Identification and Characterization of MicroRNAs in Normal Equine Tissues by Next Generation Sequencing

Abstract

The role of microRNAs (miRNAs) as a post-transcriptional gene regulator has been elucidated in a broad range of organisms including domestic animals. Characterization of miRNAs in normal tissues is an important step to investigate the functions of miRNAs in various physiological and pathological conditions. Using Illumina Next Generation Sequencing (NGS) technology, we identified a total of 292 known and 329 novel miRNAs in normal horse tissues including skeletal muscle, colon and liver. Distinct sets of miRNAs were differentially expressed in a tissue-specific manner. The miRNA genes were distributed across all the chromosomes except chromosomes 29 and 31 in the horse reference genome. In some chromosomes, multiple miRNAs were clustered and considered to be polycistronic transcript. A base composition analysis showed that equine miRNAs had a higher frequency of A+U than G+C. Furthermore, U tended to be more frequent at the 5′ end of miRNA sequences. This is the first experimental study that identifies and characterizes the global miRNA expression profile in normal horse tissues. The present study enriches the horse miRNA database and provides useful information for further research dissecting biological functions of miRNAs in horse.

Novel equine tissue miRNAs and breed-related miRNA expressed in serum

“…From five most abundantly expressed novel putative miRNA reported in equine plasma by Lee et al [37], only one miRNA was identified in our study in bone and blood tissues with a mature sequenced shorter by three nucleotides from 5’ end. From the 329 novel miRNAs reported by Kim et al [9] only 11 had exactly the same mature sequence as novel miRNAs reported here. From the 896 putative novel miRNAs included in the microarrays used by Mach et al [32] only two had exactly the same mature sequence and further 24 had few nucleotides shorter mature sequence compared to the miRNAs identified here (Additional file 4: Table S3).…”

“…Nonetheless, from the 166 tissue-specific known equine miRNAs reported in liver, colon or muscles, a total of 132 were expressed in our study and 105 of them were expressed at >10 cpm on average in at least one group. Interestingly, 21 miRNAs reported as tissue-specific in Kim et al [9] were also expressed in all groups studied here, at > 10 cpm on average. From the 31 liver-specific miRNAs reported by Kim et al [9], only one was supported by our study with our definition of tissue specificity (eca-miR-135a).…”

“…Interestingly, 21 miRNAs reported as tissue-specific in Kim et al [9] were also expressed in all groups studied here, at > 10 cpm on average. From the 31 liver-specific miRNAs reported by Kim et al [9], only one was supported by our study with our definition of tissue specificity (eca-miR-135a). On contrary, four of liver-specific miRNAs reported here were reported in Kim et al [9] as muscle (eca-miR-299, eca-miR-32, eca-miR-656) or colon-specific miRNAs (eca-miR-429).…”

“…Over 700 miRNAs have been identified in the equine genome with distinct subsets of miRNAs differentially expressed in a tissue-specific manner [9, 10]. For example, horse specific miRNA in cartilage and bone have been already reported [10] and the existence of hundreds of horse specific transcripts may suggest the existence of more horse specific miRNAs [11].…”

RNA sequencing as a powerful tool in searching for genes influencing health and performance traits of horses

“…Novel miRNAs have been mapped to chromosomes excluding chromosomes 29 and 31. Moreover, detailed analysis revealed that equine miRNA are distributed across chromosomes in 51 clusters, with 160 miRNAs corresponding to 55 % of known miRNAs (Kim et al 2014). …”