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PLoS genetics2025; 21(9); e1011835; doi: 10.1371/journal.pgen.1011835

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

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.
Copyright: © 2025 Cullen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2025-09-05 PubMed ID: 40911641PubMed Central: PMC12449019DOI: 10.1371/journal.pgen.1011835Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study developed new computational tools and a comprehensive database to identify, quantify, and visualize microRNA (miRNA) and their isoforms (isomiRs) in horses.
  • The research provides the largest equine miRNA expression atlas across many tissues, improving understanding of gene regulation in horses and aiding veterinary medicine.

Background

  • MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression post-transcriptionally, playing critical roles in development, tissue function, and disease.
  • Most miRNA research has focused on model organisms; non-model species like horses have limited miRNA databases and expression data.
  • IsomiRs, which are variants of canonical miRNAs differing in length and sequence, can have different regulatory targets and biological functions but are even less studied in horses.
  • The lack of data on miRNAs and isomiRs hampers understanding of their roles in equine biology and limits biomarker discovery and precision veterinary medicine.

Research Aims and Tools Developed

  • The authors aimed to fill the gap by creating a unified computational pipeline to identify and quantify both miRNAs and isomiRs from small RNA sequencing data.
  • They developed FARmiR (Framework for Analysis and Refinement of miRNAs), an open-source, containerized pipeline designed to process miRNA expression data efficiently and reproducibly.
  • An interactive web-based browser named AIMEE (Animal IsomiR and MiRNA Expression Explorer) was created for intuitive visualization and exploration of miRNA and isomiR expression data.
  • Both tools are species-agnostic and can be adapted for other animals beyond horses.

Data Aggregation and Analysis

  • The study compiled 461 small RNA-sequencing datasets representing 61 distinct equine tissue types.
  • Data was sourced from public repositories, a cohort of American Quarter Horses, and samples from the FAANG consortium’s Thoroughbred horse collection.
  • Applying FARmiR to this extensive dataset allowed identification and quantification of 5,781 miRNAs and isomiRs.
  • This large-scale, systematic approach represents the most comprehensive equine miRNA/isomiR expression atlas constructed to date.

Significance and Applications

  • The atlas provides detailed, tissue-specific expression profiles of miRNAs and their isoforms in horses.
  • It facilitates improved understanding of miRNA-mediated gene regulation mechanisms in equine biology and disease.
  • The AIMEE browser makes the data accessible and user-friendly for researchers, enhancing opportunities for discovery.
  • This resource supports biomarker identification efforts, enabling better diagnostics and precision treatment strategies in veterinary medicine.
  • The pipeline and browser can be extended to other species, benefiting broader non-model organism functional genomics.

Conclusions

  • This work addresses an important gap by integrating computational tools and large datasets to produce a high-resolution map of equine miRNA and isomiR expression.
  • It empowers researchers with resources to study post-transcriptional regulation in horses, aiding functional genomics and translational applications.
  • The open-source, modular design ensures adaptability and ongoing improvements for studying miRNAs in diverse animal species.

Cite This Article

APA
Cullen JN, Cieslak J, Petersen JL, Bellone RR, Finno CJ, Kalbfleisch TS, Calloe K, Capomaccio S, Cappelli K, Coleman SJ, Distl O, Durward-Akhurst SA, Giulotto E, Hamilton NA, Hill EW, Katz LM, Klaerke DA, Lindgren G, MacHugh DE, Mackowski M, MacLeod JN, Metzger J, Murphy BA, Orlando L, Raudsepp T, Silvestrelli M, Strand E, Tozaki T, Trachsel DS, Valderrama Figueroa LS, Velie BD, Wade CM, Waud B, Mickelson JR, McCue ME. (2025). Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression. PLoS Genet, 21(9), e1011835. https://doi.org/10.1371/journal.pgen.1011835

Publication

PLoS genetics
ISSN: 1553-7404
NlmUniqueID: 101239074
Country: United States
Language: English
Volume: 21
Issue: 9
Pages: e1011835
PII: e1011835

Researcher Affiliations

Cullen, Jonah N
  • Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America.
Cieslak, Jakub
  • Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.
Bellone, Rebecca R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, United States of America.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, United States of America.
Finno, Carrie J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, United States of America.
Kalbfleisch, Ted S
  • Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky, United States of America.
Calloe, Kirstine
  • Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
Capomaccio, Stefano
  • Sport Horse Research Centre, Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
Cappelli, Katia
  • Sport Horse Research Centre, Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
Coleman, Stephen J
  • Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
Distl, Ottmar
  • Institute of Animal Genomics, University of Veterinary Medicine Hannover, Hannover, Germany.
Durward-Akhurst, Sian A
  • Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America.
Giulotto, Elena
  • Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
Hamilton, Natasha A
  • Equine Genetics Research Centre, Racing Australia, Scone, New South Wales, Australia.
Hill, Emmeline W
  • UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland.
Katz, Lisa M
  • UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland.
Klaerke, Dan A
  • Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
Lindgren, Gabriella
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium.
MacHugh, David E
  • UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland.
  • UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.
Mackowski, Mariusz
  • Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland.
MacLeod, James N
  • Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky, United States of America.
Metzger, Julia
  • Institute of Animal Genomics, University of Veterinary Medicine Hannover, Hannover, Germany.
Murphy, Barbara A
  • UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland.
Orlando, Ludovic
  • Centre for Anthropobiology and Genomics of Toulouse, CNRS, Université de Toulouse, Toulouse, France.
Raudsepp, Terje
  • College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.
Silvestrelli, Maurizio
  • Sport Horse Research Centre, Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
Strand, Eric
  • Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Aas, Norway.
Tozaki, Teruaki
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan.
Trachsel, Dagmar S
  • Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
Valderrama Figueroa, Laura S
  • Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America.
Velie, Brandon D
  • Equine Genetics & Genomics Group, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
Wade, Claire M
  • School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
Waud, Bianca
  • Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia.
Mickelson, James R
  • Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, United States of America.
McCue, Molly E
  • Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America.

MeSH Terms

  • Horses / genetics
  • MicroRNAs / genetics
  • Animals
  • Gene Expression Regulation
  • Software
  • Molecular Sequence Annotation
  • Databases, Genetic
  • Computational Biology / methods
  • Gene Expression Profiling
  • Web Browser

Grant Funding

  • K12 TR004373 / NCATS NIH HHS
  • KL2 TR002492 / NCATS NIH HHS
  • UL1 TR002494 / NCATS NIH HHS
  • UM1 TR004405 / NCATS NIH HHS

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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