DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (Cyprinus carpio)

文献类型： 外文期刊

第一作者： Yu, Shuang-Ting

作者： 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;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;Yu, Shuang-Ting

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关键词： polyploidy; subgenome expression; DNA methylation; chromatin accessibility; homoeologous gene

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：5.6； 五年影响因子：6.2 ）

ISSN： 1661-6596

年卷期： 2024 年 25 卷 3 期

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收录情况： SCI

摘要： 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.

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