Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver

• Published in: Biomolecules (Basel, Switzerland) Switzerland), 2024-04, Vol.14 (4), p.427
• Main Authors: Chan, Shuheng, Wang, Yubei, Luo, Yabiao, Zheng, Meili, Xie, Fuyin, Xue, Mingming, Yang, Xiaoyang, Xue, Pengxiang, Zha, Chengwan, Fang, Meiying
• Format: Article
• Language: English
• Subjects: Adipose tissue; Adipose tissues; Agricultural research; Analysis; Androst-16-en-3-one; androstenone metabolism; Animals; Boars; Body fat; Castration; Chromatin; Chromatin - genetics; Chromatin - metabolism; enhancer; Enhancer Elements, Genetic - genetics; Enhancers; Food contamination; Gene expression; Gene Expression Regulation; Gene Regulatory Networks; Genes; Genetic aspects; Genetic transcription; Genomes; Hogs; Hormones; HSD3B1; Internet resources; Liver; Liver - metabolism; Male; Males; Meat; Meat quality; Metabolic regulation; Metabolism; Physiological aspects; Pork; Production processes; Quality; Quality control; regulatory factors; RNA; SP1; Steroid hormones; surgical castration; Swine; Testis - metabolism; Transcriptome
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom14040427

Surgical castration can effectively avoid boar taint and improve pork quality by removing the synthesis of androstenone in the testis, thereby reducing its deposition in adipose tissue. The expression of genes involved in testis-derived hormone metabolism was altered following surgical castration, but the upstream regulatory factors and underlying mechanism remain unclear. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics in liver tissue of castrated and intact full-sibling Yorkshire pigs. First, we identified 897 differentially expressed genes and 6864 differential accessible regions (DARs) using RNA- and ATAC-seq. By integrating the RNA- and ATAC-seq results, 227 genes were identified, and a significant positive correlation was revealed between differential gene expression and the ATAC-seq signal. We constructed a transcription factor regulatory network after motif analysis of DARs and identified a candidate transcription factor (TF) that targeted the gene, which was responsible for the metabolism of androstenone. Subsequently, we annotated DARs by incorporating H3K27ac ChIP-seq data, marking 2234 typical enhancers and 245 super enhancers involved in the regulation of all testis-derived hormones. Among these, four typical enhancers associated with were identified. Furthermore, an in-depth investigation was conducted on the androstenone-related enhancers, and an androstenone-related mutation was identified in a newfound candidatetypical enhancer (andEN) with dual-luciferase assays. These findings provide further insights into how enhancers function as links between phenotypic and non-coding area variations. The discovery of upstream TF and enhancers of contributes to understanding the regulatory networks of androstenone metabolism and provides an important foundation for improving pork quality.