title: Novel equine tissue miRNAs and breed-related miRNA expressed in serum.
abstract: MiRNAs regulate multiple genes at the post-transcriptional level and therefore play an important role in many biological processes. It has been suggested that miRNA exported outside the cells contribute to inter-cellular communication. Consequently, circulating miRNAs are of particular interest and are promising biomarkers for many diseases. The number of miRNAs annotated in the horse genome is much lower compared to model organisms like human and mouse. We therefore aimed to identify novel equine miRNAs for tissue types and breed in serum.
  
  
  
  We analysed 71 small RNA-seq libraries derived from nine tissues (gluteus medius, platysma, masseter muscle, heart, liver, cartilage, bone, total blood and serum) using miRDeep2 and miRdentify tools. Known miRNAs represented between 2.3 and 62.9 % of the reads in 71 libraries. A total of 683 novel miRNAs were identified. Breed and tissue type affected the number of miRNAs detected and interestingly, affected its average intensity. A total of 50 miRNAs in serum proved to be potential biomarkers to differentiate specific breed types, of which miR-122, miR-200, miR-483 were over-expressed and miR-328 was under-expressed in ponies compared to Warmbloods. The different miRNAs profiles, as well as the differences in their expression levels provide a foundation for more hypotheses based on the novel miRNAs discovered.
  
  
  
  We identified 683 novel equine miRNAs expressed in seven solid tissues, blood and serum. Additionally, our approach evidenced that such data supported identification of specific miRNAs as markers of functions related to breeds or disease tissues.
authors: Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland. alicja.pacholewska@vetsuisse.unibe.ch.|Department of Clinical Research and Veterinary Public Health, Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland. alicja.pacholewska@vetsuisse.unibe.ch.
authors: Alicja
authors: 0000-0002-4888-4883
authors: A
authors: Pacholewska
authors: Animal Genetics and Integrative Biology unit (GABI), INRA, AgroParis Tech, University of Paris-Saclay, 78350, Jouy-en-Josas, France.
authors: Núria
authors: N
authors: Mach
authors: Animal Genetics and Integrative Biology unit (GABI), INRA, AgroParis Tech, University of Paris-Saclay, 78350, Jouy-en-Josas, France.
authors: Xavier
authors: X
authors: Mata
authors: Animal Genetics and Integrative Biology unit (GABI), INRA, AgroParis Tech, University of Paris-Saclay, 78350, Jouy-en-Josas, France.
authors: Anne
authors: A
authors: Vaiman
authors: Animal Genetics and Integrative Biology unit (GABI), INRA, AgroParis Tech, University of Paris-Saclay, 78350, Jouy-en-Josas, France.
authors: Laurent
authors: L
authors: Schibler
authors: Animal Genetics and Integrative Biology unit (GABI), INRA, AgroParis Tech, University of Paris-Saclay, 78350, Jouy-en-Josas, France.
authors: Eric
authors: E
authors: Barrey
authors: Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland.
authors: Vincent
authors: V
authors: Gerber
mesh_terms: D000818:Animals; D001483:Base Sequence; D015415:Biomarkers; D001947:Breeding; D002874:Chromosome Mapping; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006736:Horses / Q000097:blood / Q000235:genetics*; D035683:MicroRNAs / Q000097:blood / Q000235:genetics*; D009690:Nucleic Acid Conformation; D009928:Organ Specificity / Q000235:genetics; D057188:Workflow
chemical_list: D015415:Biomarkers; D035683:MicroRNAs
keywords: Horse; Serum; miRNA; miRNome; microRNA; sRNA-seq