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The Human Adenovirus Type 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs.

Amanda Westergren Jakobsson1,2, Bo Segerman1,3, Ola Wallerman1

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Human adenovirus type 2 (Ad2) uses flexible splicing to create over 900 alternatively spliced mRNAs, with more than 850 being novel. This complex transcriptome, including novel E1A transcripts, highlights the virus's adaptability.

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Area of Science:

  • * Molecular Biology
  • * Virology
  • * Genomics

Background:

  • * RNA splicing and alternative splicing are fundamental to increasing the coding capacity of genomes in mammalian evolution.
  • * Adenoviruses have historically been crucial in discovering RNA splicing mechanisms.
  • * Adenoviruses are increasingly utilized as vectors in vaccines, such as for SARS-CoV-2.

Purpose of the Study:

  • * To comprehensively characterize the complexity of the human adenovirus type 2 (Ad2) transcriptome using Nanopore long-read sequencing.
  • * To identify and quantify novel alternatively spliced messenger RNAs (mRNAs) produced by Ad2.
  • * To investigate the mechanisms generating novel Ad2 transcripts, including potential novel promoters and enhancer-driven transcription.

Main Methods:

  • * Nanopore long-read sequencing platform for transcriptome analysis.
  • * Bioinformatic analysis to identify and quantify alternatively spliced mRNAs.
  • * Proteomic analysis to verify the existence of novel mRNA-derived peptides.

Main Results:

  • * Discovery of over 900 alternatively spliced mRNAs from the Ad2 transcriptome, with over 850 identified as novel.
  • * Identification of novel E1A transcripts originating upstream of the previously known start site, potentially driven by novel promoters or enhancer elements.
  • * The E3 region exhibited the highest complexity, generating over 400 alternatively spliced mRNAs, including extended and readthrough variants.

Conclusions:

  • * The Ad2 transcriptome is remarkably complex, with extensive alternative splicing generating a vast repertoire of mRNAs.
  • * Novel transcription start sites and enhancer-driven transcription contribute to the diversity of Ad2 mRNAs.
  • * Understanding Ad2's complex gene expression is critical for its application in gene therapy and vaccine development.