Equine

Epigenetic and transcriptional characterisation of oxidative versus glycolytic muscles in horses

---

Abstract

Mature equine muscle fibres are composed of varying proportions of three different fibre types. These are type 1- slow twitch oxidative, type 2A- fast twitch oxidative and type 2X-fast twitch glycolytic. Here fast/slow twitch refers to the maximal shortening velocities of the fibre, while oxidative/glycolytic refers to the primary energy pathway used. Fibre-type proportion can vary depending on primary muscle function and breed, as well as changing in response to exercise. In this research we are interested in the semimembranosus (SM) and the sacrocaudalis dorsalis medialis (SCDM), two muscles with different functions in the horse. The SM is a primarily glycolytic locomotor muscle, while the SCDM is a primarily oxidative muscle with a largely stabilising function. These muscles are also of interest for diagnosis of different diseases. The SCDM biopsied in cases where equine motor neurone disease is suspected, and the SM is biopsied to diagnose exertional rhabdomyolysis or polysaccharide storage myopathy. In this research we are looking for differences on an epigenetic and transcriptional level between the SCDM, and the SM. We aim to create transcriptional and epigenetic profiles of our muscles of interest and we are confirming fibre-type proportions in the muscles. Currently these muscles are poorly annotated, and this information can support future genetic research into equine myopathies. To investigate at an epigenetic level, we collected samples for assay for transposase accessible chromatin sequencing (ATAC-seq) giving a total of 19 samples, 10 SCDM and 9 SM. Transcription was investigated using RNA-seq in 30 samples,15 SM and 15 SCDM, from healthy thoroughbreds and warmbloods. In addition, we used immunohistochemistry to confirm fibre-type proportions in the samples. ATAC library prep was done using a commercial kit available from Active Motif and sequenced at a depth of ~100 million reads 150bp paired end, while RNA-seq data was sequenced at ~65 million reads, 150bp paired end. RNA-seq data of the samples found 727 differentially expressed genes (DEGs). Enriched genes included those involved in glycolytic processes-ADP/ATP metabolic processes, and actin binding. ATAC-seq data allowed us to identify 97 transcription factors (TFs), that were significantly differentially bound. The relationship between the differentially bound TFs and DEGs was also investigated. Immunohistochemistry confirmed fibre-type proportions for our samples, with the SCDM samples having ~75% type 1 oxidative fibres, and 2% type 2X glycolytic fibres, compared to the SM with ~ 12% type 1 fibres and 49% type 2X fibres. In conclusion our research has highlighted differences in cell apoptosis, glucose metabolism and gene regulation between SM and SCDM muscles and determined fibre-type proportions. This research is important for improving our baseline understanding of how different muscles are regulated in horses, in addition to providing a foundation for future research into equine myopathies.

Keywords: 2026

How to Cite:

Cuffe, C., Attree, E., Clark, E., Piercy, R. & Psifidi, A., (2026) “Epigenetic and transcriptional characterisation of oxidative versus glycolytic muscles in horses”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286775. doi: https://doi.org/10.31274/wcgalp.24116

Rights: 1