Genome-Wide DNA Methylation and Transcriptome Analyses Reveal Epigenetic and Genetic Mechanisms Underlying Sex Maintenance of Adult Chinese Alligator

Abstract

The sexes of Chinese alligators are determined during embryonic development and remain fixed thereafter. In this study, we investigated the genetic and epigenetic mechanisms underlying sex maintenance in Chinese alligators through RNA sequencing and bisulfite sequencing data analyses of the adult gonads. We identified the genes and pathways (e. g., DMRT1-SOX9-AMH pathway for males and oocyte meiotic maturation pathway for females) involved in male and female sex maintenance and gonadal development of adult Chinese alligators. In contrast to their expression patterns in the embryo, both DMRT1 and the steroid hormone biosynthesis related genes showed a male-biased expression in adult gonads. The overall DNA methylation density and level were higher in testes than in ovaries. Hypermethylation in the gene bodies enhanced the expression of male-biased genes (such as DMRT1-SOX9-AMH and steroid hormone biosynthesis related genes) in the testis, as opposed to the normalization of gene expression. Our results provide insights into the genetic and epigenetic mechanisms underlying sex maintenance in adult Chinese alligators, and are expected to contribute to the development of scientific programs for the successful conservation of this endangered species.

Sex-Biased miRNAs in the Gonads of Adult Chinese Alligator (Alligator sinensis) and Their Potential Roles in Sex Maintenance

“…In silico analysis revealed that 1,659 and 2,719 genes were targeted by 13 female-biased and 50 male-biased miRNAs, respectively. Previously, we identified sex-biased differentially expressed genes (DEGs) in Chinese alligator gonads by transcriptome analysis ( Lin et al, 2021 ). Here, we constructed interaction networks of DEmiRs and DEGs ( Figure 6 ).…”

“…Previously, we constructed the oocyte meiosis, steroid biosynthesis, and antagonistic sex maintenance pathway in the gonads of Chinese alligator ( Lin et al, 2021 ). However, we found that most of the target genes of sex-biased DEmiRs were concentrated in the previously constructed oocyte meiosis pathways, and a small number appear in the mutually antagonistic sex maintenance pathways, while hardly any appear in the steroid biosynthesis pathways.…”

“…Therefore, the Chinese alligator is a suitable biological model to study temperature-dependent sex determination, differentiation, and maintenance. Our previous studies on the gonads of the Chinese alligator have mainly focused on the process of sex differentiation in the embryonic stage ( Lin et al, 2018 ), the importance of hibernation to ovarian development ( Lin et al, 2020 ), and the genetic and epigenetic mechanisms of sex maintenance ( Lin et al, 2021 ). The default sex of the Chinese alligator embryo is female and the male determination is triggered by high temperature through calcium signals in the middle of the TSP, while miRNA also participates in the regulation of this process ( Lin et al, 2018 ).…”

“…The default sex of the Chinese alligator embryo is female and the male determination is triggered by high temperature through calcium signals in the middle of the TSP, while miRNA also participates in the regulation of this process ( Lin et al, 2018 ). The DMRT1 and steroid biosynthesis pathways in adult Chinese alligators show male-biased expression and maintain male sex ( Lin et al, 2021 ). However, the roles of miRNA in sexual dimorphism and gonadal sex maintenance in adult Chinese alligators is still unclear.…”

Comparison of Genome-Wide DNA Methylation Profiles of Human Fetal Tissues Conceived by in vitro Fertilization and Natural Conception

“…The Circos plot was used by the Bioconductor OmicCircos package into R environment (Hu et al, 2014b). The violin graphs were plotted using ggplot2 package (Hu, 2020;Lin et al, 2021). The heatmap with the use of "heatmap" package, after data preprocessing and normalization, was plotted to identify clusters between samples.…”