{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T05:59:27Z","timestamp":1768888767245,"version":"3.49.0"},"reference-count":36,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2019,1,7]],"date-time":"2019-01-07T00:00:00Z","timestamp":1546819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI070723"],"award-info":[{"award-number":["AI070723"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI139572"],"award-info":[{"award-number":["AI139572"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Diabetes and Digestive and Kidney Disease","award":["DK054759"],"award-info":[{"award-number":["DK054759"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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\u20135340 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.<\/jats:p>","DOI":"10.3390\/v11010033","type":"journal-article","created":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T03:06:06Z","timestamp":1547003166000},"page":"33","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium"],"prefix":"10.3390","volume":"11","author":[{"given":"Wei","family":"Zou","sequence":"first","affiliation":[{"name":"Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Xiong","sequence":"additional","affiliation":[{"name":"The Children\u2019s Mercy Hospital, School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuefeng","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Engelhardt","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziying","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9850-1695","authenticated-orcid":false,"given":"Jianming","family":"Qiu","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,1,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1086\/512196","article-title":"Human bocavirus and acute wheezing in children","volume":"44","author":"Allander","year":"2007","journal-title":"Clin. Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1128\/CMR.00040-16","article-title":"Human parvoviruses","volume":"30","author":"Qiu","year":"2017","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1750-9378-2-3","article-title":"Quantification of human bocavirus in lower respiratory tract infections in China","volume":"2","author":"Lin","year":"2007","journal-title":"Infect. Agent Cancer"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1002\/rmv.720","article-title":"Human bocavirus-the first 5 years","volume":"22","author":"Jartti","year":"2011","journal-title":"Rev. Med. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1002\/ppul.21151","article-title":"Serologically verified human bocavirus pneumonia in children","volume":"45","author":"Don","year":"2010","journal-title":"Pediatr. Pulmonol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1002\/ppul.21225","article-title":"Role of emerging respiratory viruses in children with severe acute wheezing","volume":"45","author":"Calvo","year":"2010","journal-title":"Pediatr. Pulmonol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1186\/s12879-018-3225-3","article-title":"Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: A 7-year study in a subtropical region","volume":"18","author":"Liu","year":"2018","journal-title":"BMC Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1111\/irv.12587","article-title":"Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia","volume":"12","author":"Praznik","year":"2018","journal-title":"Influenza Other Respir Viruses"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1128\/JCM.02362-10","article-title":"Human bocavirus as the cause of a life-threatening infection","volume":"49","author":"Ursic","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2303","DOI":"10.3201\/eid1712.110574","article-title":"Severe human bocavirus infection, Germany","volume":"17","author":"Korner","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1128\/JCM.05706-11","article-title":"Life-threatening respiratory tract disease with human bocavirus-1 infection in a four-year-old child","volume":"50","author":"Edner","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.3201\/eid1908.130074","article-title":"Primary and secondary human bocavirus 1 infections in a family, Finland","volume":"19","author":"Jula","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1097\/INF.0000000000000509","article-title":"Fatal human bocavirus infection in an 18-month-old child with chronic lung disease of prematurity","volume":"34","author":"Ursic","year":"2015","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1097\/INF.0000000000001681","article-title":"Severe Lower Respiratory Tract Infection Caused by Human Bocavirus 1 in an Infant","volume":"36","author":"Eskola","year":"2017","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1093\/infdis\/jix148","article-title":"Viral Pathogen Detection by Metagenomics and Pan Viral Group PCR in Children with Pneumonia Lacking Identifiable Etiology","volume":"215","author":"Schlaberg","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"7739","DOI":"10.1128\/JVI.00614-09","article-title":"Human bocavirus can be cultured in differentiated human airway epithelial cells","volume":"83","author":"Dijkman","year":"2009","journal-title":"J. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Huang, Q., Deng, X., Yan, Z., Cheng, F., Luo, Y., Shen, W., Lei-Butters, D.C., Chen, A.Y., Li, Y., and Tang, L. (2012). Establishment of a reverse genetics system for studying human bocavirus in human airway epithelia. