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Viruses 2019, 11(1), 33; https://doi.org/10.3390/v11010033

A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium

1
Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
2
The Children’s Mercy Hospital, School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
3
Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
*
Author to whom correspondence should be addressed.
Received: 11 December 2018 / Revised: 30 December 2018 / Accepted: 2 January 2019 / Published: 7 January 2019
(This article belongs to the Special Issue New Insights into Parvovirus Research)
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Abstract

Human bocavirus 1 (HBoV1) infects well-differentiated (polarized) human airway epithelium (HAE) cultured at an air-liquid interface (ALI). In the present study, we applied next-generation RNA sequencing to investigate the genome-wide transcription profile of HBoV1, including viral mRNA and small RNA transcripts, in HBoV1-infected HAE cells. We identified novel transcription start and termination sites and confirmed the previously identified splicing events. Importantly, an additional proximal polyadenylation site (pA)p2 and a new distal polyadenylation site (pA)dREH lying on the right-hand hairpin (REH) of the HBoV1 genome were identified in processing viral pre-mRNA. Of note, all viral nonstructural proteins-encoding mRNA transcripts use both the proximal polyadenylation sites [(pA)p1 and (pA)p2] and distal polyadenylation sites [(pA)d1 and (pA)dREH] for termination. However, capsid proteins-encoding transcripts only use the distal polyadenylation sites. While the (pA)p1 and (pA)p2 sites were utilized at roughly equal efficiency for proximal polyadenylation of HBoV1 mRNA transcripts, the (pA)d1 site was more preferred for distal polyadenylation. Additionally, small RNA-seq analysis confirmed there is only one viral noncoding RNA (BocaSR) transcribed from nt 5199–5340 of the HBoV1 genome. Thus, our study provides a systematic and unbiased transcription profile, including both mRNA and small RNA transcripts, of HBoV1 in HBoV1-infected HAE-ALI cultures. View Full-Text
Keywords: parvovirus; human bocavirus 1; RNA-seq; transcription profile; human airway epithelia parvovirus; human bocavirus 1; RNA-seq; transcription profile; human airway epithelia
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Zou, W.; Xiong, M.; Deng, X.; Engelhardt, J.F.; Yan, Z.; Qiu, J. A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium. Viruses 2019, 11, 33.

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