Wang Jianfang, Li Bingzhi, Yang Xinran, Liang Chengcheng, Raza Sayed Haidar Abbas, Pan Yueting, Zhang Ke, Zan Linsen
College of Animal Science and Technology, Northwest A&F University, Xianyang, China.
National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China.
Front Vet Sci. 2022 Aug 11;9:925590. doi: 10.3389/fvets.2022.925590. eCollection 2022.
As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (ME) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including , and . This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.
作为家畜的主要产物，肌肉本身在维持动物身体运动和调节新陈代谢方面发挥着不可替代的作用。因此，探索其生长、发育和再生对于提高家畜的肉产量和质量具有重要意义。在本研究中，我们试图利用RNA测序和ATAC测序技术来鉴定在牛骨骼肌中特异性表达的差异表达基因（DEG），作为研究肌肉发育调控机制的潜在候选基因。从GEO数据库中选择了8个组织样本的微阵列数据进行分析。首先，我们通过WGCNA分析获得了与每个组织相关的基因模块。通过基因本体（GO）功能注释，浅黄模块（ME）与肌肉发育密切相关，筛选出213个中心基因作为后续研究靶点。进一步的差异分析表明，除PREB外，所有其他候选中心基因均上调（肌肉组与其他组相比）。ATAC测序分析表明，肌肉特异性可及染色质区域主要位于与肌肉结构发育（GO:0061061）、肌肉细胞发育（GO:0055001）和肌肉系统过程（GO:0003012）相关的基因启动子区域，这些区域参与cAMP、CGMP-PKG、MAPK等信号通路。接下来，我们整合了RNA测序和ATAC测序分析的结果，212个候选中心基因中的54个被鉴定为骨骼肌发育中的关键调控基因。最后，通过基序分析，发现54个关键基因中的22个是转录因子MEF2C的潜在靶基因。包括 ，以及 。这为研究哺乳动物骨骼肌发育的分子机制提供了潜在参考。
