联合microRNA和mRNA组学对雄性小鼠随增龄生育力变化的生物信息学研究

Bioinformatics study on the changes of fertility of male mice with their increasing age by microRNA combined with mRNAomics

目的:通过生物信息学方法筛选出小鼠睾丸组织随增龄变化的差异表达的关键miRNA和mRNA,为精子发生的研究提供新的方向.方法:检索美国国家生物技术信息中心(NCBI)的基因表达集合(GEO)数据库中关于精子发生的miRNAs和mRNA的芯片数据,确定数据集为GSE41857和GSE41858.对数据集GSE41857进行GEO2R在线分析,获得精子发生相关的差异表达miRNAs,并利用联川生物云平台预测其靶基因.对数据集GSE41858进行GEO2R在线分析,获得精子发生相关的差异表达mRNAs.将上述获得的靶基因与miRNA的靶基因取交集获得最终的差异表达基因.运用DAVID数据库对差异表达基因进行基因本体数据库(GO)富集和京都基因与基因组百科全书数据库(KEGG)通路分析,应用STRING数据库构建差异表达基因相关的蛋白质互作网络.结果:对数据集GSE41857分析共获得差异表达miRNAs52条,其靶基因17224个.对数据集GSE41858分析共得出差异表达基因619个,最终获得交集差异表达基因485个.GO富集分析生物过程(BP),主要包括精子发生、细胞分化、纤毛组装等;细胞组成(CC)主要包括细胞质、细胞核、细胞骨架等;分子功能(MF)主要包括蛋白质结合、RNA聚合酶II序列特异性DNA结合转录因子结合、整合素结合等.差异表达基因KEGG分析获得的通路主要包括轴突引导、乙型肝炎、Hippo信号传导途径等.利用cytoscape分析前20位的hub基因分别为Tgfb1/1、Tns3、Tln1、Csk、Zyx、Capn5、Capn1、Crebbp、Plxna1、Plxna3、Plxna4、Plxnb1、Itga9、Lama5、Fras1、Pdlim3、Ccnb2、E2f1、Ncor2、Inppl1.结论:本研究构建了小鼠精子发生过程中的miRNA􀆼mRNA调控网络,并挖掘出一些可能参与精子发生的miRNAs和新基因,为进一步阐明精子发生提供新的方向.

Objective:Through bioinformatic methods screening out the key miRNAs and mRNAs differentially expressed in mouse testicular tissues with their increasing age,to provide new directions for the research of spermatogenesis.Methods:Microarray data on miRNAs and mRNAs of spermatogenesis were searched in NCBI's GEO database,and the datasets were identified as GSE41857 and GSE41858.GEO2R online analysis of the dataset GSE41857 was used to derive the differentially expression of miRNAs related to spermatogenesis,and the Lianchuan Omicstudio was used to predict their target genes.GEO2R online analysis of the dataset GSE41858 was used to derive the differentially expression of mRNAs associated with spermatogenesis.The target genes as mentioned above were intersected with the target genes of the miRNA to obtain the final differentially expressed genes.GO enrichment and KEGG pathway analysis of the differentially expressed genes were performed by DAVID,and STRING was applied to construct a protein interaction network associated with differentially expressed genes.Results:Analysis of the dataset GSE41857 yielded 52 differentially expressed miRNAs with 17,224 target genes.Analysis of the dataset GSE41858 yielded 619 differentially expressed genes,and finally 485 differentially expressed genes of intersection were obtained.GO enrichment analysis of biological processes(BP),mainly included spermatogenesis,cell differentiation,and cilia assembly,etc.Cell composition(CC)mainly included cytoplasm,nucleus,and cytoskeleton,etc.Molecular function(MF)mainly included protein binding,RNA polymerase II sequence-specific DNA binding transcription factor binding,and integrin binding,etc.The pathways obtained by KEGG analysis of differentially expressed genes mainly included axon guidance,hepatitis B,and Hippo signaling pathway,etc.The top 20 hub genes analyzed by cytoscape were Tgfb1/1,Tns3,Trn1,Csk,Zyx,Capn5,Capn1,Crebbp,Plxna1,Plxna3,Plxna4,Plxnb1,Itga9,Lama5,Fras1,Pdlim3,Ccnb2,E2f1,Ncor2,and Inppl1.Conclusion:The miRNA-mRNA regulatory network in mouse spermatogenesis has been constructed in this study,and some miRNAs and novel genes are uncovered,which may be involved in spermatogenesis.The new directions are provided for further elucidation of spermatogenesis.