Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs

Abstract

The epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in the pituitary gland of adult Bama Xiang and Large White pigs, which have divergent evolutionary histories and large phenotypic differences. We identified a total of 65,044 non-redundant regulatory regions, including 23,680 H3K4me3 peaks and 61,791 H3K27ac peaks (12,318 proximal and 49,473 distal), augmenting the catalog of pituitary regulatory elements in pigs. We found 793 H3K4me3 and 3,602 H3K27ac peaks that show differential activity between the two breeds, overlapping with genes involved in the Notch signaling pathway, response to growth hormone (GH), thyroid hormone signaling pathway, and immune system, and enriched for binding motifs of transcription factors (TFs), including JunB, ATF3, FRA1, and BATF. We further identified 2,025 non-redundant super enhancers from H3K27ac ChIP-seq data, among which 302 were shared in all samples of cover genes enriched for biological processes related to pituitary function. This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs.