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Article

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

by
Shuang-Ting Yu
1,2,
Ran Zhao
1,
Xiao-Qing Sun
1,
Ming-Xi Hou
1,
Yi-Ming Cao
1,
Jin Zhang
1,
Ying-Jie Chen
1,
Kai-Kuo Wang
1,
Yan Zhang
1,
Jiong-Tang Li
1,* and
Qi Wang
1,*
1
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
2
Chinese Academy of Agricultural Sciences, Beijing 100081, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(3), 1635; https://doi.org/10.3390/ijms25031635
Submission received: 23 December 2023 / Revised: 19 January 2024 / Accepted: 23 January 2024 / Published: 29 January 2024
(This article belongs to the Special Issue Molecular Advance on Reproduction and Fertility of Aquatic Animals)
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Abstract

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.
Keywords: polyploidy; subgenome expression; DNA methylation; chromatin accessibility; homoeologous gene polyploidy; subgenome expression; DNA methylation; chromatin accessibility; homoeologous gene

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MDPI and ACS Style

Yu, S.-T.; Zhao, R.; Sun, X.-Q.; Hou, M.-X.; Cao, Y.-M.; Zhang, J.; Chen, Y.-J.; Wang, K.-K.; Zhang, Y.; Li, J.-T.; et al. DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (Cyprinus carpio). Int. J. Mol. Sci. 2024, 25, 1635. https://doi.org/10.3390/ijms25031635

AMA Style

Yu S-T, Zhao R, Sun X-Q, Hou M-X, Cao Y-M, Zhang J, Chen Y-J, Wang K-K, Zhang Y, Li J-T, et al. DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (Cyprinus carpio). International Journal of Molecular Sciences. 2024; 25(3):1635. https://doi.org/10.3390/ijms25031635

Chicago/Turabian Style

Yu, Shuang-Ting, Ran Zhao, Xiao-Qing Sun, Ming-Xi Hou, Yi-Ming Cao, Jin Zhang, Ying-Jie Chen, Kai-Kuo Wang, Yan Zhang, Jiong-Tang Li, and et al. 2024. "DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (Cyprinus carpio)" International Journal of Molecular Sciences 25, no. 3: 1635. https://doi.org/10.3390/ijms25031635

APA Style

Yu, S.-T., Zhao, R., Sun, X.-Q., Hou, M.-X., Cao, Y.-M., Zhang, J., Chen, Y.-J., Wang, K.-K., Zhang, Y., Li, J.-T., & Wang, Q. (2024). DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (Cyprinus carpio). International Journal of Molecular Sciences, 25(3), 1635. https://doi.org/10.3390/ijms25031635

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