Yu Shuang-Ting, Zhao Ran, Sun Xiao-Qing, Hou Ming-Xi, Cao Yi-Ming, Zhang Jin, Chen Ying-Jie, Wang Kai-Kuo, Zhang Yan, Li Jiong-Tang, Wang Qi
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China.
Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Int J Mol Sci. 2024 Jan 29;25(3):1635. doi: 10.3390/ijms25031635.
DNA methylation and chromatin accessibility play important roles in gene expression, but their function in subgenome expression dominance remains largely unknown. We conducted comprehensive analyses of the transcriptome, DNA methylation, and chromatin accessibility in liver and muscle tissues of allotetraploid common carp, aiming to reveal the function of epigenetic modifications in subgenome expression dominance. A noteworthy overlap in differential expressed genes (DEGs) as well as their functions was observed across the two subgenomes. In the promoter and gene body, the DNA methylation level of the B subgenome was significantly different than that of the A subgenome. Nevertheless, differences in DNA methylation did not align with changes in homoeologous biased expression across liver and muscle tissues. Moreover, the B subgenome exhibited a higher prevalence of open chromatin regions and greater chromatin accessibility, in comparison to the A subgenome. The expression levels of genes located proximally to open chromatin regions were significantly higher than others. Genes with higher chromatin accessibility in the B subgenome exhibited significantly elevated expression levels compared to the A subgenome. Contrastingly, genes without accessibility exhibited similar expression levels in both subgenomes. This study contributes to understanding the regulation of subgenome expression dominance in allotetraploid common carp.
DNA甲基化和染色质可及性在基因表达中发挥重要作用，但其在亚基因组表达优势中的功能仍 largely 未知。我们对异源四倍体鲤鱼肝脏和肌肉组织中的转录组、DNA甲基化和染色质可及性进行了全面分析，旨在揭示表观遗传修饰在亚基因组表达优势中的功能。在两个亚基因组中观察到差异表达基因（DEGs）及其功能存在显著重叠。在启动子和基因体中，B亚基因组的DNA甲基化水平与A亚基因组显著不同。然而，DNA甲基化的差异与肝脏和肌肉组织中同源偏倚表达的变化并不一致。此外，与A亚基因组相比，B亚基因组表现出更高比例的开放染色质区域和更大的染色质可及性。位于开放染色质区域附近的基因表达水平显著高于其他基因。与A亚基因组相比，B亚基因组中具有更高染色质可及性的基因表现出显著升高的表达水平。相反，无可及性的基因在两个亚基因组中的表达水平相似。本研究有助于理解异源四倍体鲤鱼亚基因组表达优势的调控。
