Decoding the Architecture of the Varicella-Zoster Virus Transcriptome

ABSTRACT Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain. The VZV genome is densely packed and produces multitudes of overlappi...

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Autores principales:	Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	direct RNA-Seq ORF62 alphaherpesvirus kinetics transcriptome varicella-zoster virus Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/69e6362f0451459ab6b88c036fa84b1e
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spelling	oai:doaj.org-article:69e6362f0451459ab6b88c036fa84b1e2021-11-15T16:19:09ZDecoding the Architecture of the Varicella-Zoster Virus Transcriptome10.1128/mBio.01568-202150-7511https://doaj.org/article/69e6362f0451459ab6b88c036fa84b1e2020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01568-20https://doaj.org/toc/2150-7511ABSTRACT Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain. The VZV genome is densely packed and produces multitudes of overlapping transcripts deriving from both strands. While 71 distinct open reading frames (ORFs) have thus far been experimentally defined, the full coding potential of VZV remains unknown. Here, we integrated multiple short-read RNA sequencing approaches with long-read direct RNA sequencing on RNA isolated from VZV-infected cells to provide a comprehensive reannotation of the lytic VZV transcriptome architecture. Through precise mapping of transcription start sites, splice junctions, and polyadenylation sites, we identified 136 distinct polyadenylated VZV RNAs that encode canonical ORFs, noncanonical ORFs, and ORF fusions, as well as putative noncoding RNAs (ncRNAs). Furthermore, we determined the kinetic class of all VZV transcripts and observed, unexpectedly, that transcripts encoding the ORF62 protein, previously designated Immediate-Early, were expressed with Late kinetics. Our work showcases the complexity of the VZV transcriptome and provides a comprehensive resource that will facilitate future functional studies of coding RNAs, ncRNAs, and the biological mechanisms underlying the regulation of viral transcription and translation during lytic VZV infection. IMPORTANCE Transcription from herpesviral genomes, executed by the host RNA polymerase II and regulated by viral proteins, results in coordinated viral gene expression to efficiently produce infectious progeny. However, the complete coding potential and regulation of viral gene expression remain ill-defined for the human alphaherpesvirus varicella-zoster virus (VZV), causative agent of both varicella and herpes zoster. Here, we present a comprehensive overview of the VZV transcriptome and the kinetic class of all identified viral transcripts, using two virus strains and two biologically relevant cell types. Additionally, our data provide an overview of how VZV diversifies its transcription from one of the smallest herpesviral genomes. Unexpectedly, the transcript encoding the major viral transactivator protein (pORF62) was expressed with Late kinetics, whereas orthologous transcripts in other alphaherpesviruses are typically expressed during the immediate early phase. Therefore, our work both establishes the architecture of the VZV transcriptome and provides insight into regulation of alphaherpesvirus gene expression.Shirley E. BraspenningTomohiko SadaokaJudith BreuerGeorges M. G. M. VerjansWerner J. D. OuwendijkDaniel P. DepledgeAmerican Society for Microbiologyarticledirect RNA-SeqORF62alphaherpesviruskineticstranscriptomevaricella-zoster virusMicrobiologyQR1-502ENmBio, Vol 11, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	direct RNA-Seq ORF62 alphaherpesvirus kinetics transcriptome varicella-zoster virus Microbiology QR1-502
spellingShingle	direct RNA-Seq ORF62 alphaherpesvirus kinetics transcriptome varicella-zoster virus Microbiology QR1-502 Shirley E. Braspenning Tomohiko Sadaoka Judith Breuer Georges M. G. M. Verjans Werner J. D. Ouwendijk Daniel P. Depledge Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
description	ABSTRACT Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain. The VZV genome is densely packed and produces multitudes of overlapping transcripts deriving from both strands. While 71 distinct open reading frames (ORFs) have thus far been experimentally defined, the full coding potential of VZV remains unknown. Here, we integrated multiple short-read RNA sequencing approaches with long-read direct RNA sequencing on RNA isolated from VZV-infected cells to provide a comprehensive reannotation of the lytic VZV transcriptome architecture. Through precise mapping of transcription start sites, splice junctions, and polyadenylation sites, we identified 136 distinct polyadenylated VZV RNAs that encode canonical ORFs, noncanonical ORFs, and ORF fusions, as well as putative noncoding RNAs (ncRNAs). Furthermore, we determined the kinetic class of all VZV transcripts and observed, unexpectedly, that transcripts encoding the ORF62 protein, previously designated Immediate-Early, were expressed with Late kinetics. Our work showcases the complexity of the VZV transcriptome and provides a comprehensive resource that will facilitate future functional studies of coding RNAs, ncRNAs, and the biological mechanisms underlying the regulation of viral transcription and translation during lytic VZV infection. IMPORTANCE Transcription from herpesviral genomes, executed by the host RNA polymerase II and regulated by viral proteins, results in coordinated viral gene expression to efficiently produce infectious progeny. However, the complete coding potential and regulation of viral gene expression remain ill-defined for the human alphaherpesvirus varicella-zoster virus (VZV), causative agent of both varicella and herpes zoster. Here, we present a comprehensive overview of the VZV transcriptome and the kinetic class of all identified viral transcripts, using two virus strains and two biologically relevant cell types. Additionally, our data provide an overview of how VZV diversifies its transcription from one of the smallest herpesviral genomes. Unexpectedly, the transcript encoding the major viral transactivator protein (pORF62) was expressed with Late kinetics, whereas orthologous transcripts in other alphaherpesviruses are typically expressed during the immediate early phase. Therefore, our work both establishes the architecture of the VZV transcriptome and provides insight into regulation of alphaherpesvirus gene expression.
format	article
author	Shirley E. Braspenning Tomohiko Sadaoka Judith Breuer Georges M. G. M. Verjans Werner J. D. Ouwendijk Daniel P. Depledge
author_facet	Shirley E. Braspenning Tomohiko Sadaoka Judith Breuer Georges M. G. M. Verjans Werner J. D. Ouwendijk Daniel P. Depledge
author_sort	Shirley E. Braspenning
title	Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
title_short	Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
title_full	Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
title_fullStr	Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
title_full_unstemmed	Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
title_sort	decoding the architecture of the varicella-zoster virus transcriptome
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/69e6362f0451459ab6b88c036fa84b1e
work_keys_str_mv	AT shirleyebraspenning decodingthearchitectureofthevaricellazostervirustranscriptome AT tomohikosadaoka decodingthearchitectureofthevaricellazostervirustranscriptome AT judithbreuer decodingthearchitectureofthevaricellazostervirustranscriptome AT georgesmgmverjans decodingthearchitectureofthevaricellazostervirustranscriptome AT wernerjdouwendijk decodingthearchitectureofthevaricellazostervirustranscriptome AT danielpdepledge decodingthearchitectureofthevaricellazostervirustranscriptome
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Decoding the Architecture of the Varicella-Zoster Virus Transcriptome

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