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

Abstract

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

CLC Number:

S826.2

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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Weighted Gene Co-expression Network Analysis for Embryo Development of Skeletal Muscle in Chinese Merino Sheep

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