Tan Wenhua, Liu Chenxi, Liu Juan, Wen Sheng, Chen Yantong, Ren Ruimin, Gao Ning, Ding Xiaoling, He Jun, Zhang Yuebo
Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Yuelushan Laboratory, Changsha 410128, China.
Int J Mol Sci. 2025 Mar 14;26(6):2634. doi: 10.3390/ijms26062634.
Meat production traits in pigs are critical economic characteristics, primarily influenced by the formation and development of skeletal muscle. Skeletal muscle development is regulated by a complex transcriptional network, which partly relies on chromatin accessibility for initiation. Ningxiang pigs, a renowned Chinese indigenous breed, are highly valued for their tender meat. However, studies focusing on skeletal muscle development in Ningxiang pigs, particularly from the perspective of chromatin accessibility, have not yet been reported. Based on this, the present study selected several key time points in the skeletal muscle development of Ningxiang pigs to perform Transposase-Accessible Chromatin Sequencing (ATAC-seq) and RNA sequencing (RNA-seq). This was carried out to identify key open chromatin regions and genes during different growth stages, which could influence skeletal muscle development in Ningxiang pigs. We collected longissimus dorsi muscle samples at postnatal days 14 (D14), 28 (D28), 85 (D85), 165 (D165), and 250 (D250). For each age, three individuals were collected for ATAC-seq and RNA-seq. After initial differential analysis among different ages, we identified 6412 differentially accessible chromatin peaks and 1464 differentially expressed genes. To clarify the key candidate transcription factors affecting the development of skeletal muscle in Ningxiang pigs, motif analysis of differential peaks revealed potential cis-regulatory elements with binding sites for transcription factors, including and . Correlation analysis identified 56 overlapping genes and a significant positive correlation (r = 0.73, = 1 × 10) between gene expression and chromatin accessibility. Key candidate genes such as , closely related to skeletal muscle development, were specifically examined. These results enhance our understanding of the genetic and epigenetic regulatory mechanisms of porcine skeletal muscle development, providing a robust foundation for future molecular studies.
猪的肉用生产性状是关键的经济特征，主要受骨骼肌的形成和发育影响。骨骼肌发育由一个复杂的转录网络调控，该网络部分依赖于染色质可及性来启动。宁乡猪是中国著名的本土品种，以其肉质鲜嫩而备受重视。然而，尚未有针对宁乡猪骨骼肌发育，特别是从染色质可及性角度进行的研究报道。基于此，本研究选取了宁乡猪骨骼肌发育的几个关键时间点进行转座酶可及染色质测序（ATAC-seq）和RNA测序（RNA-seq）。这样做是为了确定不同生长阶段影响宁乡猪骨骼肌发育的关键开放染色质区域和基因。我们在出生后第14天（D14）、28天（D28）、85天（D85）、165天（D165）和250天（D250）采集背最长肌样本。对于每个年龄段，采集三只个体进行ATAC-seq和RNA-seq。在对不同年龄进行初步差异分析后，我们鉴定出6412个差异可及染色质峰和1464个差异表达基因。为了阐明影响宁乡猪骨骼肌发育的关键候选转录因子，对差异峰进行基序分析，揭示了具有转录因子结合位点的潜在顺式调控元件，包括 和 。相关性分析确定了56个重叠基因，并且基因表达与染色质可及性之间存在显著正相关（r = 0.73， = 1 × 10）。对与骨骼肌发育密切相关的关键候选基因如 进行了专门研究。这些结果加深了我们对猪骨骼肌发育的遗传和表观遗传调控机制的理解，为未来的分子研究提供了坚实的基础。
