title: RNA sequencing of the exercise transcriptome in equine athletes.
abstract: The horse is an optimal model organism for studying the genomic response to exercise-induced stress, due to its natural aptitude for athletic performance and the relative homogeneity of its genetic and environmental backgrounds. Here, we applied RNA-sequencing analysis through the use of SOLiD technology in an experimental framework centered on exercise-induced stress during endurance races in equine athletes. We monitored the transcriptional landscape by comparing gene expression levels between animals at rest and after competition. Overall, we observed a shift from coding to non-coding regions, suggesting that the stress response involves the differential expression of not annotated regions. Notably, we observed significant post-race increases of reads that correspond to repeats, especially the intergenic and intronic L1 and L2 transposable elements. We also observed increased expression of the antisense strands compared to the sense strands in intronic and regulatory regions (1 kb up- and downstream) of the genes, suggesting that antisense transcription could be one of the main mechanisms for transposon regulation in the horse under stress conditions. We identified a large number of transcripts corresponding to intergenic and intronic regions putatively associated with new transcriptional elements. Gene expression and pathway analysis allowed us to identify several biological processes and molecular functions that may be involved with exercise-induced stress. Ontology clustering reflected mechanisms that are already known to be stress activated (e.g., chemokine-type cytokines, Toll-like receptors, and kinases), as well as "nucleic acid binding" and "signal transduction activity" functions. There was also a general and transient decrease in the global rates of protein synthesis, which would be expected after strenuous global stress. In sum, our network analysis points toward the involvement of specific gene clusters in equine exercise-induced stress, including those involved in inflammation, cell signaling, and immune interactions.
authors.affiliation: Department of Pathology, Diagnostic and Veterinary Clinic - Sport Horse Research Centre, University of Perugia, Perugia, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Capomaccio
authors.affiliation: CRIBI, University of Padua, Complesso Vallisneri, Padova, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Vitulo
authors.affiliation: Department of Pathology, Diagnostic and Veterinary Clinic - Sport Horse Research Centre, University of Perugia, Perugia, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Verini-Supplizi
authors.affiliation: Laboratory of Genetic and Genomics, DAFNAE - University of Padova, Campus of Agripolis, Legnaro, Italy.
authors.forename: Gianni
authors.initials: G
authors.lastname: Barcaccia
authors.affiliation: CRIBI, University of Padua, Complesso Vallisneri, Padova, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Albiero
authors.affiliation: CRIBI, University of Padua, Complesso Vallisneri, Padova, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: D'Angelo
authors.affiliation: CRIBI, University of Padua, Complesso Vallisneri, Padova, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Campagna
authors.affiliation: CRIBI, University of Padua, Complesso Vallisneri, Padova, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
authors.affiliation: Department of Pathology, Diagnostic and Veterinary Clinic - Sport Horse Research Centre, University of Perugia, Perugia, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Felicetti
authors.affiliation: Department of Pathology, Diagnostic and Veterinary Clinic - Sport Horse Research Centre, University of Perugia, Perugia, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Silvestrelli
authors.affiliation: Department of Pathology, Diagnostic and Veterinary Clinic - Sport Horse Research Centre, University of Perugia, Perugia, Italy.
authors.forename: Katia
authors.initials: K
authors.lastname: Cappelli
mesh_terms: D000818:Animals; D015870:Gene Expression; D053263:Gene Regulatory Networks; D006736:Horses / Q000235:genetics* / Q000502:physiology*; D005810:Multigene Family; D010805:Physical Conditioning, Animal; D005082:Physical Exertion / Q000235:genetics; D022821:RNA Splice Sites; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome
chemical_list: D022821:RNA Splice Sites