Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)

Abstract

Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. A combined regulatory network was constructed based on 92 metabolism-related candidate target genes and 65 differentially expressed miRNAs, among which 7 miRNAs were identified as hub miRNAs. Via these mechanisms, miRNAs may play a role in maintaining intestinal homeostasis and metabolism. This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep.

Identification of Ovine Serum miRNAs Following Bacterial Lipopolysaccharide Challenge

“…Based on a search in the miRBase database, and in BLAST with other species, the DE miRNAs were found to be conserved between Homo sapiens (has-miR, chromosome 21) and Bos taurus (bta-miR, chromosome 14). Intriguingly, most of the identified DE miRNAs were located on chromosome 18 in sheep, which corroborates findings of others who have reported the highest density of miRNA on ovine chromosome 18 (2.40 miRNA loci per Mbp with a total 174 miRNA loci) based on miRNAome analysis of ovine heart, intestine, and muscle tissues [48][49][50]. Collectively, these results highlight the importance of ovine chromosome 18 in terms of unravelling the regulation of ovine innate immune response.…”

Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages

“…In addition, the miRNAs that we identified were mostly distributed in the 20-24 nt length range, with the greatest abundance of 22 nt miRNAs (Fig 1D and 1E). This finding is consistent with the typical length distribution of miRNAs found in most mammals, for example, sheep [37], pig [38], and mouse [39]. A statistical analysis of the identified miRNAs in various species revealed that 534 miRNAs were annotated in and related to humans, 489 miRNAs were related to cattle, and 263 miRNAs were related to goats, with fewer miRNAs annotated to goats than to humans and cattle ( Fig 1F).…”

Characterization of Sheep Milk Extracellular Vesicle-miRNA by Sequencing and Comparison with Cow Milk

“…The primer sequence of oar-miR-199a-3p, oar-let-7c, oar-let-7i, and oar-miR-143 referred to Jin et al [20]. The primer sequence of oar-miR-200b and oar-miR-10a referred to Hou et al [21]. The primer sequence of oar-miR-103 referred to Wu et al [22].…”