Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [RNA-seq]
DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well understood in Arabidopsis, mutations in RdDM genes cause no visible developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 in rice. Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH methylation levels. Moreover, male and female reproductive development was disturbed, which led to the sterility of osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation likely regulates the expression of multiple key genes involved in stamen development and meiosis. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH DNA methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity including OsRDR2 activity. Our results, which revealed a global increase in DNA methylation through enhancement of RdDM activity in reproductive organs, demonstrate the crucial role of OsRDR2 in the sexual reproduction of rice. Overall design: Transcriptome sequencing