MicroRNAs expression in hypothalamus and pituitary of Saanen goat

MicroRNAs (miRNA) are small, noncoding RNA molecules that regulate gene expression by targeting messenger RNAs for post-transcriptional cleavage or translational inhibition. There is still limited knowledge about miRNAs expression profiles in farm animals, especially in small ruminant species. The identification of miRNAs expressed in different brain regions of the domestic goat, Capra hircus, will contribute to a better understanding of miRNA function and the control of the physiologic pathways in this species. We sequenced miRNAs expressed in hypothalamus and pituitary gland, from 3 adult Saanen goats using Illumina high-throughput sequencing (Miseq). Reads were mapped on the Capra hircus reference genome and both known and novel pre-miRNA, mature miRNAs, and miRNA target sites were identified using existing information collected in miRBase and using specific bioinformatic tools. This analysis found 313 and 304 miRNAs in the hypothalamus and pituitary respectively, 131 of which were differentially expressed between the two tissues. Mapping these small RNAs on Capra hircus genome revealed that 61 miRNA genes from hypothalamus and 54 from hypophysis were located on goat chromosome 21, and belonged to the largest conserved mammalian miRNA gene cluster. A large miRNA gene population was also identified on chromosome X, encompassing 38 miRNAs in the hypothalamus and 36 in the pituitary. We also discovered 46 and 48 putative novel miRNAs in hypothalamus and pituitary respectively, based on structural prediction and homology with known miRNA genes from goat and other ruminants. This study produced a comprehensive miRNA profile related to the biology of two brain areas in goat. The characterization of these miRNAs contributes to a better understanding of the molecular and epigenetic mechanisms of physiology and development in this species.