Switches in transcriptome functions during seven skeletal muscle development stages from fetus to kid in Capra hircus

doi:10.1016/S2095-3119(20)63268-3

摘要/Abstract

摘要：

骨骼肌约占哺乳动物体重的40％，其发育是一个动态、复杂且精确调节的过程。转录组在调节山羊骨骼肌的发育中起着不可或缺的作用，但是在从胎儿到羔羊的多个骨骼肌发育阶段中，转录组表达谱和作用变化尚不清晰。对山羊胎儿到羔羊骨骼肌发育转录组进行细致的探讨及分析，探究转录组山羊骨骼肌早期发育过程中的角色转变，以完善了骨骼肌生长发育的调控网络。本研究使用石蜡切片和RNA-seq探究了从胎儿到出生后七个阶段（胎龄45d（F45），65d（F65），90d（F90），120d（F120）和135d（F135）的胎儿及以及出生1（B1）天和90（B90）天的孩子）的安徽白山羊背最长肌组织学和转录组表达谱。并通过WGCNA结合STEM分析，全面分析了差异表达基因（DEG）的时序表达情况，再利用GO和KEGG探究了差异mRNA的在不同时序中的功能转变。石蜡切片显示在F45时肌细胞较少，此时多为结缔组织。在F65在结缔组织间已出现大量肌细胞，且F65和F90具有初级肌纤维，而到F120及之后阶段初级肌纤维消失，完全为次级肌纤维。骨骼肌直径结果显示除F65和F90、F135和B1外，所有比较组均有显著差异（P <0.05）。所有阶段中共鉴定出4793个DEG，聚类结果显示它们在F45到F90、F135和B1之间相互聚类，而F120和B90单独聚类。石蜡切片结合RNA-seq将七个阶段划分为四个状态：F90之前，F120，F135和B1、B90。DEGs的WGCNA分析也验证了该结果。WGCNA结合STEM分析表明，F90之前的阶段与山羊骨骼肌的增殖密切相关。F120相关的DEGs通过调节tRNA参与骨骼肌结构的调节和骨骼肌的发育。F135和B1的DEGs参与调节脂肪酸的生物过程，以维持肌肉细胞的正常发育。B90的DEG通过调节肌动蛋白丝和原肌球蛋白来提供骨骼肌力量。这些结果验证了转录组在不同阶段扮演着不同角色，阐明了转录组在不同阶段对肌肉生长发育过程的潜在作用，进一步揭示了山羊骨骼肌发育中阶段特异性核心遗传网络的发展顺序。

Abstract:

Skeletal muscle accounts for about 40% of mammalian body weight, the development of which is a dynamic, complex and precisely regulated process that is critical for meat production. We here described the transcriptome expression profile in 21 goat samples collected at 7 growth stages from fetus to kid, including fetal 45 (F45), 65 (F65), 90 (F90), 120 (F120), and 135 (F135) days, and birth 1 (B1) day and 90 (B90) days kids. Paraffin sections combined with RNA-seq data of the 7 stages divided the transcriptomic functions of skeletal muscle into 4 states: before F90, F120, F135 and B1, and B90. And the dynamic expression of all 4 793 differentially expressed genes (DEGs) was identified. Furthermore, DEGs were clustered by weighted gene correlation network analysis into 4 modules (turquoise, grey, blue and brown) that corresponded to these 4 states. Functional and pathway analysis indicated that the active genes in the stages before F90 (turquoise) were closely related to skeletal muscle proliferation. The DEGs in the F120-related module (grey) were found to participate in the regulation of skeletal muscle structure and skeletal muscle development by regulating tRNA. The brown module (F135 and B1) regulated fatty acid biological processes to maintain the normal development of muscle cells. The DEGs of B90 high correlation module (blue) were involved the strengthening and power of skeletal muscle through the regulation of actin filaments and tropomyosin. Our current data thus revealed the internal functional conversion of the goat skeletal muscle in the growth from fetus to kid. The results provided a theoretical basis for analyzing the involvement of mRNA in skeletal muscle development.

Key words: mRNA , goat (Capra hircus) , transcriptome , skeletal muscle

. [J]. Journal of Integrative Agriculture, 2021, 20(1): 212-226.

LING Ying-hui, ZHENG Qi, JING Jing, SUI Meng-hua, ZHU Lu, LI Yun-sheng, ZHANG Yun-hai, LIU Ya, FANG Fu-gui, ZHANG Xiao-rong . Switches in transcriptome functions during seven skeletal muscle development stages from fetus to kid in Capra hircus[J]. Journal of Integrative Agriculture, 2021, 20(1): 212-226.

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