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| 鸡肌肉发育相关miR-133a-5p分析和关键靶基因筛选 |
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贾富民,贾羽晴,夏晶晶,税斐,曹程程,张泰康,丁元飞,郭立平,耿照玉,金四华*
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| (安徽农业大学 动物科技学院, 合肥 230036) |
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| 摘要: |
| 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。 |
| 关键词: 鸡 肌肉 miR-133a-5p 生物信息学 |
| DOI：10.11841/j.issn.1007-4333.2023.08.14 |
| 投稿时间：2022-10-29 |
| 基金项目:国家自然科学基金项目(31802028)；安徽省教育厅高校自然科学研究重点项目(2022AH050928)；高校优秀青年人才支持重点项目(gxyqZD2022017)；2022年教育部产学研合作协同育人项目(221000488095409)；安徽省重点研究与开发计划项目(202004a06020049) |
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| Analysis of miR-133a-5p related to chicken muscle development and screening of key target genes |
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JIA Fumin,JIA Yuqing,XIA Jingjing,SHUI Fei,CAO Chengcheng,ZHANG Taikang,DING Yuanfei,GUO Liping,GENG Zhaoyu,JIN Sihua*
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| (School of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China) |
| Abstract: |
| 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. |
| Key words: Chicken muscle miR-133a-5p bioinformatics |
