The super-enhancer repertoire in porcine liver

Three markers including H3K27ac, H3K4me1, and C-EBP beta were used to access and compare the characteristics of promoters, typical enhancers, and SEs in the porcine liver. The results provided novel insight on the locational, sequential, and functional, differences of cis-elements. The transcriptional initiation of genes is inextricably bound with the functions of cis-regulatory sequences. The pig is one of the most important livestock species and an ideal animal model for biomedical studies. At the same time, the liver is a critical organ with diverse and complex metabolic functions. Here, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with high-throughput sequencing to profile the chromatin landscape of histone H3 lysine 27 acetylation (H3K27ac), histone H3 lysine 4 monomethylation (H3K4me1), and CCAAT enhancer-binding protein beta (C-EBP beta) in the 70-d-old porcine liver, compared the different profiles among the three markers and their associated stitched-enhancers by stitching and sorting the peaks within 12.5 kb () and generated the porcine liver-specific super-enhancers (SEs) by the combination of three markers. Compared to typical enhancers (TEs) and other stitched-enhancers, liver-specific SEs showed a higher density of cis-motifs and SNPs, which may recruit more tissue-specific vital TFs. The expression profiles in fetal and 70-d-old pigs proved that a large proportion of SE-associated genes were up-regulated and were more related to hepatic metabolisms and detoxification pathways. Our results illustrated the difference and connection among promoter and enhancer markers, identified the features of liver SEs and their associated genes, and provided novel insight into cis-element identification, function, and liver transcriptional regulation. Lay Summary The cis-regulatory elements including promoters, enhancers, and newly identified super-enhancers (SEs), which were reported to function both promoter and enhancer capabilities, play critical roles in selective gene expression during development and disease. To reveal and compare the characteristics of these cis-elements in liver, we first performed a genome-wide profile of H3K27ac, H3K4me1, and C-EBP beta, then constructed their associated stitched-enhancers respectively. Porcine liver-specific SEs were generated by overlapping the three stitched-enhancers. The genomic and genic location, TF binding sites and SNP distribution patterns were compared among these cis-elements. We found that stitched-enhancers gather in regions with higher gene densities and locate closer to the transcription starting sites. Additionally, SEs showed higher density of TF binding sites and SNPs. To access the transcriptional consequences of liver SEs, we first analyzed the genes locationally associated with SEs. The KEGG results suggested that these genes are significantly involved in metabolisms, detoxification, and autophagy pathways. We also detected the liver gene expression profiles using RNA-seq and noticed that SE-associated genes are more likely to be up-regulated. Our results provided novel information on the identification, function, and transcriptional regulation of cis-elements in the liver.