PDF(Pubmed)
Abstract：
Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are limited. In this study, we conducted the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and Bisulfite sequencing (BS-seq) to explore the roles of epigenetic modifications in the common carp gonads. We identified 84,207 more accessible regions and 77,922 less accessible regions in ovaries compared to testes, and some sex-biased genes showed differential chromatin accessibility in their promoter regions, such as sox9a and zp3. Motif enrichment analysis showed that transcription factors (TFs) associated with embryonic development and cell proliferation were heavily enriched in ovaries, and the TFs Foxl2 and SF1 were only identified in ovaries. We also analyzed the possible regulations between chromatin accessibility and gene expression. By BS-seq, we identified 2087 promoter differentially methylated genes (promoter-DMGs) and 5264 gene body differentially methylated genes (genebody-DMGs) in CG contexts. These genebody-DMGs were significantly enriched in the Wnt signaling pathway, TGF-beta signaling pathway, and GnRH signaling pathway, indicating that methylation in gene body regions could play an essential role in sex maintenance, just like methylation in promoter regions. Combined with transcriptomes, we revealed that the expression of dmrtb1-like, spag6, and fels was negatively correlated with their methylation levels in promoter regions. Our study on the epigenetic modifications of gonads contributes to elucidating the molecular mechanism of sex differentiation and sex maintenance in the common carp.
摘要：
表观遗传修饰对于精确调节基因表达至关重要。鲤鱼（Cyprinuscarpio）是经济上重要的鱼类，女性的生长速度比男性快。然而,与鲤鱼性腺表观遗传修饰相关的研究是有限的。在这项研究中,我们进行了转座酶可访问染色质测序（ATAC-seq）和亚硫酸氢盐测序（BS-seq）测定，以探讨表观遗传修饰在鲤鱼性腺中的作用。与睾丸相比，我们在卵巢中确定了84,207个更容易进入的区域和77,922个较少进入的区域。一些性别偏倚的基因在其启动子区域显示出不同的染色质可及性，如sox9a和zp3。基序富集分析表明,与胚胎发育和细胞增殖相关的转录因子(TFs)在卵巢中大量富集,仅在卵巢中鉴定了TFsFoxl2和SF1。我们还分析了染色质可及性与基因表达之间的可能调节。通过BS-seq，我们在CG环境中鉴定了2087个启动子差异甲基化基因(启动子-DMGs)和5264个基因体差异甲基化基因(基因体-DMGs)。这些遗传体DMGs在Wnt信号通路中显著富集,TGF-β信号通路,和GnRH信号通路，表明基因体区的甲基化可能在性别维持中起重要作用，就像启动子区域的甲基化一样。结合转录组，我们揭示了dmrtb1-like的表达，spag6和fels与启动子区域的甲基化水平呈负相关。我们对性腺表观遗传修饰的研究有助于阐明鲤鱼性别分化和性别维持的分子机制。
