斑马鱼MIB1启动子及互作基因的功能富集分析

Functional enrichment analysis of MIB1 promoter and interacting genes in zebrafish

目的分析斑马鱼E3泛素蛋白连接酶1(MIB1)基因启动子区转录因子结合位点(TFBS),MIB1互作基因和互作蛋白的种类及其在信号通路中的作用,探讨MIB1基因的调控方式及潜在功能。方法利用国家基因组科学数据中心(NGDC)预测非编码RNA(ncRNA),利用Alggen与AnimalTFDB在线网站预测MIB1基因TFBS种类,使用GeneMANIA与STRING分析MIB1的互作基因与互作蛋白;通过DAVID网站获取相关数据,进行基因本体(GO)可视化分析及京都基因与基因组百科全书(KEGG)代谢通路分析。结果MIB1基因启动子区及5′非翻译区可转录出ncRNA;通过预测得到121种TFBS,并发现P53转录因子既可以结合到MIB1基因的启动子区又可与MIB1蛋白相互作用;在线预测出6种MIB1的共表达基因,筛选出20种互作基因;通过GO可视化分析发现,MIB1及其互作基因在生物过程方面具有调控细胞、组织、器官生长分化及调节NOTCH信号通路等功能,且主要在细胞质核周区、细胞膜和突触后密集区等部位被富集,具有结合NOTCH蛋白、PDZ结构域蛋白等分子功能;KEGG代谢通路分析发现,MIB1及其互作基因涉及4条代谢途径。结论MIB1包含多种TFBS,并通过与特定转录因子的相互作用,影响细胞癌变、免疫调节等多种生物学过程。MIB1还可能通过其互作基因和互作蛋白的介导,在细胞生长调控、造血干细胞分化、胚胎发育及神经元信息的传递等方面发挥重要作用。

Objective To analyze the transcription factor binding sites(TFBS)in the promoter region of E3 ubiquitin protein ligase 1(MIB1)gene in zebrafish,the types of MIB1 interacting genes and proteins and their roles in signaling pathways,and to investigate the regulatory mode and potential function of MIB1 gene.Methods Non-coding RNA(ncRNA)was predicted by National Genomics Data Center(NGDC).Alggen and AnimalTFDB online software were used to predict the TFBS types of MIB1 gene.GeneMANIA and STRING were used to analyze the interacting genes and proteins of MIB1.The related data were obtained through DAVID website,and gene ontology(GO)visual analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)metabolic pathway analysis were performed.Results ncRNA could be transcribed from the promoter region and 5′untranslated region of MIB1 gene.A total of 121 TFBS were obtained by prediction.P53 transcription factor could bind to the promoter region of MIB1 gene and interact with MIB1 protein.A total of 6 co-expressed genes of MIB1 were predicted online,and 20 interacting genes were screened.GO visual analysis showed that MIB1 and its interaction genes had functions in regulating the growth and differentiation of cells,tissues and organs and regulating the NOTCH signaling pathway in the biological process,and were mainly enriched in the cytoplasmic perinuclear region,cell membrane,postsynaptic dense area and so on.It had molecular functions such as binding NOTCH proteins and PDZ domain proteins.KEGG metabolic pathway analysis showed that MIB1 and its interacting genes were involved in 4 metabolic pathways.Conclusion MIB1 contains a variety of TFBS,and affects a variety of biological processes such as cell carcinogenesis and immune regulation by interacting with specific transcription factors.MIB1 may also play an important role in cell growth regulation,hematopoietic stem cell differentiation,embryonic development and neuronal information transmission through the mediation of its interacting genes and proteins.