Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Int J Mol Sci. 2023 Jul 4;24(13):11076. doi: 10.3390/ijms241311076.
The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, we used ATAC-seq and rRNA-depleted RNA-seq to profile open chromatin maps and transcriptional features of heart, kidney, liver, lung, skeletal muscle, and spleen in newborn pigs and porcine liver tissue in the suckling and adult stages, respectively. Specifically, by analyzing a union set of protein-coding genes (PCGs) and two types of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage. As expected, the PCGs with tissue-specific accessible promoters had active transcription and were relevant to tissue-specific functions. In addition, other non-coding tissue-specific peaks were involved in both physical activity and the morphogenesis of neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands our current understanding of epigenetic regulation in mammalian tissues and organ development, which can benefit both economic trait improvement and improve the biomedical usage of pigs.
研究不同组织和发育阶段的染色质可及性对于阐明各种表型和生物过程的转录调控至关重要。然而，新生猪多个组织和猪肝脏发育过程中的染色质可及性图谱仍未得到充分研究。在这里，我们使用 ATAC-seq 和 rRNA 耗尽 RNA-seq 分别对新生猪心脏、肾脏、肝脏、肺、骨骼肌和脾脏的开放染色质图谱和转录特征，以及哺乳期和成年期猪肝脏组织进行了分析。具体来说，通过分析一个包含蛋白质编码基因（PCGs）和两种类型转录本（lncRNAs 和 TUCPs）的联合数据集，我们获得了每个组织和发育阶段的共识 ATAC-seq 峰的全面注释。正如预期的那样，具有组织特异性可及启动子的 PCGs 具有活跃的转录，并与组织特异性功能相关。此外，其他非编码组织特异性峰参与了新生组织的物理活动和形态发生。我们还对阶段特异性峰进行了表征，并观察到染色质可及性的动态与肝内发育过程中肝功能的转变密切相关。总的来说，这项研究扩展了我们对哺乳动物组织和器官发育中表观遗传调控的现有认识，这对经济性状的改良和猪在生物医学中的应用都有好处。
