Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [ATAC-seq]

Landscape of chromatin accessibility across tissues and developmental stages is essential to elucidate the transcriptional regulation in various biological processes and phenotypes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development have been seldomly investigated. Here, we profiled open chromatin maps and transcriptional features of the heart, kidney, liver, lung, skeletal muscle, and spleen tissues in newborn pigs and that of porcine liver tissue at suckling and adult stages using ATAC-seq and rRNA-depleted RNA-seq, respectively. Employing a union set of protein coding genes (PCGs) and two kinds of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue or developmental stage. The PCGs with tissue-specific accessible promoters, as expected, had active transcription and were relevant to tissue-specific functions. Other non-coding tissue-specific peaks were involved in both physical activities and morphogenesis in the 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 the understanding of epigenetic regulation in mammalian tissue functions and organ development, which can benefit both economic trait improvement and better biomedical use of pigs. We analyzed the chromatin accessibility and transcriptomic profiles for six tissues (heart, kidney, liver, lung, skeletal muscle [longissimus dorsi muscle], and spleen) of newborn (one-day-old) pigs, and characterized the dynamic chromatin accessibility and concomitant transcriptional changes in liver during development, i.e., from newborn to suckling at postnatal 28 days and adult at postnatal 180 days. We identified tissue-specific and stage-specific accessible regions, and found these segments played important regulatory roles in tissue-specific functions and hepatic function transition during development. Our study not only confirmed the transcriptional regulatory role of chromatin accessibility across promoter and other non-coding regions in tissue-specific physical activities and organ development, but also enriched the epigenetic profiling and genome regulation of pigs regarding diverse tissues and developmental stages.