Mutation of a major CG methylase alters genome-wide lncRNA expression in rice

文献类型： 外文期刊

第一作者： Li, Juzuo

作者： Li, Juzuo;Li, Ning;Zhu, Ling;Zhang, Zhibin;Li, Xiaochong;Wang, Jinbin;Zhao, Jing;Wang, Xiaofei;Wang, Tianya;Liu, Bao;Gong, Lei;Xun, Hongwei;Wang, Hongyan;Li, Yu

作者机构：

关键词： long non-coding RNAs (lncRNAs); DNA methylation; transposable element; OsMET1-2; small interference RNA (siRNA); RNA-directed DNA methylation (RdDM)

期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：2.781； 五年影响因子：3.026 ）

ISSN： 2160-1836

年卷期： 2021 年 11 卷 4 期

页码：

收录情况： SCI

摘要： Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and IncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (C-5m) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2(-/)(-)) and its isogenic wild type (OsMET1-2(+/+)). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2(+/+), was transcriptionally de-repressed in OsMET1-2(-/-) due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5'-upstream genomic regions of lncRNAs in OsMET1-2(-/)(-). The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.

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