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

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.

Automated summary

In this study, the profiles of genome-wide lncRNA of a rice DNA methyltransferase mutant and its wild type were characterized and compared, revealing that erasure of CG methylation leads to increased production of specific lncRNAs and CHH hypermethylation is involved in the regulation of lncRNA expression.