6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication

文献类型： 外文期刊

第一作者： Zhang, Yue

作者： Zhang, Yue;Chen, Jinming;Shi, Tao;Zhang, Yue;Chen, Jinming;Shi, Tao;Zhang, Qian;Gu, Xiaofeng;Yang, Xingyu;Yang, Xingyu

作者机构：

关键词： N-6-methyladenine; gene duplication; gene expression; Nelumbo nucifera

期刊名称：PLANTS-BASEL （ 影响因子：4.5； 五年影响因子：4.8 ）

ISSN：

年卷期： 2023 年 12 卷 10 期

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收录情况： SCI

摘要： N-6-methyladenine (6mA) DNA methylation has emerged as an important epigenetic modification in eukaryotes. Nevertheless, the evolution of the 6mA methylation of homologous genes after species and after gene duplications remains unclear in plants. To understand the evolution of 6mA methylation, we detected the genome-wide 6mA methylation patterns of four lotus plants (Nelumbo nucifera) from different geographic origins by nanopore sequencing and compared them to patterns in Arabidopsis and rice. Within lotus, the genomic distributions of 6mA sites are different from the widely studied 5mC methylation sites. Consistently, in lotus, Arabidopsis and rice, 6mA sites are enriched around transcriptional start sites, positively correlated with gene expression levels, and preferentially retained in highly and broadly expressed orthologs with longer gene lengths and more exons. Among different duplicate genes, 6mA methylation is significantly more enriched and conserved in whole-genome duplicates than in local duplicates. Overall, our study reveals the convergent patterns of 6mA methylation evolution based on both lineage and duplicate gene divergence, which underpin their potential role in gene regulatory evolution in plants.

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