Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality

Abstract

Cytosine methylation at CG sites ( m CG) plays critical roles in development, epigenetic inheritance, and genome stability in mammals and plants. In the dicot model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal CG methylase, functions to maintain m CG during DNA replication, with its null mutation resulting in global hypomethylation and pleiotropic developmental defects. Null mutation of a critical CG methylase has not been characterized at a whole-genome level in other higher eukaryotes, leaving the generality of the Arabidopsis findings largely speculative. Rice is a model plant of monocots, to which many of our important crops belong. Here we have characterized a null mutant of OsMet1-2, the major CG methylase in rice. We found that seeds homozygous for OsMet1-2 gene mutation (OsMET1-2 −/− ), which directly segregated from normal heterozygote plants (OsMET1-2 +/− ), were seriously maldeveloped, and all germinated seedlings underwent swift necrotic death. Compared with wild type, genome-wide loss of m CG occurred in the mutant methylome, which was accompanied by a plethora of quantitative molecular phenotypes including dysregulated expression of diverse protein-coding genes, activation and repression of transposable elements, and altered small RNA profiles. Our results have revealed conservation but also distinct functional differences in CG methylases between rice and Arabidopsis.Oryza sativa L. | monocotyledons C ytosine methylation is an evolutionarily conserved epigenetic modification across biological kingdoms (1-3). However, fundamental differences exist for this epigenetic mark between animals and plants in many aspects (1-3). For example, in mammalian somatic cells, methylated cytosines ( m Cs) occur almost exclusively in a CG sequence context, and CG methylation ( m CG) is maintained during DNA replication by a single CG methylase, DNA methyltransferase 1 (DNMT1). Cytosine methylation in plants is more complex, occurs in all sequence contexts (CG, CHG, and CHH; where H is A, T, or C), and is established and maintained by multiple enzymes that have distinct but also overlapping functions (2, 4-6). Nevertheless, m CG stands out as the most pervasive type (2). In the dicot model plant Arabidopsis thaliana, m CG is maintained by a major CG methylase, namely DNA methyltransferase 1 (MET1), the homolog of mammalian DNMT1 (2, 7-11). Null mutation of MET1 (the homozygous met1 mutant) virtually eliminates genome-wide m CG to 1.7% that of wild type (WT), that is, from 24.6% in WT to 0.42% in mutant (12, 13). Homozygous null met1 mutant can be obtained from selfed progenies of heterozygotes (MET1 +/− ) but was often at much lower frequencies than expected by Mendelian segregation (11). Homozygous Arabidopsis met1 plants show pleiotropic developmental abnormalities of variable penetrance, which aggravate in frequency and severity with inbreeding (11). Although conditional knockout DNMT1 mutants were established in human colorectal carcinoma cell lines (14) and loss-of-function DNA methyltran...

Genetic Perturbation of the Maize Methylome

“…There is evidence that this may also be true for rice (Oryza sativa) as homozygous met1 mutant individuals were not recovered (Hu et al, 2014). The increased requirement for DNA methylation to successfully complete embryo development in maize but not Arabidopsis could be due to the increased transposon content and higher frequency of genes being located very near to transposons in maize (Schnable et al, 2009).…”

Epigenetic Regulation of Abiotic Stress Tolerance in Plants

“…In fact, DNA methyl transferases and DNA demethylase mutations in rice showed more severe defects compared with the corresponding mutants in Arabidopsis. [43][44][45][46] Gene manipulation for stress-tolerant transgenic plant development via DNA methylation initially needs a proper selection of the gene. Evaluating promoter sequence of the target gene for RdDM-associated features can be done using starPRO database.…”

Genomic DNA methylation analyses reveal the distinct profiles in castor bean seeds with persistent endosperms

“…Increasing evidence demonstrates that DNA methylation plays crucial roles in the control of seed development and seed size (Xiao et al, 2006a(Xiao et al, , 2006bHu et al, 2014;Xing et al, 2015). In particular, DNA methylation was considered as a major regulator of gene imprinting that mainly manifests itself in the endosperm of angiosperm plants, closely associated with endosperm and seed development, such as the imprinted genes MEA (Grossniklaus et al, 1998;Köhler et al, 2003), FWA (Kinoshita et al, 2004), and FIS2 (Jullien et al, 2006).…”