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Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression

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dc.abstract.enMicroRNAs (miRNAs) are essential regulators of gene expression, yet few comprehensive databases exist for miRNA expression in non-model species, limiting our ability to characterize their roles in gene regulation, development, and disease. Similarly, isomiRs - length and sequence isoforms of canonical miRNAs with potentially altered regulatory targets and functions - have received even less attention in non-model species, including the horse, leaving a critical gap in our understanding of their biological significance. To address these challenges, we developed an open-source, containerized pipeline for identifying and quantifying miRNAs and isomiRs (FARmiR: Framework for Analysis and Refinement of miRNAs), and an associated interactive browser (AIMEE: Animal IsomiR and MiRNA Expression Explorer). AIMEE was developed to make miRNA expression data more accessible and user-friendly, a feature often lacking from other expression atlases. These tools were developed using equine data but can be readily extended to other species. Using these tools, we aggregated 461 small RNA-seq datasets, spanning 61 distinct tissues, integrating data from public repositories, an American Quarter Horse cohort, and the Functional Annotation of ANimal Genome (FAANG) consortium Thoroughbred samples, predicting 5,781 miRNAs and isomiRs. This work represents the largest systematically curated atlas of equine miRNA expression to date, providing a valuable resource that will enhance our understanding of miRNA and isomiR functions in tissue-specific regulation and ultimately improve biomarker discovery, functional genomics, and precision veterinary medicine.
dc.affiliationWydział Medycyny Weterynaryjnej i Nauk o Zwierzętach
dc.affiliation.instituteKatedra Genetyki i Podstaw Hodowli Zwierząt​​
dc.contributor.authorCullen, Jonah N.
dc.contributor.authorCieślak, Jakub
dc.contributor.authorPetersen, Jessica L.
dc.contributor.authorBellone, Rebecca R.
dc.contributor.authorFinno, Carrie J.
dc.contributor.authorKalbfleisch, Ted S.
dc.contributor.authorCalloe, Kirstine
dc.contributor.authorCapomaccio, Stefano
dc.contributor.authorCappelli, Katia
dc.contributor.authorColeman, Stephen J.
dc.contributor.authorDistl, Ottmar
dc.contributor.authorDurward-Akhurst, Sian A.
dc.contributor.authorGiulotto, Elena
dc.contributor.authorHamilton, Natasha A.
dc.contributor.authorHill, Emmeline W.
dc.contributor.authorKatz, Lisa M.
dc.contributor.authorKlaerke, Dan A.
dc.contributor.authorLindgren, Gabriella
dc.contributor.authorMacHugh, David E.
dc.contributor.authorMaćkowski, Mariusz
dc.contributor.authorMacLeod, James N.
dc.contributor.authorMetzger, Julia
dc.contributor.authorMurphy, Barbara A.
dc.contributor.authorOrlando, Ludovic
dc.contributor.authorRaudsepp, Terje
dc.contributor.authorSilvestrelli, Maurizio
dc.contributor.authorStrand, Eric
dc.contributor.authorTozaki, Teruaki
dc.contributor.authorTrachsel, Dagmar S.
dc.contributor.authorValderrama Figueroa, Laura S.
dc.contributor.authorVelie, Brandon D.
dc.contributor.authorWade, Claire M.
dc.contributor.authorWaud, Bianca
dc.contributor.authorMickelson, James R.
dc.contributor.authorMcCue, Molly E.
dc.date.access2025-09-24
dc.date.accessioned2025-09-30T11:08:09Z
dc.date.available2025-09-30T11:08:09Z
dc.date.copyright2025-09-05
dc.date.issued2025
dc.description.abstract<jats:p>MicroRNAs (miRNAs) are essential regulators of gene expression, yet few comprehensive databases exist for miRNA expression in non-model species, limiting our ability to characterize their roles in gene regulation, development, and disease. Similarly, isomiRs - length and sequence isoforms of canonical miRNAs with potentially altered regulatory targets and functions - have received even less attention in non-model species, including the horse, leaving a critical gap in our understanding of their biological significance. To address these challenges, we developed an open-source, containerized pipeline for identifying and quantifying miRNAs and isomiRs (FARmiR: Framework for Analysis and Refinement of miRNAs), and an associated interactive browser (AIMEE: Animal IsomiR and MiRNA Expression Explorer). AIMEE was developed to make miRNA expression data more accessible and user-friendly, a feature often lacking from other expression atlases. These tools were developed using equine data but can be readily extended to other species. Using these tools, we aggregated 461 small RNA-seq datasets, spanning 61 distinct tissues, integrating data from public repositories, an American Quarter Horse cohort, and the Functional Annotation of ANimal Genome (FAANG) consortium Thoroughbred samples, predicting 5,781 miRNAs and isomiRs. This work represents the largest systematically curated atlas of equine miRNA expression to date, providing a valuable resource that will enhance our understanding of miRNA and isomiR functions in tissue-specific regulation and ultimately improve biomarker discovery, functional genomics, and precision veterinary medicine.</jats:p>
dc.description.accesstimeat_publication
dc.description.bibliographyil., bibliogr.
dc.description.financepublication_nocost
dc.description.financecost0,00
dc.description.if3,7
dc.description.number9
dc.description.points140
dc.description.versionfinal_published
dc.description.volume21
dc.identifier.doi10.1371/journal.pgen.1011835
dc.identifier.eissn1553-7390
dc.identifier.issn1553-7404
dc.identifier.urihttps://sciencerep.up.poznan.pl/handle/item/5052
dc.identifier.weblinkhttps://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011835
dc.languageen
dc.relation.ispartofPLoS Genetics
dc.relation.pagese1011835
dc.rightsCC-BY
dc.sciencecloudnosend
dc.share.typeOPEN_JOURNAL
dc.titleCharting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression
dc.typeJournalArticle
dspace.entity.typePublication
oaire.citation.issue9
oaire.citation.volume21