College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Genes (Basel). 2024 Mar 18;15(3):372. doi: 10.3390/genes15030372.
As more and more of the available genomic data have been published, several databases have been developed for deciphering early mammalian embryogenesis; however, less research has been conducted on the regulation of the expression of natural immunity genes during early embryonic development in dairy cows. To this end, we explored the regulatory mechanism of innate immunity genes at the whole-genome level. Based on comparative genomics, 1473 innate immunity genes in cattle were obtained by collecting the latest reports on human innate immunity genes and updated bovine genome data for comparison, and a preliminary database of bovine innate immunity genes was constructed. In order to determine the regulatory mechanism of innate immune genes in dairy cattle early embryos, we conducted weighted co-expression network analysis of the innate immune genes at different developmental stages of dairy cattle early embryos. The results showed that specific module-related genes were significantly enriched in the MAPK signaling pathway. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 10 of the highest connectivity genes were chosen as potential hub genes. Finally, combined with the results for differential expressed genes (DEGs), , , , , , , , , , , and were identified as the key genes of innate immunity in dairy cattle early embryos. In conclusion, the bovine innate immunity gene set was determined and the co-expression network of innate immunity genes in the early embryonic stage of dairy cattle was constructed by comparing and analyzing the whole genome of bovines and humans. The findings in this study provide the basis for exploring the involvement and regulation of innate immune genes in the early embryonic development of dairy cattle.
随着越来越多的可用基因组数据被发表，已经开发了几个数据库用于破译早期哺乳动物胚胎发生；然而，对于奶牛早期胚胎发育中天然免疫基因表达的调控研究较少。为此，我们在全基因组水平上探讨了天然免疫基因的调控机制。基于比较基因组学，通过收集人类天然免疫基因的最新报道和更新的牛基因组数据进行比较，获得了牛的 1473 个天然免疫基因，并构建了牛天然免疫基因的初步数据库。为了确定奶牛早期胚胎中天然免疫基因的调控机制，我们对奶牛早期胚胎不同发育阶段的天然免疫基因进行了加权共表达网络分析。结果表明，特定模块相关基因在 MAPK 信号通路中显著富集。蛋白质-蛋白质相互作用（PPI）分析显示每个特定模块中的基因相互作用，并选择了 10 个最高连通性的基因作为潜在的枢纽基因。最后，结合差异表达基因（DEGs）的结果，确定了 、 、 、 、 、 、 、 、 和 为奶牛早期胚胎天然免疫的关键基因。总之，通过比较和分析牛和人类的全基因组，确定了牛的天然免疫基因集，并构建了奶牛早期胚胎天然免疫基因的共表达网络。本研究为探索天然免疫基因在奶牛早期胚胎发育中的作用和调控机制提供了依据。
