| Title: |
Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression |
| Authors: |
Cullen, Jonah, N; Cieslak, Jakub; Petersen, Jessica, L; Bellone, Rebecca, R; Finno, Carrie, J; Kalbfleisch, Ted, S; Calloe, Kirstine; Capomaccio, Stefano; Cappelli, Katia; Coleman, Stephen, J; Distl, Ottmar; Durward-Akhurst, Sian, A; Giulotto, Elena; Hamilton, Natasha, A; Hill, Emmeline, W; Katz, Lisa, M; Klaerke, Dan, A; Lindgren, Gabriella; Machugh, David, E; Mackowski, Mariusz; Macleod, James, N; Metzger, Julia; Murphy, Barbara, A; Orlando, Ludovic; Raudsepp, Terje; Silvestrelli, Maurizio; Strand, Eric; Tozaki, Teruaki; Trachsel, Dagmar, S; Valderrama Figueroa, Laura, S; Velie, Brandon, D; Wade, Claire, M; Waud, Bianca; Mickelson, James, R; Mccue, Molly, E |
| Contributors: |
University of Minnesota System (UMN); AGH University of Science and Technology Krakow, PL (AGH UST); University of Minnesota Morris (UMM); Department of Population Health and Reproduction and the Veterinary Genetics Laboratory; University of California Davis (UC Davis); University of California (UC)-University of California (UC); University of California (UC); Københavns Universitet = University of Copenhagen = Université de Copenhague (UCPH); University of Leeds; Inst Anim Breeding & Genet; University of Veterinary Medecine Hannover; Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso; Università degli Studi di Pavia Italia = University of Pavia Italy = Université de Pavie Italie (UNIPV); University College Dublin Dublin (UCD); Faculty of Health and Medical Sciences; Department of Animal Bredding and Genetics; Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet (SLU); Department of Biosystems, Division of Livestock-Nutrition-Quality; Université Catholique de Louvain = Catholic University of Louvain (UCL); Institute of Animal Breeding and Genetics; Max Planck Institute for Molecular Genetics (MPIMG); Max-Planck-Gesellschaft; Centre d'anthropobiologie et de génomique de Toulouse (CAGT); Centre National de la Recherche Scientifique (CNRS)-Université de Toulouse (EPE UT); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse); Department of Veterinary Anatomy and Public Health; Texas A&M University System; Fac Vet Med; Università degli Studi di Perugia = University of Perugia (UNIPG); Dept Mol Genet; Laboratory of Racing Chemistry; École nationale vétérinaire d'Alfort (ENVA); Centre d'Imagerie et de Recherche sur les Affections Locomotrices Equines - Center of Imaging and Research in Locomotor Affections on Equines ENVA (CIRALE) |
| Source: |
ISSN: 1553-7390. |
| Publisher Information: |
CCSD; Public Library of Science |
| Publication Year: |
2025 |
| Collection: |
Université Toulouse III - Paul Sabatier: HAL-UPS |
| Subject Terms: |
[SDV]Life Sciences [q-bio] |
| Description: |
International audience ; 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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1371/journal.pgen.1011835 |
| Availability: |
https://hal.science/hal-05343164; https://hal.science/hal-05343164v1/document; https://hal.science/hal-05343164v1/file/journal.pgen.1011835.pdf; https://doi.org/10.1371/journal.pgen.1011835 |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.5BC080B4 |
| Database: |
BASE |