中国农业科学 ›› 2020, Vol. 53 ›› Issue (3): 642-657.doi: 10.3864/j.issn.0578-1752.2020.03.015

• 畜牧·兽医·资源昆虫 • 上一篇    下一篇

基于全转录组测序的绵羊胚胎不同发育阶段 骨骼肌circRNA的分析与鉴定

石田培,王欣悦,侯浩宾,赵志达,尚明玉,张莉()   

  1. 中国农业科学院北京畜牧兽医研究所,北京100193
  • 收稿日期:2019-03-01 接受日期:2019-05-30 出版日期:2020-02-01 发布日期:2020-02-13
  • 通讯作者: 张莉
  • 作者简介:石田培,E-mail:yangstp@foxmail.com。
  • 基金资助:
    国家自然科学基金联合基金重点支持项目NSFC(U1503285);中央级公益性科研院所基本科研业务费专项(Y2017XM02)

Analysis and Identification of circRNAs of Skeletal Muscle at Different Stages of Sheep Embryos Based on Whole Transcriptome Sequencing

SHI TianPei,WANG XinYue,HOU HaoBin,ZHAO ZhiDa,SHANG MingYu,ZHANG Li()   

  1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193
  • Received:2019-03-01 Accepted:2019-05-30 Online:2020-02-01 Published:2020-02-13
  • Contact: Li ZHANG

摘要:

【目的】肉用性状是家养动物的重要性状,尤其是产肉性能与骨骼肌的发育密切相关,对多数动物而言,骨骼肌的生长取决于肌纤维的早期发育。本研究将揭示绵羊(Ovis aries)胚胎期骨骼肌组织发育重要节点、肌纤维的形成及转换机制,探究骨骼肌在动物胚胎期的生长对后续发育潜力的影响。【方法】在前期绵羊胚胎期组织结构试验的基础上,选择肌纤维发育及类型转换的3个重要时间节点:胎龄85 d(D85)、105 d(D105)、135 d(D135),并对处于这些节点期的中国美利奴绵羊胚胎背最长肌进行全转录组测序。通过生物信息学分析和功能预测筛选出差异表达显著的circRNA,采用实时荧光定量 PCR(qRT-PCR)对其进行验证。【结果】通过条件筛选(|log2| ≥1且P≤0.05)获得差异表达circRNA 1 126个。将3组进行比较,在各时间节点都发现较多的特异性表达circRNA。在D85 vs D135比较组中,特异性差异表达数量最多:共发现差异表达circRNA 374个,上调表达201个,下调表达173个,其中具有4倍以上差异的基因167个,占差异基因的44.7%。对这些差异性表达的circRNA进行GO和KEGG功能分析和靶向预测,富集到与肌肉分化和肌纤维发育相关的能量代谢和信号转导通路,包括MAPK、PI3K-Akt、Ras、Regulation of actin cytoskeleton等。结果表明:在D85至D105期间富集到的差异circRNA多与肌细胞发育调控、细胞增殖和存活、细胞周期等相关,而在D105至D135期间富集到的通路则主要与能量转换、物质运输、RNA转运和DNA修复有关。靶向预测结果通过Cytoscape软件绘制出可视化共表达网络,筛选到circRNA8239、circRNA19073,circRNA2765、circRNA1616等核心调控转录物,并在D105找到调节快慢肌类型转换的关键因子circRNA7527,其靶向作用于bta-miR-135a、bta-miR-615、chi-miR-133a-5p进而调控MEF2C基因。通过3个时间节点的差异表达情况和功能预测描述选取了与肌肉发育相关的4个核心circRNA和其靶向的4个miRNA进行qRT-PCR分析,其基因表达趋势与测序数据一致。【结论】本试验在转录水平上验证了绵羊胚胎发育D85至D105是肌纤维数量的稳定发生期,而D105至D135则是肌纤维的肥大期,由此推断D105可能是绵羊胚胎发育的关键时间窗口。本研究首次基于全转录组测序构建了绵羊胚胎期骨骼肌发育的circRNA图谱,揭示了不同发育阶段的转录组差异,并对绵羊胚胎骨骼肌发育期间重要的调控因子进行挖掘和验证,发现了以MEF2C为靶基因的多个circRNA和miRNA参与MAPK信号通路,为绵羊肌纤维发育分子机制以及其它家畜非编码RNA的研究提供了参考。

关键词: 绵羊, 胚胎, 全转录组, 骨骼肌, 生长发育, circRNA

Abstract:

【Objective】The meat production of livestock, which is closely related to the development of skeletal muscle, is an important economic trait to measure the quality of livestock. For mammals, the skeletal muscle development depends on the growth and differentiation of embryonic myocyte, which has a significant impact on the subsequent growing potential. In this study, the developmental mode of skeletal muscle, the important transformation nodes, the formation of muscle fibers and the molecular regulation mechanism of transformation were mainly explored. 【Method】 Based on the previous research, the important nodes D85, D105 and D135 related to the myotube development were used in the experiment, and the longissimus dorsi muscles were sequenced by whole transcriptome sequencing. The differentially expressed (DE) circRNAs were screened by bioinformatics analysis and verified by quantitative real-time PCR (qRT-PCR). 【Result】 1 126 DE circRNAs were obtained by conditional screening (|log2| ≥1 and P≤0.05). The 3 groups were compared and many specific expressions of circRNA were found at each stage, but in the D85 vs D135 group, the amount was the most. 374 DE circRNAs were obtained, which contained 201 up-regulated and 173 down-regulated, and 44.7% of the DE genes were differentially expressed with a difference of more than 4 times. These DE circRNAs were subjected to run GO and KEGG functional analysis and targeted prediction, and they were enriched into some pathways, such as energy metabolism and signal transduction, which involved in muscle differentiation and muscle fiber development, including MAPK, PI3K-Akt, Ras, regulation of actin cytoskeleton and other signal transduction pathways. According to the results, it was confirmed that the DE circRNAs enriched during D85 to D105 were mostly associated with cell proliferation and survival, regulation of myocyte development and cell cycle, while D105 to D135 were mainly related to energy conversion, material transport, RNA transport, and DNA repair. By drawing co-expression visualization network with the targeted prediction results used by Cytoscape, the core regulatory transcripts, such as circRNA8239, circRNA19073, circRNA2765 and circRNA1616, were identified. In the D105 period, a key factor circRNA7527 that regulated the conversion of fast and slow muscle types was found, which targets the bta-miR-135a, bta-miR-615, and chi-miR-133a-5p to regulate the MEF2C gene. According to the differential expression and functional prediction in three comparison groups, 4 circRNAs related to muscle development and 4 target miRNA were selected for qRT-PCR, and the results showed that the gene expression trend was consistent with the sequencing data. 【Conclusion】 It was verified that the stabilization of the number of muscle fibers occurred between sheep embryos at D85 and D105, and muscle fiber hypertrophy happened during the D105 to D135 period, which lead to the conclusion that D105 was probably a key time point. In this study, we firstly constructed a circRNA map in sheep embryonic skeletal muscle development based on the whole transcriptome sequencing. The transcriptome differences at key stages were revealed, and multiple circRNAs and miRNAs targeting MEF2C that involved in the MAPK signaling pathway were found, which provided reference for livestock myofiber development research and other research on non-coding RNA.

Key words: sheep, embryo, whole transcriptome, skeletal muscle, growth and development, circRNA