viruses Article A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium Wei Zou 1, Min Xiong 2, Xuefeng Deng 1, John F. Engelhardt 3, Ziying Yan 3 and Jianming Qiu 1,* 1 Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA;
[email protected] (W.Z.);
[email protected] (X.D.) 2 The Children’s Mercy Hospital, School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA;
[email protected] 3 Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA;
[email protected] (J.F.E.);
[email protected] (Z.Y.) * Correspondence:
[email protected]; Tel.: +1-913-588-4329 Received: 11 December 2018; Accepted: 2 January 2019; Published: 7 January 2019 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.