Establishing the super-enhancer landscape in chicken adipose tissue

Enhancers are cis-regulatory elements that control spatiotemporal gene expression patterns. Super-enhancers (SEs), which function as clustered regulatory elements, play crucial roles in establishment and maintenance of cellular identity. Accumulating evidence highlights the importance of SEs in mammalian adipogenesis and fat deposition. However, adipocyte-specific SEs (ASSEs) in chicken adipose tissue have not been systematically characterized at the genome-wide level. In this study, we performed the Cleavage Under Targets and Tag mentation (CUT&Tag) profiling of H3K4me1, H3K27ac, and PPARγ binding in chicken adipose tissue. Integration of these three datasets led to the identification of 278 ASSEs, which were associated with 1,129 genes within ±100 kb window. Functional enrichment analysis revealed that these ASSE-associated genes (ASSEAGs) are implicated in key signaling pathways, including PI3K-Akt, PPAR, Hippo, and JAK-STAT. To evaluate the potential role of ASSEs in chicken adipose tissue, we intersected the ASSEAGs with the differentially expressed genes from abdominal adipose tissues of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). This analysis identified 93 overlapping genes. Furthermore, transcription factor binding site enrichment analysis showed significant overrepresentation of binding sites for PPARγ, C/EBPα, C/EBPβ, CTCF, EBF2, and KLFs within the ASSEs. Additionally, the identified ASSEs overlapped with 1,125 quantitative trait loci (QTLs) related to various chicken traits. Collectively, our findings provide a comprehensive characterization of chicken ASSEs and offer new insights into the regulatory mechanisms underlying adipogenesis and adipose tissue development in chickens.