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Related Concept Videos

MicroRNAs01:22

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing

Jonah N Cullen1, Jakub Cieslak2, Jessica L Petersen3

  • 1Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America.

Plos Genetics
|September 5, 2025
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Summary
This summary is machine-generated.

We created tools to analyze microRNAs (miRNAs) and their variants (isomiRs) in horses. This provides the largest equine miRNA expression atlas, aiding research in gene regulation and disease.

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology and Genetics

Background:

  • MicroRNAs (miRNAs) and isomiRs are crucial gene regulators, but data for non-model species like horses is scarce.
  • Limited understanding of miRNA and isomiR roles in equine development and disease hinders biological insights.

Purpose of the Study:

  • To develop accessible tools for identifying and quantifying miRNAs and isomiRs in non-model organisms.
  • To create the most comprehensive equine miRNA expression atlas to date.
  • To facilitate research in equine functional genomics and precision veterinary medicine.

Main Methods:

  • Developed FARmiR (Framework for Analysis and Refinement of miRNAs), an open-source pipeline for miRNA and isomiR analysis.
  • Created AIMEE (Animal IsomiR and MiRNA Expression Explorer), an interactive browser for user-friendly data access.
  • Integrated 461 small RNA-seq datasets from diverse equine tissues and sources.

Main Results:

  • Predicted 5,781 unique equine miRNAs and isomiRs.
  • Established the largest systematically curated atlas of equine miRNA expression.
  • Demonstrated the utility of FARmiR and AIMEE for comprehensive small RNA analysis.

Conclusions:

  • The developed tools and equine atlas significantly advance the study of miRNA and isomiR biology in non-model species.
  • This resource will accelerate biomarker discovery and enhance understanding of tissue-specific gene regulation.
  • Facilitates future research in equine functional genomics and personalized veterinary medicine.