鸡肌肉发育相关miR-133a-5p分析和关键靶基因筛选

Analysis of miR-133a-5p related to chicken muscle development and screening of key target genes

为筛选miR-133a-5p影响鸡肌肉发育的关键靶基因,本研究利用在线数据库预测miR-133a-5p靶基因,并对靶基因进行富集分析和构建蛋白-蛋白相互作用(Protein-protein interaction,PPI)网络,寻找网络图中有意义的模块。通过单因素方差分析,比较分析肌肉和其他组织中的miR-133a-5p表达量;再依据microRNA与靶基因负相关的作用机制,将miR-133a-5p靶基因与肌肉中相对下调基因取交集,筛选关键靶基因。最后,通过RNA22 v2对筛选结果进行评估。结果表明:(1)共获得157个靶基因;(2)GO富集分析显示,靶基因参与多个生物合成过程的调控和代谢过程;KEGG富集结果包括MAPK信号通路等多种信号通路,也包括肌动蛋白细胞骨架等与肌肉发育直接相关的通路;(3)PPI网络图共筛选到4个有意义模块,涉及17个基因;(4)miR-133a-5p在肌肉中表达显著上调(相对肺、肝脏和肾脏),与肌肉相对下调基因取交集后,筛选到SOX5(SRY-box 5)、PRTFDC1(Phosphoribosyl transferase domain containing 1)、THRB(Thyroid hormone receptor beta)、THBS2(Thrombospondin 2)和ARRDC3(Arrestin domain containing 3)5个基因;(5)在GSE93855的表达谱中,PRTFDC1和THRB在肌肉中表达量最低,而RNA22 v2评估结果显示,仅SOX5和THRB存在P<0.05的结合位点。综上,miR-133a-5p很可能是通过SOX5、PRTFDC1、THRB、THBS2和ARRDC3影响肌肉发育,其中SOX5和THRB尤为重要。本研究为进一步研究鸡miR-133a-5p提供了理论基础和数据支撑。

In order to screen the key target genes of miR-133a-5p affecting chicken muscle development,in this study,the online database was used to predict the target genes of miR-133a-5p,enriched and analyzed the target genes,and constructed the protein-protein interaction(PPI)network to find meaningful modules in the network diagram.The expression of miR-133a-5p in muscle and other tissues was compared and analyzed by one-way ANOVA.Then,according to the mechanism of negative correlation between microRNA and target genes,the intersection of miR-133a-5p target genes and relatively down-regulated genes in muscle was to screen the key target genes.Finally,the screening results were evaluated by RNA22 v2.The results showed that:(1)A total of 157 target genes were obtained;(2)GO enrichment analysis showed that the target genes were involved in the regulation of multiple biosynthetic and metabolic processes;KEGG enrichment results included a variety of signaling pathways such as MAPK signaling pathway,as well as pathways directly related to muscle development such as actin cytoskeleton;(3)A total of 4 meaningful modules were screened by PPI network map,involving 17 genes;(4)miR-133a-5p expression was significantly up-regulated in muscle(relative to lung,liver and kidney),and interlaced with relative down-regulated genes in muscle,SOX5(SRY-box 5),PRTFDC1(Phosphoribosyl transferase domain containing 1)and THRB(Thyroid hormone receptor)were obtained beta),THBS2(Rhrombospondin 2),ARRDC3(Arrestin domain containing 3);(5)In the GSE93855 expression profile,PRTFDC1 and THRB had the lowest expression in muscle,while the evaluation results of RNA22 v2 showed that only SOX5 and THRB had P<0.05 binding sites.In conclusion,miR-133a-5p may affect muscle development through SOX5,PRTFDC1,THRB,THBS2,and ARRDC3,of which SOX5 and THRB are particularly important.This study provides theoretical basis and data support for further study of chicken miR-133a-5p.