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Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses
Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007360/ https://www.ncbi.nlm.nih.gov/pubmed/35363834 http://dx.doi.org/10.1371/journal.ppat.1010401 |
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author | Nomburg, Jason Zou, Wei Frost, Thomas C. Datta, Chandreyee Vasudevan, Shobha Starrett, Gabriel J. Imperiale, Michael J. Meyerson, Matthew DeCaprio, James A. |
author_facet | Nomburg, Jason Zou, Wei Frost, Thomas C. Datta, Chandreyee Vasudevan, Shobha Starrett, Gabriel J. Imperiale, Michael J. Meyerson, Matthew DeCaprio, James A. |
author_sort | Nomburg, Jason |
collection | PubMed |
description | Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families. |
format | Online Article Text |
id | pubmed-9007360 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-90073602022-04-14 Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses Nomburg, Jason Zou, Wei Frost, Thomas C. Datta, Chandreyee Vasudevan, Shobha Starrett, Gabriel J. Imperiale, Michael J. Meyerson, Matthew DeCaprio, James A. PLoS Pathog Research Article Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families. Public Library of Science 2022-04-01 /pmc/articles/PMC9007360/ /pubmed/35363834 http://dx.doi.org/10.1371/journal.ppat.1010401 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Nomburg, Jason Zou, Wei Frost, Thomas C. Datta, Chandreyee Vasudevan, Shobha Starrett, Gabriel J. Imperiale, Michael J. Meyerson, Matthew DeCaprio, James A. Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
title | Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
title_full | Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
title_fullStr | Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
title_full_unstemmed | Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
title_short | Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
title_sort | long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007360/ https://www.ncbi.nlm.nih.gov/pubmed/35363834 http://dx.doi.org/10.1371/journal.ppat.1010401 |
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