{"doi":"10.3390/ijms25010399","title":"Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection","abstract":"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.","journal":"International Journal of Molecular Sciences","year":2023,"id":340493,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9167,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1075555,"name":"Azeem Saifee","orcid":null,"position":1,"is_corresponding":false},{"id":699673,"name":"Leanne E. Henry","orcid":"0009-0003-7554-079X","position":2,"is_corresponding":false},{"id":332765,"name":"Leo Tunkle","orcid":null,"position":3,"is_corresponding":false},{"id":1074999,"name":"Alexander Popescu","orcid":"0000-0002-8856-9300","position":4,"is_corresponding":false},{"id":889017,"name":"Philip Huang","orcid":"0000-0002-0194-3882","position":5,"is_corresponding":false},{"id":1075556,"name":"Jibiana Jakpor","orcid":null,"position":6,"is_corresponding":false},{"id":1075000,"name":"Ava Barbano","orcid":"0009-0006-5236-6065","position":7,"is_corresponding":false},{"id":889738,"name":"Rohit Goru","orcid":null,"position":8,"is_corresponding":false},{"id":1075001,"name":"Audrey Gunawan","orcid":"0009-0004-4884-0639","position":9,"is_corresponding":false},{"id":1075002,"name":"María Sicilia Piñero","orcid":"0000-0002-1731-4570","position":10,"is_corresponding":false},{"id":1075557,"name":"Mori Ono","orcid":null,"position":11,"is_corresponding":false},{"id":326649,"name":"Xiaoyong Bao","orcid":"0000-0002-6884-2584","position":12,"is_corresponding":false},{"id":326648,"name":"Inhan Lee","orcid":"0000-0001-5840-3900","position":13,"is_corresponding":false},{"id":889506,"name":"Isabella Imirowicz","orcid":"0009-0007-6100-2594","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T01:10:54.145367Z","pmid":"38203569","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}