Genomic structure, polymorphism and expression of the horse alpha-actinin-3 gene

Gene characterization is an important feature for genome annotation and more particularly for candidate genes that could be selected in domestic species. Associations between an alpha-actinin-3 gene polymorphism and muscle performance were reported in humans involving a nonsense mutation (R577X) and in mice after inactivation of the gene. Here, we characterized the equine alpha-actinin-3 (ACTN3) gene by sequencing and transcript analysis. The cDNA was determined to be 3.47 kb in length with an open reading frame of 2709 bp expectedly encoding a protein 902 amino acids long. The ACTN3 gene is 13.2 kb long and contains 21 exons. The equine ACTN3 gene has a ubiquitous expression but it is overexpressed in skeletal muscles with fast fibers of type IIb. No alternative transcripts were observed. Sequencing the cDNA revealed 8 SNPs, 6 in the coding and 2 in the 3′ non-coding regions with no amino acid change and not affecting potential miRNA targets. The equine in silico promoter sequence reveals a structure with two regions similar to those of other mammalian species.

► Cloning and sequencing the full ACTN3 horse cDNA states annotation and informs about the functionality of this equine gene. ► Comparison of nucleotide and protein sequences in seven species revealed a great level of conservation. ► Higher expression of the ACTN3 gene in gluteus medius and platysma in accordance with a high proportion of fiber type IIb. ► Analysis of the ACTN3 gene promoters of different species highlights conservation of transcription factors potential binding sites.