Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection
The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. In the context of...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.821137/full |
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| author | Wenzhe Wu Eun-Jin Choi Binbin Wang Ke Zhang Awadalkareem Adam Gengming Huang Leo Tunkle Leo Tunkle Leo Tunkle Philip Huang Philip Huang Rohit Goru Rohit Goru Isabella Imirowicz Isabella Imirowicz Leanne Henry Leanne Henry Inhan Lee Jianli Dong Jianli Dong Tian Wang Tian Wang Tian Wang Xiaoyong Bao Xiaoyong Bao Xiaoyong Bao |
| author_facet | Wenzhe Wu Eun-Jin Choi Binbin Wang Ke Zhang Awadalkareem Adam Gengming Huang Leo Tunkle Leo Tunkle Leo Tunkle Philip Huang Philip Huang Rohit Goru Rohit Goru Isabella Imirowicz Isabella Imirowicz Leanne Henry Leanne Henry Inhan Lee Jianli Dong Jianli Dong Tian Wang Tian Wang Tian Wang Xiaoyong Bao Xiaoyong Bao Xiaoyong Bao |
| author_sort | Wenzhe Wu |
| collection | DOAJ |
| description | The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. In the context of viral infections, small non-coding RNAs (sncRNAs) are known to play important roles in regulating the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK‐RNA‐seq, a modified next-generation sequencing (NGS), we found that sncRNA profiles in human nasopharyngeal swabs (NPS) samples are significantly impacted by SARS-CoV-2. Among impacted sncRNAs, tRFs are the most significantly affected and most of them are derived from the 5′-end of tRNAs (tRF5). Such a change was also observed in SARS-CoV-2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several small virus-derived ncRNAs (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3′-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs. |
| first_indexed | 2024-12-13T12:53:58Z |
| format | Article |
| id | doaj.art-3e9d29887cb14e22a87d8a99be7fcfa3 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-12-13T12:53:58Z |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-3e9d29887cb14e22a87d8a99be7fcfa32022-12-21T23:45:14ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-02-01910.3389/fmolb.2022.821137821137Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 InfectionWenzhe Wu0Eun-Jin Choi1Binbin Wang2Ke Zhang3Awadalkareem Adam4Gengming Huang5Leo Tunkle6Leo Tunkle7Leo Tunkle8Philip Huang9Philip Huang10Rohit Goru11Rohit Goru12Isabella Imirowicz13Isabella Imirowicz14Leanne Henry15Leanne Henry16Inhan Lee17Jianli Dong18Jianli Dong19Tian Wang20Tian Wang21Tian Wang22Xiaoyong Bao23Xiaoyong Bao24Xiaoyong Bao25Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Pathology, The University of Texas Medical Branch, Galveston, TX, United StatesmiRcore, Ann Arbor, MI, United StatesDepartment of Nuclear Engineering and Radiological Sience, University of Michigan, Ann Arbor, MI, United StatesDepartment of Computer Science, University of Michigan, Ann Arbor, MI, United StatesmiRcore, Ann Arbor, MI, United StatesDepartment of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United StatesmiRcore, Ann Arbor, MI, United StatesDepartment of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United StatesmiRcore, Ann Arbor, MI, United StatesDepartment of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United StatesmiRcore, Ann Arbor, MI, United StatesDepartment of Computer Science, University of Michigan, Ann Arbor, MI, United StatesmiRcore, Ann Arbor, MI, United StatesDepartment of Pathology, The University of Texas Medical Branch, Galveston, TX, United StatesThe Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Pathology, The University of Texas Medical Branch, Galveston, TX, United StatesThe Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United StatesDepartment of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United StatesThe Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United StatesThe Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United StatesThe ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. In the context of viral infections, small non-coding RNAs (sncRNAs) are known to play important roles in regulating the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK‐RNA‐seq, a modified next-generation sequencing (NGS), we found that sncRNA profiles in human nasopharyngeal swabs (NPS) samples are significantly impacted by SARS-CoV-2. Among impacted sncRNAs, tRFs are the most significantly affected and most of them are derived from the 5′-end of tRNAs (tRF5). Such a change was also observed in SARS-CoV-2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several small virus-derived ncRNAs (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3′-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs.https://www.frontiersin.org/articles/10.3389/fmolb.2022.821137/fullSARS-CoV-2TRFSARS-CoV-2-derived sncRNAstRF5DCviral replication and SARS-CoV-2-derived sncRNAs |
| spellingShingle | Wenzhe Wu Eun-Jin Choi Binbin Wang Ke Zhang Awadalkareem Adam Gengming Huang Leo Tunkle Leo Tunkle Leo Tunkle Philip Huang Philip Huang Rohit Goru Rohit Goru Isabella Imirowicz Isabella Imirowicz Leanne Henry Leanne Henry Inhan Lee Jianli Dong Jianli Dong Tian Wang Tian Wang Tian Wang Xiaoyong Bao Xiaoyong Bao Xiaoyong Bao Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection Frontiers in Molecular Biosciences SARS-CoV-2 TRF SARS-CoV-2-derived sncRNAs tRF5DC viral replication and SARS-CoV-2-derived sncRNAs |
| title | Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection |
| title_full | Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection |
| title_fullStr | Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection |
| title_full_unstemmed | Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection |
| title_short | Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection |
| title_sort | changes of small non coding rnas by severe acute respiratory syndrome coronavirus 2 infection |
| topic | SARS-CoV-2 TRF SARS-CoV-2-derived sncRNAs tRF5DC viral replication and SARS-CoV-2-derived sncRNAs |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.821137/full |
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