期刊
G3-GENES GENOMES GENETICS
卷 11, 期 4, 页码 -出版社
OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkab049
关键词
long non-coding RNAs (lncRNAs); DNA methylation; transposable element; OsMET1-2; small interference RNA (siRNA); RNA-directed DNA methylation (RdDM)
资金
- National Natural Science Foundation of China [31670220, 31700187]
- Recruitment Program of Global Youth Experts
- Program of Changbai Mountain Scholar
The study demonstrates that CG methylation negatively regulates the TE-related expression of lncRNA, while CHH methylation is also involved in the regulation of lncRNA expression.
Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA 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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