Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination

The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between cyp19a1a methylation and expression is relevant to the epigenetic regulation of vertebrate sex, and we report the evidence of such relationship only below a methylation threshold, ~ 80%, and that it was sex-specific: negatively correlated in females but positively correlated in males. From parents to offspring, the methylation in gonads was midway between oocytes and sperm, with bias towards oocytes for amh-r2, er-β2, fsh-r and cyp19a1a. In contrast, dmrt1 levels resembled those of sperm. The methylation of individual CpGs from foxl2, er-β2 and nr3c1 were conserved from parents to offspring, whereas those of cyp19a1a, dmrt1 and amh-r2 were affected by temperature. Utilizing a machine-learning procedure based on the methylation levels of a selected set of CpGs, we present the first, to our knowledge, system based on epigenetic marks capable of predicting sex in an animal with ~ 90% accuracy and discuss possible applications.

将基因组与环境影响整合至甲基化模式以产生表型，是发育表观遗传学的核心研究议题，但诸多细节仍未明确。本研究使用的物种欧洲海鲈（European sea bass）的性比由遗传因素与温度共同决定。我们从已知可产生不同性比后代的亲本中构建了4个家系，将幼鱼暴露于雄性化温度环境中，并通过靶向测序技术检测了幼鱼性腺中7个与性发育相关基因的DNA甲基化水平。受遗传与环境共同影响最显著的基因为cyp19a1a与dmrt1，二者呈现出截然相反的性别特异性甲基化模式与温度响应特征。cyp19a1a的甲基化与表达量之间的关联与脊椎动物性别表观调控密切相关，本研究发现该关联仅在甲基化水平低于约80%的阈值时存在，且具有性别特异性：在雌性中呈负相关，而在雄性中呈正相关。从亲本到子代，性腺甲基化水平介于卵母细胞与精子之间；其中amh-r2、er-β2、fsh-r与cyp19a1a的甲基化偏向卵母细胞，而dmrt1的甲基化水平则与精子相近。foxl2、er-β2与nr3c1的单个CpG位点甲基化水平在亲子代间具有保守性，而cyp19a1a、dmrt1与amh-r2的甲基化则受温度影响。本研究基于一组筛选出的CpG位点甲基化水平构建了机器学习流程，据我们所知，这是首个基于表观遗传标记、可在动物中以约90%的准确率预测性别的系统，并对其潜在应用场景进行了讨论。