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

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.

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Publication Details

Journal
PLoS Genetics
Published
2025-09-05
DOI
https://doi.org/10.1371/journal.pgen.1011835
Primary Topic
MicroRNA in disease regulation
Type
article
Field-Weighted Citation Impact
0.00

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article

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

Bianca Waud, Lisa M. Katz, Maurizio Silvestrelli, Emmeline W. Hill et al.
1 links
PLoS Genetics
MicroRNA in disease regulation
article

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

Bianca Waud, Lisa M. Katz, Maurizio Silvestrelli, Emmeline W. Hill, O. Distl, Ludovic Orlando, Sian A. Durward-Akhurst, S. J. Coleman, James N. MacLeod, Claire M. Wade, Brandon D. Velie, Barbara A. Murphy, Gabriella Lindgren, Teruaki Tozaki, Elena Giulotto, Ted Kalbfleisch, Dagmar S. Trachsel, Kirstine Calløe, David E. MacHugh, Jonah N. Cullen, Julia Metzger, Natasha A. Hamilton, James R. Mickelson, Rebecca R. Bellone, Dan A. Klærke, Molly E. McCue, Jessica L. Petersen, J. Cieślak, Terje Raudsepp, Stefano Capomaccio, Mariusz Mackowski, Katia Cappelli, Carrie J. Finno, Eric Strand, Laura S. Valderrama Figueroa
article en

Abstract

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.

PLoS GeneticsVol. 21(9)
University College Dublin (IE), University of Nebraska–Lincoln (US), University of Copenhagen (DK), Centre National de la Recherche Scientifique (FR), The University of Sydney (AU), University of Minnesota (US), University of Kentucky (US), Université Fédérale de Toulouse Midi-Pyrénées (FR), University of Veterinary Medicine Hannover, Foundation (DE), University of Pavia (IT), University of Perugia (IT), Racing Victoria (AU), Swedish University of Agricultural Sciences (SE), UNSW Sydney (AU), Laboratory of Racing Chemistry (JP), Norwegian University of Life Sciences (NO), University of Life Sciences in Poznań (PL), University of California, Davis (US), Texas A&M University (US), Colorado State University (US), KU Leuven (BE)
U.S. Department of Agriculture, Grayson-Jockey Club Research Foundation, University of Minnesota, National Institutes of Health, National Institute of Food and Agriculture, University of California, Davis, College of Veterinary Medicine, University of Minnesota, National Center for Advancing Translational Sciences, UC Davis Center for Equine Health
Openalex Percentile: Top 71%
MicroRNA in disease regulation
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