Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues

Abstract

Background A growing body of evidence has revealed that the mammalian genome is organized into hierarchical layers that are closely correlated with and may even be causally linked with variations in gene expression. Recent studies have characterized chromatin organization in various porcine tissues and cell types and compared them among species and during the early development of pigs. However, how chromatin organization differs among pig breeds is poorly understood. Results In this study, we investigated the 3D genome organization and performed transcriptome characterization of two adipose depots (upper layer of backfat [ULB] and greater omentum [GOM]) in wild boars and Bama pigs; the latter is a typical indigenous pig in China. We found that over 95% of the A/B compartments and topologically associating domains (TADs) are stable between wild boars and Bama pigs. In contrast, more than 70% of promoter-enhancer interactions (PEIs) are dynamic and widespread, involving over a thousand genes. Alterations in chromatin structure are associated with changes in the expression of genes that are involved in widespread biological functions such as basic cellular functions, endocrine function, energy metabolism and the immune response. Approximately 95% and 97% of the genes associated with reorganized A/B compartments and PEIs in the two pig breeds differed between GOM and ULB, respectively. Conclusions We reported 3D genome organization in adipose depots from different pig breeds. In a comparison of Bama pigs and wild boar, large-scale compartments and TADs were mostly conserved, while fine-scale PEIs were extensively reorganized. The chromatin architecture in these two pig breeds was reorganized in an adipose depot-specific manner. These results contribute to determining the regulatory mechanism of phenotypic differences between Bama pigs and wild boar.

Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis

“…In this study, we generated 11 in situ Hi-C libraries ( Table S1 ) using the same experimental protocols as the Hi-C dataset that we previously reported ( 87 ). Briefly, 1 g of ATs were cross-linked with a final concentration of 4% freshly prepared formaldehyde (Sigma Aldrich) for 30 min at room temperature, followed by quenching with glycine (Amresco) at a final concentration of 0.25 mol l −1 .…”

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig

“…The main emerging challenges for understanding the molecular mechanisms of specific expression patterns is to identify the transcriptional regulatory elements at a genome‐wide scale. Recently, the chromatin 3D genome architecture of porcine has been investigated in porcine LDM (Yuan et al, 2021) and adipose tissues (Zhang et al, 2022), using the Hi‐C method. The results indicate that A/B compartments and topologically associating domains are relatively stable and conserved in different pig breeds or embryonic development stages, but the promoter enhancer interactions are more dynamic and widespread.…”

A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

“…Studies have revealed that changes in 3D chromatin structure during growth and development, as well as long-range interactions within speci c breeds or tissues, play regulatory roles in gene expression [20]. In a comparison of Bama pigs and wild boar, chromatin architecture contributes to determining the regulatory mechanism of phenotypic differences between Bama pigs and wild boar [21]. Furthermore, the chromatin architecture had contributed to the analyses of pig phenotypes [9,22].…”