牛miR-2439-5p的转录因子-miRNA-mRNA调控网络预测与组织表达谱分析

Transcription factor-miRNA-mRNA regulatory network prediction and tissue expression profile analysis of bovine miR-2439-5p

关键词:  牛  miR-2439-5p  “转录因子-miRNA-mRNA”调控网络  组织表达谱分析

Key words:  bovine  miR-2439-5p  “transcription factor-miRNA-mRNA” regulatory network  tissue expression profile analysis

摘要:

为了解牛miR-2439-5p的生物学信息和初步探索其与宿主基因MRTFA(Myocardin related transcription factor A，心肌素相关转录因子A)是否存在互作功能，以及进一步了解牛miR-2439-5p的组织表达规律，利用物种间保守性分析、上游序列CpG岛分析、启动子预测、转录因子预测、靶基因预测、基因本体论富集分析和信号通路富集分析等生物信息学方法对miR-2439-5p进行“转录因子-miRNA-mRNA”调控网络预测，并进行组织表达谱分析。结果表明:1)miR-2439-5p是牛特异性miRNA、内含子miRNA和miRNA^*(相对低表达miRNA)；2)miR-2439-5p可能受C/EBPβ和RARα等转录因子调控，预测其共有621个靶基因，显著富集在AMPK信号通、mTOR信号通路和不饱和脂肪酸合成等信号通路；3)miR-2439-5p在28月龄郏县红牛的肾组织中相对高表达，与肌肉和背脂组织存在显著性差异(P<0.01)；其在28月龄和牛的背脂组织中相对高表达，与肝和脾组织存在显著性差异(P<0.05)；其在28月龄固原黄牛的各组织表达量无显著性差异(P>0.05)。综上，miR-2439-5p可能反馈调节宿主基因MRTFA，从而调控牛脂肪细胞分化，为进一步探究miR-2439-5p的功能和作用机制提供研究方向和理论依据。

Abstract:

In order to understand the biological information of bovine miR-2439-5p, preliminarily explore the interaction between miR-2439-5p and host gene MRTFA(Myocardin related transcription factor A), and further understand the tissue expression of miR-2439-5p, bioinformatics methods such as species conservation analysis, upstream sequence CpG island analysis, promoter prediction, transcription factor prediction, target gene prediction, gene ontology enrichment analysis and signal pathway enrichment analysis were used to predict “transcription factor-miRNA-mRNA” regulatory network of miR-2439-5p and the tissue expression profile of miR-2439-5p was also analyzed. The results showed that: 1)miR-2439-5p was bovine-specific miRNA, intron miRNA and miRNA^*. 2)miR-2439-5p may be regulated by transcription factors such as C/EBPβ and RARα. 621 target genes were predicted to be enriched in AMPK signaling pathway, mTOR signaling pathway and biosynthesis of unsaturated fatty acids. 3)miR-2439-5p was relatively highly expressed in the kidney tissue of 28-month-old Jiaxian Red cattle, which was significantly different from that in muscle and back fat(P<0. 01); it was relatively highly expressed in back fat of 28-month-old Wagyu, which was significantly different from that in liver and spleen(P<0. 05); there was no significant difference in different tissues of 28-month-old Guyuan cattle(P>0. 05). In conclusion, miR-2439-5p may feedback regulate host gene MRTFA, thereby regulate bovine adipocyte differentiation. This study provides research direction and theoretical basis for further exploration of the function and mechanism of miR-2439-5p.