Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea.
Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Korea.
Genes (Basel). 2021 Oct 21;12(11):1662. doi: 10.3390/genes12111662.
Interferon-induced transmembrane protein 3 (IFITM3), a crucial effector of the host's innate immune system, prohibits an extensive range of viruses. Previous studies have reported that single nucleotide polymorphisms (SNPs) of the gene are associated with the expression level and length of the IFITM3 protein and can impact susceptibility to infectious viruses and the severity of infection with these viruses. However, there have been no studies on polymorphisms of the bovine gene. In the present study, we finely mapped the bovine gene and annotated the identified polymorphisms. We investigated polymorphisms of the bovine gene in 108 Hanwoo and 113 Holstein cattle using direct sequencing and analyzed genotype, allele, and haplotype frequencies and linkage disequilibrium (LD) between the genes of the two cattle breeds. In addition, we analyzed transcription factor-binding sites and transcriptional capacity using PROMO and luciferase assays, respectively. Furthermore, we analyzed the effect of a nonsynonymous SNP of the gene using PolyPhen-2, PANTHER, and PROVEAN. We identified 23 polymorphisms in the bovine gene and found significantly different genotype, allele, and haplotype frequency distributions and LD scores between polymorphisms of the bovine gene in Hanwoo and Holstein cattle. In addition, the ability to bind the transcription factor Nkx2-1 and transcriptional capacities were significantly different depending on the c.-193T > C allele. Furthermore, nonsynonymous SNP (F121L) was predicted to be benign. To the best of our knowledge, this is the first genetic study of bovine polymorphisms.
干扰素诱导跨膜蛋白 3（IFITM3）是宿主固有免疫系统的关键效应因子，可抑制广泛的病毒。先前的研究报道，基因的单核苷酸多态性（SNP）与 IFITM3 蛋白的表达水平和长度有关，并可能影响对传染性病毒的易感性和感染这些病毒的严重程度。然而，目前还没有关于牛基因多态性的研究。在本研究中，我们精细地定位了牛基因并注释了鉴定出的多态性。我们使用直接测序法研究了 108 头韩牛和 113 头荷斯坦牛的牛基因多态性，并分析了两个牛品种基因的基因型、等位基因和单倍型频率以及连锁不平衡（LD）。此外，我们分别使用 PROMO 和荧光素酶测定法分析了转录因子结合位点和转录能力。此外，我们还使用 PolyPhen-2、PANTHER 和 PROVEAN 分析了基因的非同义 SNP 的影响。我们在牛基因中鉴定出 23 个多态性，发现韩牛和荷斯坦牛基因多态性的基因型、等位基因和单倍型频率分布以及 LD 评分存在显著差异。此外，转录因子 Nkx2-1 的结合能力和转录能力因 c.-193T > C 等位基因而异。此外，非同义 SNP（F121L）预测为良性。据我们所知，这是首次对牛基因多态性进行的遗传研究。
