Integrated ChIP-seq and RNA-seq analyses highlight critical roles of H3K4me3 in the sexual dimorphism and gonadal development of Paralichthys olivaceus

Abstract

Recently, epigenetic regulation has been shown to be important in the differentiation and development of fish gonads. Compared to the numerous studies focused on roles of DNA methylation, regulation of histone modification on fish sexual dimorphism and gonad development has been still scarcely studied. Thus, chromatin immunoprecipitation and sequencing (ChIP-seq) and RNA sequencing (RNA-seq) were conducted to comprehensively explore the epigenetic regulatory roles of H3K4me3 adjustments in sexual dimorphism and development of the Paralichthys olivaceus gonads in this study. A total of 13, 423 differential modified peaks (DMPs) were screened out. The DMPs were significantly enriched in regulating the actin cytoskeleton and the MAPK, Wnt, Calcium, and Activin signaling pathways. Transcriptome analysis identified 13, 660 differentially expressed genes (DEGs) in testes, which were enriched in several pathways (e.g., the cytokine-cytokine receptor interaction pathway, Cell adhesion molecules, steroid hormone biosynthesis, MAPK signaling pathway). Further integrated ChIP-seq and RNA-seq analyses determined 4, 444 genes overlapping with DEGs and DMPs. The overlapping genes with positive correlations between H3K4me3 and gene expression were enriched in multiple key sex-correlated KEGG pathways including the BMP signaling, Wnt signaling, MAPK signaling, and Steroid hormone biosynthesis. The regulatory role of H3K4me3 on the gene expressions was further verified by in vitro culture of gonadal tissues treated with a specific H3K4 methylation inhibitor (MTA), showing that inhibition of H3K4me3 modification significantly caused decreased expressions of nine sex-related genes ( daam2 , rspo2 , bmpr1a , acvr2a , mmp2 , sts , cyp17a , sox9 and dmrt1 ) in the MTA-treated testis, and seven sex-related genes ( daam2 , fbxw11 , bmpr1a , egfr , hsd17b1 , sts and dmrt1 ) in the MTA-treated ovary. This investigation systematically elucidated the epigenetic regulatory mechanism of H3K4me3 in the sexual dimorphism and gonad development in P. olivaceus , which will contribute to better understanding of teleost reproductive biology.

The authors' abstract, as published at the source. Aquaculture Reports, 2026 · DOI ↗