Mutation of a major CG methylase alters genome-wide lncRNA expression in rice. Issue 4 (22nd February 2021)

• Record Type: Journal Article
• Authors: Li, Juzuo; Li, Ning; Zhu, Ling; Zhang, Zhibin; Li, Xiaochong; Wang, Jinbin; Xun, Hongwei; Zhao, Jing; Wang, Xiaofei; Wang, Tianya; Wang, Hongyan; Liu, Bao; Li, Yu; Gong, Lei
• Editors: Andrews, B
• Is Part Of: G3. Volume 11:Issue 4(2021)
• Publication Date: 2021-02-22
• Subjects: long non-coding RNAs (lncRNAs) -- DNA methylation -- transposable element -- OsMET1-2 -- small interference RNA (siRNA) -- RNA-directed DNA methylation (RdDM); Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1093/g3journal/jkab049
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: 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 ( 5m C) 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.