journal
|January 7, 2022
PubMed
Summary

This study reveals novel Epstein-Barr virus (EBV) transcripts, including non-coding RNAs and splice isoforms, by integrating long-read and short-read sequencing data for a comprehensive EBV transcriptome analysis.

Keywords:
Epstein–Barr virusHerpesvirusLong-read sequencingNanopore sequencingPacBio sequencingSplice variantTranscript isoformTranscription end siteTranscription start siteTranscriptome

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Area of Science:

  • Virology
  • Genomics
  • Transcriptomics

Background:

  • Epstein-Barr virus (EBV) is a human gammaherpesvirus with carcinogenic potential.
  • Previous EBV transcriptome analyses utilized Illumina short-read and PacBio long-read sequencing.
  • Multiplatform approaches are valuable for comprehensive transcriptomic studies due to technique-specific strengths and limitations.

Purpose of the Study:

  • To provide a more complete picture of the EBV transcriptomic architecture.
  • To identify novel EBV transcripts and transcriptional features.
  • To leverage multi-platform sequencing for enhanced EBV transcriptome analysis.

Main Methods:

  • Applied Oxford Nanopore Technologies MinION (long-read sequencing) for novel data generation.
  • Integrated MinION data with existing long-read (Pacific Biosciences RSII) and short-read (Illumina CAGE-Seq, Poly(A)-Seq) data.
  • Utilized both amplified and non-amplified cDNA sequencing with different priming methods, and annotated transcripts using the LoRTIA software suite.

Main Results:

  • Discovered novel genes within host genes, potentially encoding truncated proteins.
  • Identified numerous novel non-coding RNAs and transcript length isoforms.
  • Reported novel splice isoforms, replication-origin-associated transcripts, and mono-/multigenic transcripts, revealing complex transcriptional overlaps.

Conclusions:

  • An integrative approach using multiple sequencing technologies is effective for reliable identification of complex transcriptomes.
  • Combining different sequencing techniques allows for validation of findings and overcomes individual method limitations.
  • This study enhances the understanding of the intricate EBV transcriptome.