Genetic characteristics and polymorphisms in the chicken interferon-induced transmembrane protein (IFITM3) gene
Genetic characteristics and polymorphisms in the chicken interferon-induced transmembrane protein (IFITM3) gene
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DOI：
10.1007/s11259-019-09762-y
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发表时间：
2019-11-01
影响因子：
2.2
通讯作者：
Jeong, Byung-Hoon
中科院分区：
文献类型：
--
作者：
Kim, Yong-Chan;Jeong, Min-Ju;Jeong, Byung-Hoon
干扰素诱导的跨膜蛋白3 （IFITM3）基因被归类为干扰素刺激的小基因，并与多种致命包膜病毒（包括甲型流感病毒（iav））的广泛抗病毒功能相关。人类IFITM3基因rs12252单核苷酸多态性（SNP）与2009年H1N1流感大流行的易感性有关。此外，IFITM3蛋白的过表达能有效抑制鸭和鸡体内的高致病性H5N1禽流感病毒。虽然鸡是流感病毒的主要宿主，IFITM3基因参与宿主抗病毒系统，但对鸡IFITM3基因的研究很少。为了研究鸡IFITM3基因的遗传特征，我们对108个Dekalb White和72个Ross品种进行了直接测序和比对。我们还研究了IFITM3基因多态性的基因型和单倍型频率以及连锁不平衡，并评估了非同义snp是否有害。我们发现Dekalb White和Ross两个鸡品种的基因型、等位基因和单倍型频率显著不同。此外，我们还将鸡IFITM3基因的启动子结构与几种物种进行了比较分析。我们发现，与哺乳动物相比，鸟类的IFITM3蛋白具有较长的c端结构域和倒置的拓扑结构。我们还在鸡IFITM3基因中发现了14个遗传多态性。L100 M和N125H被预测为“可能有害”，L100 M可以改变其保守的细胞内环（CIL）的长度。此外，鸡在这一启动子区域含有CpG岛（cgi），而哺乳动物不含。
The interferon-induced transmembrane protein 3 (IFITM3) gene is classified as a small interferon-stimulated gene and is associated with a broad spectrum of antiviral functions against several fatal enveloped viruses, including influenza A viruses (IAVs). The rs12252 single nucleotide polymorphism (SNP) of the IFITM3 gene in humans was associated with susceptibility to H1N1 influenza in a 2009 pandemic. In addition, overexpression of the IFITM3 protein potently inhibits the highly pathogenic avian influenza H5N1 virus in ducks and chickens. Although chickens are a major host of influenza viruses and the IFITM3 gene participates in the host antiviral system, studies on chicken IFITM3 gene are very rare. To investigate the genetic characteristics of the chicken IFITM3 gene, we performed direct sequencing and alignment in 108 Dekalb White and 72 Ross breeds. We also investigated the genotype and haplotype frequencies and linkage disequilibrium of the IFITM3 gene polymorphisms and evaluated whether the non-synonymous SNPs are deleterious. We found significantly different genotype, allele and haplotypes frequencies between two chicken breeds, Dekalb White and Ross. Furthermore, we compared and analyzed the promoter structure of the chicken IFITM3 gene with that of several species. We found that birds have a long C-terminal domain and inverted topology of the IFITM3 protein compared to mammals. We also identified fourteen genetic polymorphisms in the chicken IFITM3 gene. L100 M and N125H were predicted as 'probably damaging' and L100 M can alter the length of its conserved intracellular loop (CIL). Furthermore, chickens, but not mammals, contain CpG islands (CGIs) in this promoter region.