Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Int J Mol Sci. 2023 Dec 21;25(1):158. doi: 10.3390/ijms25010158.
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (, , and ) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
在出生后阶段，骨骼肌发育经历一系列精细调节的基因表达变化。然而，很少有研究利用染色质可及性来揭示控制牦牛物种肌肉发育的潜在分子机制。因此，我们进行了基因表达水平和染色质可及性分析，以全面描述天祝白牦牛肌肉生长和发育过程中全基因组染色质可及性的动态变化，从而阐明整个过程中可及染色质区域的特征。最初，我们比较了两组之间染色质可及性的差异，发现小牛的染色质可及性水平高于成年牛，特别是在转录起始位点（TSS）±2 kb 内。为了研究染色质可及区域的变化与基因表达水平变化之间的相关性，我们采用了 ATAC-seq 和 RNA-seq 技术的组合，鉴定出 18 个核心转录因子（TFs）和 110 个具有显著影响的关键基因。通过进一步分析，我们成功鉴定了几个 TF，包括 Sp1、YY1、MyoG、MEF2A 和 MEF2C，以及一些候选基因（、、和），它们可能与肌肉生长和发育密切相关。此外，我们构建了一个包含与肌肉生长和发育相关的枢纽 TF 和关键基因的交互式网络程序。这种创新方法为天祝白牦牛出生后阶段骨骼肌发育的分子机制提供了有价值的见解，为未来的牦牛肌肉发育研究奠定了坚实的理论基础。
