静原鸡miR-107的靶基因预测及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2020.09.001

摘要/Abstract

摘要： 为探究miR-107在静原鸡肌肉组织肌苷酸特异性沉积过程中的调控机制，本研究利用相关生物信息学软件和数据库对静原鸡miR-107进行了靶基因预测与生物信息学分析。通过转录组测序获取静原鸡miR-107序列，进行序列比对和保守性分析；通过TargetScan、miRDB和PicTar预测结果的交集并结合miRTarbase中已证实的靶基因集合，取二者并集，采用OmicShare工具对基因集合进行GO功能富集和信号通路富集分析，并讨论HMED数据库中miR-107在不同组织和疾病中的表达水平。结果显示，miR-107序列在各物种间高度保守，miR-107调控的靶基因GO功能富集主要包括细胞过程、生物调节、代谢过程、刺激反应等生物学过程和结合、催化活性、转录调节活性等分子功能；靶基因存在于细胞的多个组分中，包括细胞器、细胞膜、含蛋白质复合物。信号转导通路显著富集于癌症中的microRNAs途径（microRNAs in cancer）、人乳头瘤病毒感染（human papillomavirus infection）、癌症中途径（pathways in cancer）、PI3K-Akt信号通路（PI3K-Akt signaling pathway）中（P<0.05）。miRNA-靶基因互作分析发现，miR-107主要通过与靶基因mRNA的非翻译区靶向结合抑制靶基因的表达。根据HMED数据库中miR-107在不同组织和疾病中的表达数据，发现miR-107在黑素瘤（melanoma）中的表达水平最高，在扁桃体（tonsil）和肌肉（muscle）等组织中表达水平较低。通过对静原鸡miR-107靶基因的生物信息学分析，为miR-107功能及调控机制的深入研究提供参考依据，也为进一步研究miR-107在静原鸡肌肉发育中的作用奠定基础。

关键词: 静原鸡; miR-107; 靶基因; 生物信息学

Abstract: To explore the regulatory mechanism of miR-107 in the process of inosine acid specific deposition of muscle tissue in Jingyuan chickens,the bioinformatics software and databases were used to bioinformatically analyze and predict target genes of miR-107 in Jingyuan chickens in this study.The transcriptome sequencing technology was used to obtain the sequence of miR-107 in Jingyuan chickens,perform sequence alignment and analyze its conservation.TargetScan,miRDB and PicTar were applied to predict target genes of miR-107.The intersection of the three results and validated targets from miRTarbase database were demonstrated by Gene Ontology and signal pathway enrichment analysis using OmicShare tool,and discussed the expression level of miR-107 in different tissues and diseases in HMED database.The results showed that miR-107 sequence of Jingyuan chickens was highly conserved among all species,and the biological functions of target genes regulated by miR-107 mainly included basic biological function,such as cellular processes,biological regulation,metabolic processes,response to stimulus and molecular functions were enriched in binding,catalytic activity,transcription regulator activity and so on.Target genes existed in various components of the cell,including organelles,cell membranes and protein-containing complexes.The signal transduction pathway was significantly enriched in the microRNAs in cancer,human papillomavirus infection,pathways in cancer and PI3K-Akt signaling pathway (P<0.05).miRNA-target gene interaction analysis found that miR-107 mainly inhibited the expression of target genes through targeted binding to the untranslated region of the target gene mRNA.According to the expression data of miR-107 in different tissues and diseases in the HMED database,it was found that the expression level of miR-107 was the highest in melanoma,and was lower in tonsil,muscle and other tissues.The prediction and bioinformatics analysis of miR-107 target genes provided a reference for in-depth study of the function and regulatory mechanism,and laid the basis to study the role of miR-107 of muscle development in Jingyuan chickens.

Key words: Jingyuan chickens; miR-107; target gene; bioinformatics

中图分类号:

禹保军, 何金童, 姚婷婷, 吴昊, 樊希雅, 虎红红, 王卫振, 郭菊, 顾亚玲, 蔡正云, 辛国省, 张娟. 静原鸡miR-107的靶基因预测及生物信息学分析[J]. 中国畜牧兽医, 2020, 47(9): 2695-2705.

YU Baojun, HE Jintong, YAO Tingting, WU Hao, FAN Xiya, HU Honghong, WANG Weizhen, GUO Ju, GU Yaling, CAI Zhengyun, XIN Guosheng, ZHANG Juan. Prediction and Bioinformatic Analysis of miR-107 Target Genes in Jingyuan Chickens[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(9): 2695-2705.

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