Integration of ATAC-seq and RNA-seq unravels chromatin accessibility associated with gonad development after sex reversal in GIFT tilapia

The epigenetic mechanisms regulating gonadal development and maintenance in fish following hormone-induced sex reversal remain poorly understood. In order to address this knowledge gap, an integrated multi-omics analysis was conducted in GIFT tilapia . The present study compared three distinct groups: normal females (CF; genetically female, XX), normal males (CM; genetically male, XY), and pseudo-females (S; estrogen-treated genetically males, XY). The S group demonstrated intermediate growth traits and sex hormone levels that fell between those observed in the CF and CM groups. In comparison with the CF group, the S group exhibited delayed development, characterized by diminished ovarian volume, reduced oocyte numbers, and diminished oocyte quality. ATAC-seq analysis revealed unique patterns of chromatin accessibility in pseudo-female gonads, thus identifying key transcription factors, including ZNF148, ZNF281, and SP9. Integration of chromatin accessibility changes with transcriptional reprogramming has been shown to result in the identification of co-regulated genes that are enriched in critical pathways, including binding and catalytic activities, apoptosis, metabolism, and homologous recombination. Subsequent analysis identified several genes associated with gonadal development, including ncoa4 and gdf9 . It is noteworthy that ncoa4 emerged as a potential core hub gene whose expression correlates with the enrichment of ZNF148/SP9 motifs and alterations in chromatin accessibility. This gene may interact with other factors, such as esr2 , to potentially influence oocyte development. These findings may provide new insights into the epigenetic and transcriptional regulatory mechanisms associated with gonadal development following sex reversal, thereby laying a theoretical foundation for the optimization of sex control strategies in aquaculture. • Pseudo-females exhibit an incomplete ovarian phenotype and a distinct intermolecular state, differing from both normal sexes. • Integrating ATAC-seq and RNA-seq to identify key differentially expressed genes and their potential cis-regulatory elements in ovarian development of female fish following exploratory reversal. • A regulatory network centered on ZNF148 and SP9 was constructed with ncoa4 as the core, regulating gonadal development.