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Regulatory link between DNA methylation and active demethylation in Arabidopsis
Saturday, 2015/03/21 | 06:02:08

Mingguang Lei, Huiming Zhang, Russell Julian, Kai Tang, Shaojun Xie, and Jian-Kang Zhu




DNA methylation is critical for transposon silencing and gene regulation. DNA methylation levels are determined by the combined activities of DNA methyltransferases and demethylases. This study found a 39-bp DNA methylation monitoring sequence (MEMS) in the promoter of the DNA demethylase REPRESSOR OF SILENCING 1 (ROS1) gene of Arabidopsis plants. DNA methylation of MEMS is responsive to both RNA-directed DNA methylation and ROS1-dependent active demethylation. Thus, MEMS can sense DNA methylation and demethylation activities, and it regulates genomic DNA methylation by adjusting ROS1 expression levels. Our results suggest that the ROS1 promoter, with the MEMS and an adjacent helitron transposon element, functions as a “methylstat” that senses and regulates genomic DNA methylation levels.




De novo DNA methylation through the RNA-directed DNA methylation (RdDM) pathway and active DNA demethylation play important roles in controlling genome-wide DNA methylation patterns in plants. Little is known about how cells manage the balance between DNA methylation and active demethylation activities. Here, we report the identification of a unique RdDM target sequence, where DNA methylation is required for maintaining proper active DNA demethylation of the Arabidopsis genome. In a genetic screen for cellular antisilencing factors, we isolated several REPRESSOR OF SILENCING 1 (ros1) mutant alleles, as well as many RdDM mutants, which showed drastically reduced ROS1 gene expression and, consequently, transcriptional silencing of two reporter genes. A helitron transposon element (TE) in the ROS1 gene promoter negatively controls ROS1 expression, whereas DNA methylation of an RdDM target sequence between ROS1 5′ UTR and the promoter TE region antagonizes this helitron TE in regulating ROS1 expression. This RdDM target sequence is also targeted by ROS1, and defective DNA demethylation in loss-of-function ros1 mutant alleles causes DNA hypermethylation of this sequence and concomitantly causes increased ROS1 expression. Our results suggest that this sequence in the ROS1 promoter region serves as a DNA methylation monitoring sequence (MEMS) that senses DNA methylation and active DNA demethylation activities. Therefore, the ROS1 promoter functions like a thermostat (i.e., methylstat) to sense DNA methylation levels and regulates DNA methylation by controlling ROS1 expression.


See: http://www.pnas.org/content/112/11/3553.abstract.html?etoc

PNAS March 17, 2015 vol. 112 no. 11 3553-3557


Fig. 1.

Mutations in ROS1 resulted in transcriptional silencing of marker transgenes. (A) Schematic diagram of the construct harboring the 35S::SUC2 and 2 × 35S::HPTII cassettes that were transformed in the parental line. Black rectangles represent exons. (B) Comparison of root growth of Col-0, WT, and seven ros1 mutants. Expression of SUC2 (C) and HPTII (D) transgenes in ros1 mutants. Values are mean ± SD of three biological replicates and are normalized to transcript levels in WT. (E) DNA methylation status at the 35S promoter in WT, ros1-13, and nrpd1-12 mutants. The result from whole-genome bisulfite sequencing is shown. Vertical bars on each track indicate DNA methylation levels.

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