Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages

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.

Automated summary

The study used ATAC-seq and rRNA-depleted RNA-seq to analyze the chromatin accessibility and transcriptional features in multiple tissues of newborn pigs and during porcine liver development. The researchers obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage, and found that tissue-specific accessible promoters were associated with active transcription and tissue-specific functions. Additionally, they observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. This study expands our understanding of epigenetic regulation in mammalian tissues and organ development.