Differentially Expressed Candidate miRNAs of Day 16 Bovine Embryos on the Regulation of Pregnancy Establishment in Dairy Cows

SIMPLE SUMMARY: MicroRNAs (miRNAs) are small, noncoding RNAs and their role in embryo implantation is unknown. The study objective was to identify differentially expressed (DE) miRNAs between day 16 competent, elongated embryos from normal cows and day 16 noncompetent, tubular embryos from repeat breeder cows, integrate DE-miRNAs to their target genes, and categorize the target genes based on predicted biological functions. Out of 84 bovine-specific, prioritized miRNAs analyzed by RT-PCR, 19 were differentially expressed in the competent embryos compared to noncompetent ones (p ≤ 0.05; fold regulation ≥ 2 magnitudes). Top-ranked integrated genes of DE-miRNAs predicted to regulate various biological and molecular functions, cellular processes, and pathways. The categorized groups of genes may be associated with crucial signaling pathways regulating the development of embryo, placenta, and various organs. In conclusion, DE-miRNAs in day 16 bovine embryos may control pregnancy establishment, interacting with genes and transcription factors. ABSTRACT: Recent advances in high-throughput in silico techniques translate experimental data into meaningful biological networks through which the role of individual proteins, interactions, and their biological functions are comprehended. The study objective was to identify differentially expressed (DE) miRNAs between the day 16 competent, elongated embryo from normal cows and the day 16 noncompetent, tubular embryos from repeat breeder cows, assimilate DE-miRNAs to their target genes, and group target genes based on biological function using in silico methods. The 84 prioritized bovine-specific miRNAs were investigated by RT-PCR, and the results showed that 19 were differentially expressed (11 up- and 8 down-regulated) in the competent embryos compared to noncompetent ones (p ≤ 0.05; fold regulation ≥ 2 magnitudes). Top-ranked integrated genes of DE-miRNAs predicted various biological and molecular functions, cellular processes, and signaling pathways. Further, analysis of the categorized groups of genes showed association with signaling pathways, turning on or off key genes and transcription factors regulating the development of embryo, placenta, and various organs. In conclusion, highly DE-miRNAs in day 16 bovine conceptus regulated the embryogenesis and pregnancy establishment. The elucidated miRNA-mRNA interactions in this study were mostly based on predictions from public databases. Therefore, the causal regulations of these interactions and mechanisms require further functional characterization.