Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo
Abstract Background In addition to the well-known coronavirus genomes and subgenomic mRNAs, the existence of other coronavirus RNA species, which are collectively referred to as noncanonical transcripts, has been suggested; however, their biological characteristics have not yet been experimentally v...
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-023-02201-0 |
| _version_ | 1797453918537515008 |
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| author | Ching-Hung Lin BoJia Chen Day-Yu Chao Feng-Cheng Hsieh Chien-Chen Lai Wei-Chen Wang Cheng-Yu Kuo Chun-Chun Yang Hsuan-Wei Hsu Hon-Man-Herman Tam Hung-Yi Wu |
| author_facet | Ching-Hung Lin BoJia Chen Day-Yu Chao Feng-Cheng Hsieh Chien-Chen Lai Wei-Chen Wang Cheng-Yu Kuo Chun-Chun Yang Hsuan-Wei Hsu Hon-Man-Herman Tam Hung-Yi Wu |
| author_sort | Ching-Hung Lin |
| collection | DOAJ |
| description | Abstract Background In addition to the well-known coronavirus genomes and subgenomic mRNAs, the existence of other coronavirus RNA species, which are collectively referred to as noncanonical transcripts, has been suggested; however, their biological characteristics have not yet been experimentally validated in vitro and in vivo. Methods To comprehensively determine the amounts, species and structures of noncanonical transcripts for bovine coronavirus in HRT-18 cells and mouse hepatitis virus A59, a mouse coronavirus, in mouse L cells and mice, nanopore direct RNA sequencing was employed. To experimentally validate the synthesis of noncanonical transcripts under regular infection, Northern blotting was performed. Both Northern blotting and nanopore direct RNA sequencing were also applied to examine the reproducibility of noncanonical transcripts. In addition, Northern blotting was also employed to determine the regulatory features of noncanonical transcripts under different infection conditions, including different cells, multiplicities of infection (MOIs) and coronavirus strains. Results In the current study, we (i) experimentally determined that coronavirus noncanonical transcripts were abundantly synthesized, (ii) classified the noncanonical transcripts into seven populations based on their structures and potential synthesis mechanisms, (iii) showed that the species and amounts of the noncanonical transcripts were reproducible during regular infection but regulated in altered infection environments, (iv) revealed that coronaviruses may employ various mechanisms to synthesize noncanonical transcripts, and (v) found that the biological characteristics of coronavirus noncanonical transcripts were similar between in vitro and in vivo conditions. Conclusions The biological characteristics of noncanonical coronavirus transcripts were experimentally validated for the first time. The identified features of noncanonical transcripts in terms of abundance, reproducibility and variety extend the current model for coronavirus gene expression. The capability of coronaviruses to regulate the species and amounts of noncanonical transcripts may contribute to the pathogenesis of coronaviruses during infection, posing potential challenges in disease control. Thus, the biology of noncanonical transcripts both in vitro and in vivo revealed here can provide a database for biological research, contributing to the development of antiviral strategies. |
| first_indexed | 2024-03-09T15:29:48Z |
| format | Article |
| id | doaj.art-ff3f1f4251d44b85b63a233ba6668592 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-03-09T15:29:48Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-ff3f1f4251d44b85b63a233ba66685922023-11-26T12:20:37ZengBMCVirology Journal1743-422X2023-10-0120111610.1186/s12985-023-02201-0Biological characterization of coronavirus noncanonical transcripts in vitro and in vivoChing-Hung Lin0BoJia Chen1Day-Yu Chao2Feng-Cheng Hsieh3Chien-Chen Lai4Wei-Chen Wang5Cheng-Yu Kuo6Chun-Chun Yang7Hsuan-Wei Hsu8Hon-Man-Herman Tam9Hung-Yi Wu10Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityDoctoral Program in Microbial Genomics, National Chung Hsing University and Academia SinicaGraduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityInstitute of Molecular Biology, College of Life Sciences, National Chung Hsing UniversityInstitute of Molecular Biology, College of Life Sciences, National Chung Hsing UniversityInstitute of Molecular Biology, College of Life Sciences, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityGraduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing UniversityAbstract Background In addition to the well-known coronavirus genomes and subgenomic mRNAs, the existence of other coronavirus RNA species, which are collectively referred to as noncanonical transcripts, has been suggested; however, their biological characteristics have not yet been experimentally validated in vitro and in vivo. Methods To comprehensively determine the amounts, species and structures of noncanonical transcripts for bovine coronavirus in HRT-18 cells and mouse hepatitis virus A59, a mouse coronavirus, in mouse L cells and mice, nanopore direct RNA sequencing was employed. To experimentally validate the synthesis of noncanonical transcripts under regular infection, Northern blotting was performed. Both Northern blotting and nanopore direct RNA sequencing were also applied to examine the reproducibility of noncanonical transcripts. In addition, Northern blotting was also employed to determine the regulatory features of noncanonical transcripts under different infection conditions, including different cells, multiplicities of infection (MOIs) and coronavirus strains. Results In the current study, we (i) experimentally determined that coronavirus noncanonical transcripts were abundantly synthesized, (ii) classified the noncanonical transcripts into seven populations based on their structures and potential synthesis mechanisms, (iii) showed that the species and amounts of the noncanonical transcripts were reproducible during regular infection but regulated in altered infection environments, (iv) revealed that coronaviruses may employ various mechanisms to synthesize noncanonical transcripts, and (v) found that the biological characteristics of coronavirus noncanonical transcripts were similar between in vitro and in vivo conditions. Conclusions The biological characteristics of noncanonical coronavirus transcripts were experimentally validated for the first time. The identified features of noncanonical transcripts in terms of abundance, reproducibility and variety extend the current model for coronavirus gene expression. The capability of coronaviruses to regulate the species and amounts of noncanonical transcripts may contribute to the pathogenesis of coronaviruses during infection, posing potential challenges in disease control. Thus, the biology of noncanonical transcripts both in vitro and in vivo revealed here can provide a database for biological research, contributing to the development of antiviral strategies.https://doi.org/10.1186/s12985-023-02201-0CoronavirusNoncanonical transcriptPathogenesisGene expressionCoronavirus genome |
| spellingShingle | Ching-Hung Lin BoJia Chen Day-Yu Chao Feng-Cheng Hsieh Chien-Chen Lai Wei-Chen Wang Cheng-Yu Kuo Chun-Chun Yang Hsuan-Wei Hsu Hon-Man-Herman Tam Hung-Yi Wu Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo Virology Journal Coronavirus Noncanonical transcript Pathogenesis Gene expression Coronavirus genome |
| title | Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo |
| title_full | Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo |
| title_fullStr | Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo |
| title_full_unstemmed | Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo |
| title_short | Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo |
| title_sort | biological characterization of coronavirus noncanonical transcripts in vitro and in vivo |
| topic | Coronavirus Noncanonical transcript Pathogenesis Gene expression Coronavirus genome |
| url | https://doi.org/10.1186/s12985-023-02201-0 |
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