ssc-miR-486靶基因预测及生物信息学分析

Target Gene Prediction and Bioinformatics Analysis of ssc-miR-486

通过对ssc-miR-486进行靶基因预测及生物信息学分析,以探索其影响猪脂肪沉积的作用机制。首先利用实时荧光定量PCR技术对脂肪沉积能力相差较大的莱芜猪和大白猪皮下脂肪组织中ssc-miR-486表达情况进行比较研究,然后利用miRBase、Ensembl、NCBI等数据库及miRanda、PITA、RNAhybrid、Cytoscape、JASPAR、Promoter Scan等软件对ssc-miR-486进行生物信息学分析,包括保守性分析、转录因子结合位点预测、靶基因预测、GO富集分析和KEGG信号通路富集分析。结果表明,ssc-miR-486在脂肪沉积能力较强的莱芜猪皮下脂肪组织中发生显著上调。生物信息学分析结果发现,miR-486在各物种间非常保守,ssc-miR-486启动子区域有SREBP1、SREBP2等多个转录因子结合位点,获得的229个靶基因显著富集于脂质代谢、脂质生物合成、细胞代谢等生物学过程及类固醇生物合成、磷脂肌醇代谢、PPAR等信号转导通路中。结果表明,ssc-miR-486参与了猪脂肪沉积或脂肪代谢的调控,为今后研究脂肪沉积提供基础理论支撑。

The target gene prediction and bioinformatics analysis of ssc-miR-486 were performed to explore its effects on the porcine fat deposition. First,the Real-time PCR was applied to detect differential expression of sscmiR-486 in the subcutaneous adipose tissue of Laiwu pig and Large White pig which were quite different in terms of fat deposition capability. Then we performed bioinformatics analysis of ssc-miR-486 including the prediction of the target genes and transcription factor binding sites,the analysis of sequence conservation and involved Gene Ontology and KEGG pathway of its target genes using the databases such as miRBase,Ensembl and NCBI and bioinformatic softwares such as miRanda,PITA,RNAhybrid,Cytoscape,JASPAR and Promoter Scan. ssc-miR-486 was significantly upregulated in the subcutaneous adipose tissue of Laiwu pig with easily fat accumulation. The bioinformatics analysis showed that miR-486 was very conservative among various species and multiple transcription factor binding sites such as SREBP1 and SREBP2 were predicted in the promoter area of ssc-miR-486. Additionally the obtained 229 target genes of ssc-miR-486 were significantly enriched in many biological processes,for example lipid metabolism,lipid biosynthesis and cell metabolism,et al and signal transduction pathways such as steroid biosynthesis,inositol phospholipid metabolism and PPAR signaling pathway. The results suggest that ssc-miR-486 plays a certain role in fat deposition and lipid metabolism of pigs and provide a basis for fat deposition research in the future.