DNA Methylation Difference between Female and Male Ussuri Catfish (Pseudobagrus ussuriensis) in Brain and Gonad Tissues

Abstract

DNA methylation has been found to be involved in sex determination and differentiation in many aquaculture species. The Ussuri catfish (Pseudobagrus ussuriensis) is a popular aquaculture fish in China with high economic value in which male-biased sex dimorphism was observed in terms of body size and body weight. In this study, DNA methylation-sensitive RAD sequencing (Methyl-RAD) was used to explore the epigenetic difference between adult male and female samples in brain and gonad tissues. In brain tissues, 5,442,496 methylated cytosine sites were found and 9.94% of these sites were from symmetric CCGG or CCWGG sites. Among these sites, 321 differential DNA methylation sites (DMSs) in 171 genes were identified, while in gonad tissues, 4,043,053 methylated cytosines sites were found in total and 11.70% of them were from CCGG or CCWGG. Among these sites, 78 differential DNA methylation sites were found which were located in 64 genes. We also found several sex-determination genes among these differential methylated genes, such as amh, gsdf and hsd11b2 in brain tissues and slco3a1, socs2 and trim47 in gonad tissues. These results provided evidence for understanding the function of DNA methylation in the sex differentiation in Pseudobagrus ussuriensis, which further deepens the relationship between gene regulation and epigenetics.

DNA methylation difference in the liver of a fish with female-biased sexual-size dimorphism, Ancherythroculter nigrocauda

“…Previous study also reported this pattern in gonad tissue of another sh with female-biased SSD, Cynoglossus semilaevis [36]. But no whole genome methylation difference was found in brain tissue between different sexes of Ussuri cat sh (Pseudobagrus ussuriensis), which might be caused by the tissue-speci c gene expression and regulation [25]. Differentially methylated gene analysis showed that there are 1,137 DMGs with more than 3…”

“…In this study, we used MethylRAD to study the epigenetic difference between female and male liver tissue for Ancherythroculter nigrocauda, a sh with female-biased SSD. MethylRAD had been used in many epigenetic studies which aimed at nding methylation difference between various phenotypes [25,35]. It has many advantages compared with whole genome bisul te sequencing or reduced represented bisul te sequencing, such as it doesn't need to convert m C to T before library construction.…”

“…And only methylation sites with more than 3 reads in at least 6 samples were kept in following differential methylation analysis. Differential methylated sites (DMSs) were identi ed with qCML method in R package edgeR between male and female group [24,25]. Genes with more than 3 DMSs in the 2kb upstream of transcript start site were kept as differential methylated genes in this study [26].…”

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

“…Such induced expression was found to be regulated by DNA methylation ( Veron et al, 2018 ). Similarly, reduced levels of methylation in the promoter regions of STAT3 and VEGFA genes were found to be correlated with their increased expression under hypoxic conditions ( Li et al, 2022a ).…”

Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback

“…Seven genes are involved in gene expression modulation and affect either DNA methylation, transcription, or alternative splicing. If fish, sex-specific methylation is known for its role in modulating the expression level of reproduction-related genes (Laing et al, 2018;Li, Chen, et al, 2022) and in sex determinism (Gemmell et al 2019). Similarly, sex-specific transcript usage can provide an alternative route from gene regulation to generate sexual dimorphism (Telonis- Scott et al, 2009;Naftaly et al, 2021).…”