Kasimanickam Vanmathy R, Kasimanickam Ramanathan K
Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA.
AARVEE Animal Biotech LLC, Corvallis, OR 97333, USA.
Animals (Basel). 2023 Sep 28;13(19):3052. doi: 10.3390/ani13193052.
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 ( ≤ 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.
高通量计算机模拟技术的最新进展将实验数据转化为有意义的生物网络，通过该网络可以理解单个蛋白质的作用、相互作用及其生物学功能。本研究的目的是鉴定正常母牛第16天有能力的伸长胚胎与重复配种母牛第16天无能力的管状胚胎之间差异表达的（DE）miRNA，将DE-miRNA与其靶基因进行同化，并使用计算机模拟方法根据生物学功能对靶基因进行分组。通过RT-PCR研究了84个优先排序的牛特异性miRNA，结果表明，与无能力胚胎相比，有能力胚胎中有19个差异表达（11个上调和8个下调）（≤0.05；调控倍数≥2倍）。DE-miRNA的排名靠前的整合基因预测了各种生物学和分子功能、细胞过程及信号通路。此外，对分类基因组的分析表明其与信号通路相关，开启或关闭调控胚胎、胎盘和各种器官发育的关键基因和转录因子。总之，第16天牛孕体中高度差异表达的miRNA调控胚胎发生和妊娠建立。本研究中阐明的miRNA-mRNA相互作用大多基于公共数据库的预测。因此，这些相互作用和机制的因果调控需要进一步的功能表征。
