中国美利奴羊胚胎骨骼肌发育的加权基因共表达网络分析

doi:10.11843/j.issn.0366-6964.2020.03.006

摘要/Abstract

摘要： 旨在对绵羊胚胎骨骼肌lncRNAs（long non-coding RNA）进行鉴定分析，以阐明其在肌纤维类型转换与肌纤维增粗过程中的调控机制。本研究选取体重相近的成年中国美利奴母羊进行同期发情和人工授精，通过全转录组测序技术对其妊娠第85（D85N）、105（D105N）和135天（D135N）的胎儿背最长肌组织进行测序，设置D85N vs D105N、D105N vs D135N和D85N vs D135N 3个比较组，通过比较筛选出显著差异表达的lncRNA与mRNA。利用加权基因共表达网络分析（weighted gene co-expression network analysis，WGCNA）方法构建共表达模块，使用DAVID在线工具和R-package进行GO和KEGG富集分析以找到与肌肉发育相关的模块。最后从目标模块中筛选出高连通度的lncRNAs和mRNAs，通过它们与miRNAs间的靶向预测关系建立lncRNA-miRNA-mRNA共表达网络。根据WGCNA分析结果，共得到25个模块。功能富集显示，模块中的核心基因主要富集于细胞粘附、Wnt、紧密连接、mTOR、AMPK及ECM-受体相互作用等肌肉发育相关的信号通路，选出模块中连通度高的lncRNAs和mRNAs构建子网络，得到TNNI2、PIP5K1A、PDK4等关键相关基因，预测出MSTRG.3903、MSTRG.10154、MSTRG.1629、MSTRG.10496、MSTRG.9559、MSTRG.10178、MSTRG.10521、MSTRG.3911、MSTRG.4586、MSTRG.7232等10个与肌肉发育、肌肉疾病、细胞增殖相关的lncRNAs。本研究成功构建了肌纤维发育相关的lncRNA-miRNA-mRNA共表达网络，找到多个与妊娠后期胚胎骨骼肌发育相关的潜在候选基因，为深入研究lncRNA在中国美利奴羊胚胎发育过程中骨骼肌的发育调控机制奠定了基础，也为其他家畜骨骼肌发育机制的研究提供了参考和方向。

关键词: lncRNA-miRNA-mRNA, 共表达, WGCNA, 中国美利奴羊, 骨骼肌发育

Abstract: In this study, the long non-coding RNAs (lncRNAs)of sheep embryonic skeletal muscle were identified and analyzed to clarify its regulatory mechanism in myofiber switching and hypertrophy. Chinese Merino ewes with similar body weight were selected for simultaneous estrus and artificial insemination, and the fetal longissimus dorsi at the 85th(D85N), 105th (D105N), and 135th day (D135N) of pregnancy were sampled and sequenced by whole transcriptome sequencing technology. Three comparison groups (D85N vs D105N, D105N vs D135N, and D85N vs D135N) were set up, and the significantly differentially expressed lncRNA and mRNA were selected by comparison. Co-expression modules were constructed using the weighted gene co-expression network analysis (WGCNA) method. GO and KEGG enrichment analysis were performed using DAVID online tools and R-package to find modules related to muscle development. Finally, lncRNAs and mRNAs with high connectivity were selected from the target modules, and the lncRNA-miRNA-mRNA co-expression network was established through the predicted targeting relationship between mRNAs and miRNAs. A total of 25 modules were obtained according to the WGCNA analysis. The core genes in the related functional modules were mainly enriched in cell adhesion, Wnt, tight junction, mTOR, AMPK, and ECM-receptor signaling pathways. lncRNAs and mRNAs with high connectivity in modules were selected to establish a sub-network in which some genes such as TNNI2, PIP5K1A, PDK4, etc., and 10 lncRNAs (MSTRG.3903, MSTRG.10154, MSTRG.1629, MSTRG.10496, MSTRG.9559, MSTRG.10178, MSTRG.10521, MSTRG.3911, MSTRG.4586, MSTRG.7232) related to muscle development, muscle disease, and cell proliferation were found successfully. The lncRNA-miRNA-mRNA co-expression network related to myofiber development in Merino sheep was constructed, and several potential candidate genes related to embryonic skeletal muscle development in late pregnancy were found. All above results provided the solid basis for studying the regulatory mechanism of lncRNA during Merino sheep embryo development and references for the same study in other livestocks.

Key words: lncRNA-miRNA-mRNA, co-expression, WGCNA, Chinese Merino sheep, skeletal muscle development

中图分类号:

S826.2

石田培, 侯浩宾, 王欣悦, 赵志达, 尚明玉, 张莉. 中国美利奴羊胚胎骨骼肌发育的加权基因共表达网络分析[J]. 畜牧兽医学报, 2020, 51(3): 452-464.

SHI Tianpei, HOU Haobin, WANG Xinyue, ZHAO Zhida, SHANG Mingyu, ZHANG Li. Weighted Gene Co-expression Network Analysis for Embryo Development of Skeletal Muscle in Chinese Merino Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(3): 452-464.

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