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Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

View ORCID ProfileAlexander M. Price, Katharina E. Hayer, View ORCID ProfileDaniel P. Depledge, View ORCID ProfileAngus C. Wilson, View ORCID ProfileMatthew D. Weitzman
doi: https://doi.org/10.1101/2019.12.13.876037
Alexander M. Price
1Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA
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Katharina E. Hayer
2Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA
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Daniel P. Depledge
3Department of Medicine, New York University School of Medicine, New York, NY
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Angus C. Wilson
4Department of Microbiology, New York University School of Medicine, New York, NY
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Matthew D. Weitzman
1Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA
5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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  • For correspondence: weitzmanm@email.chop.edu
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Abstract

Adenovirus is a common human pathogen that relies on host cell processes for production and processing of viral RNA. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. The canonical viral early and late RNA cassettes were confirmed, but analysis of splice junctions within long RNA reads revealed an additional 20 novel viral transcripts. These RNAs include seven new splice junctions which lead to expression of canonical open reading frames (ORF), as well as 13 transcripts encoding for messages that potentially alter protein functions through truncations or the fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.

Footnotes

  • https://github.com/dandepledge/Ad5-annotation

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 13, 2019.
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Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts
Alexander M. Price, Katharina E. Hayer, Daniel P. Depledge, Angus C. Wilson, Matthew D. Weitzman
bioRxiv 2019.12.13.876037; doi: https://doi.org/10.1101/2019.12.13.876037
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Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts
Alexander M. Price, Katharina E. Hayer, Daniel P. Depledge, Angus C. Wilson, Matthew D. Weitzman
bioRxiv 2019.12.13.876037; doi: https://doi.org/10.1101/2019.12.13.876037

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