Integrated chromatin accessibility and DNA methylation analysis to reveal the critical epigenetic modification and regulatory mechanism in gonadal differentiation of the sequentially hermaphroditic fish, Monopterus albus

Abstract

Background Monopterus albus is a hermaphroditic and economically farmed fish that undergoes sex reversal from ovary to testis via ovotestis during gonadal development. The epigenetic changes that are associated with gonadal development in this species remain unclear. Methods We produced DNA methylome, transcriptome, and chromatin accessibility maps of the key stages of gonad development: ovary, ovotestis, and testis. The expression of the key candidate genes was detected using qRT-PCR and in situ hybridization and the methylation levels were analysed using bisulphite sequencing PCR. Promoter activity and regulation were assessed using dual-luciferase reporter assays. Results Gonadal development exhibits highly dynamic transcriptomic, DNA methylation, and chromatin accessibility changes. We found that DNA methylation status, especially of the transcription start site, was significantly negatively correlated with gene expression while chromatin accessibility exhibited no correlation with gene expression during gonadal development. The epigenetic signatures revealed many novel regulatory elements and genes involved in sex reversal, which were validated. DNA methylation detection and site mutation of plastin-2 promoter, as a candidate gene, revealed that DNA methylation could impact the binding of transcription factor dmrt1 and foxl2 through methylation and demethylation to regulate plastin-2 expression during gonadal development. Conclusions These data provide novel insights into epigenetic modification and help elucidate the potential molecular mechanism by which dynamic modification of DNA methylation plays a crucial role in gonadal development.

Analysis of Chromatin Accessibility and DNA Methylation to Reveal the Functions of Epigenetic Modifications in Cyprinus carpio Gonads

“…Chromatin accessibility reflects the regulatory capacity of gene expression, which is involved in various biological processes. Chromatin accessibility varies considerably between ovaries and testes [ 35 , 36 ]. In the common carp, our ATAC-seq data analysis identified 120,701 peaks in ovaries and 193,469 peaks in testes, respectively.…”

Regulatory mechanism of LncRNAs in gonadal differentiation of hermaphroditic fish, Monopterus albus

“…17α-methyltestosterone (MT) was used to treat M. albus at 60 dpf to produce sex reversal in M. albus as described in previous studies[ 26 ], and no treatment was applied to the control group. Larvae were immersed in water containing MT at concentrations of 100 µg/L (MT1), 200 µg/L (MT2) and 300 µg/L (MT3) for approximately 12 h daily.…”