Samuel Behailu, Dinka Hunduma
Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia.
Department of Animal Science, Faculty of Agriculture, Salale University, Fitche, Ethiopia.
Nucleosides Nucleotides Nucleic Acids. 2020;39(6):853-865. doi: 10.1080/15257770.2020.1711524. Epub 2020 Feb 6.
Identifications of transcription start sites (TSSs) and promoter regions are first step to understand the regulation mechanisms of gene expression and association with genetic variations in the regions. This analysis was conducted with the objectives to identify TSSs, determine the promoter regions, identify common candidate motifs and transcription factors (TFs), and search for CpG islands (CGIs) in cattle olfactory receptors (ORs) genes promoter regions. In the analysis, TSSs of cattle olfactory genes were first identified. The locations for 60% of the TSSs were below -500 bp relative to the start codon and five candidate motifs (MOR1, MOR2, MOR3, MOR4, and MOR5) were identified that are shared by at least 50% of the cattle ORs promoter input sequences from both strands. Among the five candidate motifs, MOR4 was revealed as the common promoter motif for 85.71% of cattle ORs genes that serves as binding sites for TFs involved in the expression regulation of these genes. MOR4 was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF by using the TOMTOM web application. Hence, it was revealed that MOR4 may serve as the binding site mainly for the Zinc finger (ZNF) TF gene family to regulate expression of cattle ORs genes. Further gene ontology analysis for MOR4 demonstrated ORs belong to the G-protein-coupled receptor superfamily and MOR4 tend to be located near the genes involved in the detection of chemical stimulus involved in sensory perception and in innate immune responses such as cytokine-mediated signaling. In silico digestion of cattle OR sequences was performed using restriction enzyme . CGIs from OR10K1 and OR2L13 gene was found. In the present analysis, the poor CGIs observed might suggest their gene expression regulation pattern is in tissue specific manner.
转录起始位点（TSSs）和启动子区域的鉴定是了解基因表达调控机制以及该区域遗传变异关联的第一步。本分析旨在鉴定牛嗅觉受体（ORs）基因启动子区域的TSSs、确定启动子区域、识别常见候选基序和转录因子（TFs），并搜索CpG岛（CGIs）。在分析中，首先鉴定了牛嗅觉基因的TSSs。60%的TSSs位置相对于起始密码子在-500 bp以下，并且鉴定出了五个候选基序（MOR1、MOR2、MOR3、MOR4和MOR5），来自两条链的至少50%的牛ORs启动子输入序列共享这些基序。在这五个候选基序中，MOR4被揭示为85.71%的牛ORs基因的共同启动子基序，作为参与这些基因表达调控的TFs的结合位点。还使用TOMTOM网络应用程序将MOR4与公开可用数据库中注册的基序进行比较，以查看它们是否与已知的TF调控基序相似。因此，发现MOR4可能主要作为锌指（ZNF）TF基因家族的结合位点来调节牛ORs基因的表达。对MOR4的进一步基因本体分析表明，ORs属于G蛋白偶联受体超家族，并且MOR4倾向于位于参与感觉感知中化学刺激检测以及细胞因子介导信号传导等先天免疫反应相关基因附近。使用限制性内切酶对牛OR序列进行了电子消化。发现了来自OR10K1和OR2L13基因的CGIs。在本分析中，观察到的较差的CGIs可能表明它们的基因表达调控模式是组织特异性的。
