{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T04:58:53Z","timestamp":1772773133939,"version":"3.50.1"},"reference-count":33,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T00:00:00Z","timestamp":1703721600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 AI116812"],"award-info":[{"award-number":["R01 AI116812"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21 AG069226"],"award-info":[{"award-number":["R21 AG069226"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21 AI166543"],"award-info":[{"award-number":["R21 AI166543"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21 AI166543-02S1"],"award-info":[{"award-number":["R21 AI166543-02S1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Pilot Grant from the Institute for Human Infections and Immunity (IHII) at UTMB","award":["R01 AI116812"],"award-info":[{"award-number":["R01 AI116812"]}]},{"name":"Research Pilot Grant from the Institute for Human Infections and Immunity (IHII) at UTMB","award":["R21 AG069226"],"award-info":[{"award-number":["R21 AG069226"]}]},{"name":"Research Pilot Grant from the Institute for Human Infections and Immunity (IHII) at UTMB","award":["R21 AI166543"],"award-info":[{"award-number":["R21 AI166543"]}]},{"name":"Research Pilot Grant from the Institute for Human Infections and Immunity (IHII) at UTMB","award":["R21 AI166543-02S1"],"award-info":[{"award-number":["R21 AI166543-02S1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Unlike other coronaviruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly infected the global population, with some suffering long-term effects. Thanks to extensive data on SARS-CoV-2 made available through global, multi-level collaborative research, investigators are getting closer to understanding the mechanisms of SARS-CoV-2 infection. Here, using publicly available total and small RNAseq data of Calu3 cell lines, we conducted a comparative analysis of the changes in tRNA fragments (tRFs; regulatory small noncoding RNAs) in the context of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 infections. We found extensive upregulation of multiple tRFs in SARS-CoV-2 infection that was not present in SARS-CoV or other virus infections our group has studied. By comparing the total RNA changes in matching samples, we identified significant downregulation of TRDMT1 (tRNA methyltransferase), only in SARS-CoV-2 infection, a potential upstream event. We further found enriched neural functions among downregulated genes with SARS-CoV-2 infection. Interestingly, theoretically predicted targets of the upregulated tRFs without considering mRNA expression data are also enriched in neural functions such as axon guidance. Based on a combination of expression data and theoretical calculations, we propose potential targets for tRFs. For example, among the mRNAs downregulated with SARS-CoV-2 infection (but not with SARS-CoV infection), SEMA3C is a theoretically calculated target of multiple upregulated tRFs and a ligand of NRP1, a SARS-CoV-2 receptor. Our analysis suggests that tRFs contribute to distinct neurological features seen in SARS-CoV-2.<\/jats:p>","DOI":"10.3390\/ijms25010399","type":"journal-article","created":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T03:30:34Z","timestamp":1703734234000},"page":"399","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection"],"prefix":"10.3390","volume":"25","author":[{"given":"Isabella","family":"Imirowicz","sequence":"first","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Azeem","family":"Saifee","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leanne","family":"Henry","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leo","family":"Tunkle","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8856-9300","authenticated-orcid":false,"given":"Alexander","family":"Popescu","sequence":"additional","affiliation":[{"name":"miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0194-3882","authenticated-orcid":false,"given":"Philip","family":"Huang","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jibiana","family":"Jakpor","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"},{"name":"miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ava","family":"Barbano","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"},{"name":"miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rohit","family":"Goru","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4884-0639","authenticated-orcid":false,"given":"Audrey","family":"Gunawan","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Sicilia","sequence":"additional","affiliation":[{"name":"miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mori","family":"Ono","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6884-2584","authenticated-orcid":false,"given":"Xiaoyong","family":"Bao","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX 77555, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inhan","family":"Lee","sequence":"additional","affiliation":[{"name":"Outreach Division, miRcore, Ann Arbor, MI 48104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/s41579-020-00459-7","article-title":"Characteristics of SARS-CoV-2 and COVID-19","volume":"19","author":"Hu","year":"2021","journal-title":"Nat. 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