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002899"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4097","DOI":"10.1128\/JVI.03132-12","article-title":"In vitro modeling of human bocavirus 1 infection of polarized primary human airway epithelia","volume":"87","author":"Deng","year":"2013","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.jviromet.2013.10.012","article-title":"Human bocavirus 1 infects commercially available primary human airway epithelium cultures productively","volume":"195","author":"Deng","year":"2014","journal-title":"J. Virol. Methods"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Deng, X., Yan, Z., Cheng, F., Engelhardt, J.F., and Qiu, J. (2016). Replication of an Autonomous Human Parvovirus in Non-dividing Human Airway Epithelium Is Facilitated through the DNA Damage and Repair Pathways. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1005399"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3956","DOI":"10.1128\/JVI.02569-08","article-title":"Molecular characterization of infectious clones of the minute virus of canines reveals unique features of bocaviruses","volume":"83","author":"Sun","year":"2009","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"12080","DOI":"10.1128\/JVI.00815-07","article-title":"The transcription profile of the bocavirus bovine parvovirus is unlike those of previously characterized parvoviruses","volume":"81","author":"Qiu","year":"2007","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.virol.2010.04.014","article-title":"Characterization of the gene expression profile of human bocavirus","volume":"403","author":"Chen","year":"2010","journal-title":"Virology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"10097","DOI":"10.1128\/JVI.01374-15","article-title":"Identification and Functional Analysis of Novel Non-structural Proteins of Human Bocavirus 1","volume":"89","author":"Shen","year":"2015","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"4658","DOI":"10.1128\/JVI.02964-15","article-title":"Nonstructural Protein NP1 of Human Bocavirus 1 Plays a Critical Role in the Expression of Viral Capsid Proteins","volume":"90","author":"Zou","year":"2016","journal-title":"J. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e02375-16","DOI":"10.1128\/JVI.02375-16","article-title":"Parvovirus Expresses a Small Noncoding RNA That Plays an Essential Role in Virus Replication","volume":"91","author":"Wang","year":"2017","journal-title":"J. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3781","DOI":"10.1016\/S0021-9258(18)53762-5","article-title":"Expression of the cystic fibrosis transmembrane conductance regulator from a novel adeno-associated virus promoter","volume":"268","author":"Flotte","year":"1993","journal-title":"J. Biol. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"12435","DOI":"10.1128\/JVI.76.24.12435-12447.2002","article-title":"Characterization of the transcription profile of adeno-associated virus type 5 reveals a number of unique features compared to previously characterized adeno-associated viruses","volume":"76","author":"Qiu","year":"2002","journal-title":"J. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1101\/gad.9.21.2672","article-title":"The 160-kD subunit of human cleavage-polyadenylation specificity factor coordinates pre-mRNA 3\u2032-end formation","volume":"9","author":"Murthy","year":"1995","journal-title":"Genes Dev."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Stutika, C., Mietzsch, M., Gogol-Doring, A., Weger, S., Sohn, M., Chen, W., and Heilbronn, R. (2016). Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0161454"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1128\/JVI.02627-12","article-title":"Characterization of the nonstructural proteins of the bocavirus minute virus of canines","volume":"87","author":"Sukhu","year":"2013","journal-title":"J. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1128\/JVI.02618-15","article-title":"NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing","volume":"90","author":"Fasina","year":"2015","journal-title":"J. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"e00260-17","DOI":"10.1128\/JVI.00260-17","article-title":"The minute virus of canines (MVC) NP1 protein governs the expression of a subset of essential NS proteins via its role in RNA processing","volume":"91","author":"Fasina","year":"2017","journal-title":"J. Virol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e01187-18","DOI":"10.1128\/JVI.01187-18","article-title":"The Human Bocavirus 1 NP1 Protein Is a Multifunctional Regulator of Viral RNA Processing","volume":"92","author":"Dong","year":"2018","journal-title":"J. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1128\/MMBR.63.2.405-445.1999","article-title":"Formation of mRNA 3\u2032 ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis","volume":"63","author":"Zhao","year":"1999","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e02026-16","DOI":"10.1128\/JVI.02026-16","article-title":"Alternative Polyadenylation of Human Bocavirus at Its 3\u2032 End Is Regulated by Multiple Elements and Affects Capsid Expression","volume":"91","author":"Hao","year":"2017","journal-title":"J. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/1\/33\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:24:00Z","timestamp":1760185440000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/1\/33"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,7]]},"references-count":36,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,1]]}},"alternative-id":["v11010033"],"URL":"https:\/\/doi.org\/10.3390\/v11010033","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,7]]}}}