{"data":{"id":"10.6084/m9.figshare.1296270","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1296270","prefix":"10.6084","suffix":"m9.figshare.1296270","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Ahmed, Firoz","nameType":"Personal","givenName":"Firoz","familyName":"Ahmed","affiliation":[],"nameIdentifiers":[]},{"name":"Muthappa Senthil-Kumar","affiliation":[],"nameIdentifiers":[]},{"name":"Seonghee Lee","affiliation":[],"nameIdentifiers":[]},{"name":"Xinbin Dai","affiliation":[],"nameIdentifiers":[]},{"name":"Kirankumar S Mysore","affiliation":[],"nameIdentifiers":[]},{"name":"Zhao, Patrick Xuechun","nameType":"Personal","givenName":"Patrick Xuechun","familyName":"Zhao","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in \u003ci\u003eArabidopsis thaliana\u003c/i\u003e"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2014,"subjects":[{"subject":"Biophysics"},{"subject":"Biochemistry"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"80699 Information Systems not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Science Policy"}],"contributors":[],"dates":[{"date":"2015-01-28","dateType":"Created"},{"date":"2020-08-25","dateType":"Updated"},{"date":"2014","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2014.996474","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["3957245 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from \u003ci\u003eArabidopsis\u003c/i\u003e to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in \u003ci\u003eArabidopsis\u003c/i\u003e. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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