{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:46:34Z","timestamp":1753890394539,"version":"3.41.2"},"reference-count":56,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,1,31]],"date-time":"2024-01-31T00:00:00Z","timestamp":1706659200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>In recent years, a population of small RNA fragments derived from non-coding RNAs (sfd-RNAs) has gained significant interest due to its functional and structural resemblance to miRNAs, adding another level of complexity to our comprehension of small-RNA-mediated gene regulation. Despite this, scientists need more tools to test the differential expression of sfd-RNAs since the current methods to detect miRNAs may not be directly applied to them. The primary reasons are the lack of accurate small RNA and ncRNA annotation, the multi-mapping read (MMR) placement, and the multicopy nature of ncRNAs in the human genome. To solve these issues, a methodology that allows the detection of differentially expressed sfd-RNAs, including canonical miRNAs, by using an integrated copy-number-corrected ncRNA annotation was implemented. This approach was coupled with sixteen different computational strategies composed of combinations of four aligners and four normalization methods to provide a rank-order of prediction for each differentially expressed sfd-RNA. By systematically addressing the three main problems, we could detect differentially expressed miRNAs and sfd-RNAs in dengue virus-infected human dermal microvascular endothelial cells. Although more biological evaluations are required, two molecular targets of the hsa-mir-103a and hsa-mir-494 (CDK5 and PI3\/AKT) appear relevant for dengue virus (DENV) infections. Here, we performed a comprehensive annotation and differential expression analysis, which can be applied in other studies addressing the role of small fragment RNA populations derived from ncRNAs in virus infection.<\/jats:p>","DOI":"10.3389\/fbinf.2024.1293412","type":"journal-article","created":{"date-parts":[[2024,1,31]],"date-time":"2024-01-31T04:42:51Z","timestamp":1706676171000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells"],"prefix":"10.3389","volume":"4","author":[{"given":"Aimer","family":"Gutierrez-Diaz","sequence":"first","affiliation":[]},{"given":"Steve","family":"Hoffmann","sequence":"additional","affiliation":[]},{"given":"Juan Carlos","family":"Gallego-G\u00f3mez","sequence":"additional","affiliation":[]},{"given":"Clara Isabel","family":"Bermudez-Santana","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,1,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.virusres.2018.10.018","article-title":"Dengue virus potentially promotes migratory responses on endothelial cells by enhancing pro-migratory soluble factors and miRNAs","volume":"259","author":"Alvarez-Diaz","year":"2019","journal-title":"Virus Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1186\/1471-2164-11-270","article-title":"Genomic organization of eukaryotic tRNAs","volume":"11","author":"Bermudez-Santana","year":"2010","journal-title":"BMC Genomics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"93.2","DOI":"10.4049\/jimmunol.204.supp.93.2","article-title":"Respiratory syncytial virus induces a functional tRNA-derived fragment to promote infection by targeting SYNE2","volume":"204","author":"Chen","year":"2020","journal-title":"J. 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