牛骨骼肌不同发育阶段miRNA测序及生物信息学分析

doi:10.11843/j.issn.0366-6964.2025.06.015

摘要/Abstract

摘要：

为明确牛骨骼肌不同发育阶段miRNA表达情况，筛选影响牛骨骼肌发育的关键miRNA。本研究利用胚胎切割和胚胎移植技术获得的来源相同、遗传背景高度一致的3月龄、6月龄胚胎肌肉组织和9月龄胎儿肌肉组织进行RNA-seq测序分析，运用生物信息学筛选差异表达的miRNA，并进行靶基因预测和功能富集分析。6月龄vs.3月龄、9月龄vs.6月龄、9月龄vs.3月龄分别筛选出262个(上调130个，下调132个)、397个(上调199个，下调198个)、448个(上调224个，下调224个)差异表达miRNA，同时分别预测到靶基因3 854个、7 434个、8 167个。对这些靶基因进行功能注释及信号通路分析，发现6月龄vs.3月龄差异表达miRNA靶基因主要参与肌肉细胞中的细胞骨架、焦点粘连以及动物自噬等5条与肌肉发育相关通路；9月龄vs. 6月龄差异表达miRNA靶基因主要参与肌肉细胞中的细胞骨架、焦点粘连以及生长激素的合成、分泌和作用等4条与肌肉发育相关通路；9月龄vs.3月龄差异表达miRNA靶基因主要参与肌肉细胞中的细胞骨架、焦点粘连以及肌动蛋白细胞骨架的调节等6条与肌肉发育相关通路；构建差异表达miRNAs与骨骼肌发育相关功能靶基因的调控网络图，发现其中bta-miR-139、bta-miR-499、bta-miR-7、bta-miR-148a、bta-miR-204等38个miRNA可能在牛不同时期骨骼肌生长发育中起调控作用。本研究结果为深入理解牛骨骼肌发育的分子机制提供重要的理论依据，同时为后续牛骨骼肌miRNA研究提供了基础资料。

关键词: 牛, 骨骼肌发育, miRNA测序, 靶基因预测

Abstract:

The study aimed to clarify the expression of miRNA in bovine skeletal muscle tissues at different developmental stages and screen the key miRNAs affecting bovine skeletal muscle development. The present study conducted RNA sequencing analysis on muscle tissues from 3-month-old and 6-month-old embryos, as well as 9-month-old fetal muscle tissues obtained through embryo splitting and embryo transfer techniques, all originating from the same source with highly consistent genetic backgrounds. Bioinformatics approaches were applied to screen for differentially expressed miRNAs, followed by target gene prediction and functional enrichment analysis. Compared with muscle tissue at 3 months old, 262 differentially expressed miRNAs (130 up-regulated and 132 down-regulated) were screened in muscle tissue at 6 months old; Compared with muscle tissue at 6 months old, 397 differentially expressed miRNAs (199 up-regulated and 198 down-regulated) were screened in muscle tissue at 9 months old; And compared with muscle tissue at 3 months old, 448 differentially expressed miRNAs (224 up-regulated and 224 down-regulated) were screened in muscle tissue at 9 months old. Meanwhile, 3 854, 7 434 and 8 167 target genes were predicted, respectively. Functional annotation and pathway analysis of the target genes revealed that the differentially expressed miRNAs between the 6-month and 3-month stages were predominantly involved in 5 muscle development-related pathways, including cytoskeleton in muscle cells, focal adhesion, autophagy-animal, etc. Similarly, the differentially expressed miRNAs between the 9-month and 6-month stages were primarily associated with 4 muscle development-related pathways, such as cytoskeleton in muscle cells, focal adhesion and growth hormone synthesis, secretion and action, etc. Furthermore, the differentially expressed miRNAs between the 9-month and 3-month stages were significantly enriched in 6 muscle development-related pathways, including cytoskeleton in muscle cells, focal adhesion, regulation of the actin cytoskeleton, etc. A regulatory network of differentially expressed miRNAs and functional target genes associated with skeletal muscle development was constructed, identifying 38 miRNAs, including bta-miR-139, bta-miR-499, bta-miR-7, bta-miR-148a and bta-miR-204, which might play regulatory roles in the growth and development of bovine skeletal muscle at different stages. The results of this study provide an important theoretical basis for in depth understanding of the molecular mechanism of bovine skeletal muscle development, and also provide basic data for subsequent miRNA research on bovine skeletal muscle.

Key words: cattle, skeletal muscle development, miRNA sequencing, target gene prediction

中图分类号:

S823.2

石闪闪, 万琼飞, 许赢心, 王秋硕, 张林林, 郭益文, 胡德宝, 郭宏, 丁向彬, 李新. 牛骨骼肌不同发育阶段miRNA测序及生物信息学分析[J]. 畜牧兽医学报, 2025, 56(6): 2701-2710.

SHI Shanshan, WAN Qiongfei, XU Yingxin, WANG Qiushuo, ZHANG Linlin, GUO Yiwen, HU Debao, GUO Hong, DING Xiangbin, LI Xin. Sequencing and Bioinformatics Analysis of miRNAs at Different Developmental Stages of Bovine Skeletal Muscle[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(6): 2701-2710.

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样品编号 Sample	原始序列数量Raw reads		过滤后序列数量Valid reads
样品编号 Sample	Total	Unique	Total	Unique
3月龄胚胎ET3_SM	11 193 282	969 370	8 593 571	426 864
6月龄胚胎ET6_SM	13 187 757	426 202	7 604 666	107 484
9月龄胎儿ET9_SM	13 353 677	1 151 579	9 490 944	221 957

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