Control of chloroplast development by active DNA demethylation

Abstract

DNA methylation is an epigenetic modification regulating genome stability and diverse biological processes. In plants, RNA-dependent DNA methylation (RdDM) establishes de novo DNA methylation, whereas DNA demethylases remove established DNA methylation. ROS1, DML2, DML3 (RDD) are DNA demethylases known to function in somatic cells. Despite of their significant effect on the DNA methylation pattern, only a few biological processes, such as development of stomata or trachea element and immune responses, have been associated with DNA demethylation. Here, we report that chloroplast development can be controlled by DNA demethylation pathway. From the suppressor mutant screening of mild chloroplast protease mutant clpt, we identified suppressor of clpt1 (soct1) as a mutant allele of INCREASED DNA METHYLATION3 (IDM3) a subunit of IDM complex which regulates targeting of ROS1. Mutants of ROS1 and IDM complex also suppressed clpt, which was mediated by DNA hypermethylation in the mutants. We also dentified soct2/3/4 as mutant alleles of NRPD1 or RDR2 which are components of 24-nt sRNA biogenesis pathway. The suppression of clpt by soct2/3/4 probably is associated with reduced ROS1 expression, which is caused by loss-of DNA methylation at the promoter of ROS1 (MEMS). In addition, unexpectedly, clpt DNA was hypermethylated at RdDM target sites. The clpt DNA hypermethylation was largely rescued in clpt mbd7, suggesting that chloroplast developmental defect induced RdDM-mediated DNA methylation in clpt. These results show that chloroplast development can be regulated by DNA demethylation pathway. Also, it suggests RdDM-mediated DNA methylation as a stress response against chloroplast developmental defect. Thus, this study offers a novel relationship between chloroplast development and DNA methylation.