苜蓿miR156及其靶基因生物信息学分析

Bioinformatics analysis of alfalfa miR156 and its target genes

【目的】分析苜蓿miR156(mtr-miR156)基因家族的序列组成及基因表达功能,为mtr-miR156跨界调控的研究提供理论基础。【方法】应用PmiREN数据库检索并分析mtr-miR156家族成员成熟序列、茎环序列和成熟序列染色体定位信息,weblogo在线网站对mtr-miR156家族成熟序列、茎环序列进行保守性分析,DNAMAN软件分析茎环序列同源性,同时利用联川生物云平台和TargentScan在线网站预测并下载获得mtr-miR156a的靶基因、靶基因GO功能富集分析和KEGG通路富集分析,通过RNAhybrid在线网站比对预测到的所有靶基因与mtr-miR156a的结合位点和结合自由能值,选择符合自由能值的靶基因进行靶基因功能分析。【结果】PmiREN数据库共检索到10个mtr-miR156家族成员;10个成员成熟序列共定位在3条染色体上;10个成员中有8个成员成熟序列完全一致,其余2个成员成熟序列高度保守;10个成员茎环序列中位于成熟序列位置的碱基与成熟序列完全一致;茎环序列同源树分析结果显示10个成员共分为3个分支,mtr-miR156g与其他成员的亲缘关系最远;经过GO功能富集分析发现,预测到牛体内的靶基因显著富集于转录调控功能、细胞膜组成以及ATP合成等;利用KEGG通路注释表明,预测到牛体内的靶基因显著集中于脂肪酸降解通路和Ras信号通路调节等通路中。【结论】苜蓿miR156基因家族可能会通过相关靶基因跨界调控奶牛体内脂肪酸降解、ATP合成、细胞炎症、乳脂乳蛋白合成代谢等作用。

【Objective】The present study aimed to analyze the sequence composition and gene expression function of alfalfa miR156(mtr-miR156)gene family,so as to provide a theoretical basis for the study of transboundary regulation of mtr-miR156.【Method】PmiREN database was used to retrieve and analyze mature sequences of mtr-miR156 family members,stem loop sequences and the chromosome location information of mature sequences.Weblogo online website was used to analyze the conservation of mature sequences and stem loop sequences of mtr-miR156 family members.Stem-loop sequences homology was analyzed by the DNAMAN.Meanwhile,the target genes of mtr-miR156a,target gene GO functional enrichment analysis and KEGG pathway enrichment analysis were predicted and downloaded by Lianchuan Biocloud platform and TargentScan online website.The binding sites and binding free energy values of all the predicted target genes and mtr-miR156a were compared by RNAhybrid online website,and the target genes meeting the free energy values were selected for functional analysis of target genes.【Result】A total of 10 mtr-miR156 family members were retrieved from PmiREN database.The mature sequences of 10 members were co-localized on 3 chromosomes.The mature sequences of 8 out of 10 members were completely consistent,and the mature sequences of the other 2 members were highly conserved.In the stem-loop sequence of 10 members,the bases located in the mature sequence were identical with the mature sequence.Stem-loop sequence homology tree analysis showed that the 10 members were divided into three branches,and mtr-miR156g was the furthest related to other members.GO functional enrichment analysis showed that the predicted target genes in bovine were significantly enriched in transcriptional regulatory function,cell membrane composition and ATP synthesis.KEGG pathway annotation showed that the predicted target genes in cattle were significantly concentrated in fatty acid degradation pathway and Ras signaling pathway regulation.【Conclusion】The alfalfa miR156 gene family may regulate fatty acid degradation,ATP synthesis,cellular inflammation,milk fat,milk protein anabolism and other effects in dairy cows through related target genes.