Global reinforcement of DNA methylation through enhancement of RNA-directed DNA methylation ensures sexual reproduction in rice

Abstract

<jats:title>Abstract</jats:title><jats:p>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 <jats:italic>de novo</jats:italic> DNA methylation in plants. In Arabidopsis, however, mutations in RdDM genes cause no visible developmental defects, which raising the question of the biological significance of RdDM in plant development. Here, we isolated and cloned <jats:italic>Five Elements Mountain 1</jats:italic> (<jats:italic>FEM1</jats:italic>), which encodes an RNA-dependent RNA polymerase. Mutation in <jats:italic>FEM1</jats:italic> substantially decreased genome-wide CHH methylation levels and abolished the accumulation of 24-nt small interfering RNAs. Moreover, male and female reproductive development was disturbed, which led to the sterility of <jats:italic>fem1</jats:italic> mutants. In wild-type (WT) plants but not in <jats:italic>fem1</jats:italic> 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 attributed to enhancement of RdDM activity including FEM1 activity. More than half of all encoding genes in the rice genome overlapped with hypermethylated regions in the sexual organs of the WT, and many of them appear to be directly regulated by an increase in DNA methylation.</jats:p><jats:p>Our results demonstrate that a global increase of DNA methylation through enhancement of RdDM activity in reproductive organs ensures sexual reproduction of rice.</jats:p>

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

“…Map-Based Cloning of Five Elements Mountain 3. OsGA2ox1 encodes a gibberellin metabolism enzyme (41), and its ectopic expression in a japonica variety, TP309, resulted in transgenic plants (GAE) showing GA deficiency and dwarfism (38) (Fig. 1 A and B and SI Appendix, Fig.…”

“…S1A). Spontaneous silencing of the transgene 35S::OsGA2ox1 in the transgenic plants resulted in plants (GAS) with normal plant height (38) (Fig. 1 A and B and SI Appendix, Fig.…”

“…Beside the exogenous 35S promoter, six endogenous RdDM loci (38) were examined for the effect of FEM3 on CHH methylation. Chop-PCR assay showed that, like in fem1, CHH methylation in fem3 was substantially lower than in GAS (Fig.…”

“…Here, we used a genetic screen to identify and clone OsNRPE1 as a key component in the silencing of transgene in rice. Mutation in OsNRPE1, which encodes the largest subunit of Pol V, greatly reduced seed setting, suggesting that Pol V as well as OsRDR2 and Pol IV play a vital role in the reproductive development of rice (38)(39)(40). Depletion of Pol V led to a substantial loss of CHH methylation on short transposons near genes.…”

Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains

“…Further to validate if this feature of aberrant sRNAs in kd is associated with other pol IV machineries in vegetative tissues as well, we analysed the published sRNA datasets from rice seedlings from nrpd1, rdr2 and nrpe1 backgrounds (Wang et al, 2020b;Zheng et al, 2021). We indeed observed the same trend as in reproductive tissues in the nrpd1 and rdr2 but not in nrpe1 seedlings (Fig.…”