Yu Congying, Zhong Bingzhou, Zhang Yuqiao, Zhao Haiquan, Wu Jinhua, Yu Haiyi, Yu Hui, Li Hua
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Animal Science and Technology College, Foshan University, Foshan, Guangdong, 528225, China.
Zhongshan Baishi Pig Farm Co., Ltd.r, Zhongshan, 528463, China.
BMC Genomics. 2025 May 6;26(1):447. doi: 10.1186/s12864-025-11613-x.
Disorders of Sex Development (DSD) are caused by congenital abnormalities in the chromosomes, and subsequent development of gonads or sexual anatomy. XX-DSD pigs exhibit a series of adverse symptoms such as sterility, genital infections, and decline in meat quality, leading to significant economic losses in the breeding industry. However, the understanding of the etiology and pathogenesis of XX-DSD in pigs remains limited. To investigate the molecular mechanisms underlying abnormal gonadal development in XX-DSD pigs, we analyzed the gonads of 1-month-old XX-DSD pigs, normal females, and normal males using RNA-seq and ATAC-seq techniques.
From RNA-seq, we identified potential genes involved in gonadal development in XX-DSD pigs, including SOX9, HSD3B1, CYP19A1, CCNB2, CYP11A1, DMRT1, and MGP. Following this, we analyzed ATAC-seq data and identified 14,820 differential accessible chromatin peaks. Then, by integrating the ATAC-seq and RNA-seq analysis results, we identified several candidate genes (SOX9, COL1A1, COL1A2, FDX1, COL6A1, HSD3B1, FSHR, and CYP17A1) that might be associated with sex development. Through PPI (Protein-Protein Interaction Networks) analysis, we found that SOX9 gene was the top hub gene. Furthermore, we confirmed the effect of the open chromatin region on SOX9 gene expression by a dual-luciferase reporter assay, thus further validating the critical role of this open region in regulating SOX9 expression.
This study elucidates the critical regulatory role of specific open chromatin structures in the SOX9 gene promoter region (8647563-8648475) in gonadal development of XX-DSD pigs. Additionally, we identify that genes such as SOX9, HSD3B1, and CYP19A1 act in concert to participate in gonadal development. These findings provide molecular evidence for the dynamic chromatin regulatory network underlying gonadal dysgenesis in XX-DSD and lay the foundation for subsequent mechanistic studies.
性发育障碍（DSD）由染色体先天性异常以及随后性腺或性解剖结构的发育异常引起。XX-DSD猪表现出一系列不良症状，如不育、生殖器感染和肉质下降，给养殖业造成重大经济损失。然而，对猪XX-DSD的病因和发病机制的了解仍然有限。为了研究XX-DSD猪性腺发育异常的分子机制，我们使用RNA测序（RNA-seq）和染色质转座酶可及性测序（ATAC-seq）技术分析了1月龄XX-DSD猪、正常雌性猪和正常雄性猪的性腺。
通过RNA测序，我们鉴定出参与XX-DSD猪性腺发育的潜在基因，包括SOX9、HSD3B1、CYP19A1、CCNB2、CYP11A1、DMRT1和MGP。随后，我们分析了ATAC-seq数据，鉴定出14820个差异可及染色质峰。然后，通过整合ATAC-seq和RNA-seq分析结果，我们鉴定出几个可能与性发育相关的候选基因（SOX9、COL1A1、COL1A2、FDX1、COL6A1、HSD3B1、FSHR和CYP17A1）。通过蛋白质-蛋白质相互作用网络（PPI）分析，我们发现SOX9基因是首要的枢纽基因。此外，我们通过双荧光素酶报告基因检测证实了开放染色质区域对SOX9基因表达的影响，从而进一步验证了该开放区域在调节SOX9表达中的关键作用。
本研究阐明了特定开放染色质结构在XX-DSD猪性腺发育中对SOX9基因启动子区域（8647563-8648475）的关键调控作用。此外，我们确定SOX9、HSD3B1和CYP19A1等基因协同作用参与性腺发育。这些发现为XX-DSD中性腺发育异常的动态染色质调控网络提供了分子证据，并为后续的机制研究奠定了基础。
