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Density of cytosine methylation and repeats in the genome of plants is high in heterochromatin regions surrounding centromeres where remnants of transposons accumulate, but the extent of bias in the distribution of cytosine methylation and repeats on chromosomes varies in different plant species and plants containing larger genomes tend to have broader distributions of cytosine methylation and repeats. DECREASE IN DNA METHYLATION1 (DDM1) in Arabidopsis thaliana is a chromatin remodeling factor that maintains cytosine methylation mainly in CG and CHG contexts around centromeres. However, function of DDM1 in higher plants other than Arabidopsis thaliana is poorly understood and, especially, its action in maintenance of cytosine methylation in the genomes that carry broader distribution of cytosine methylation is unknown. Towards understanding mechanism in maintenance of silent chromatin in plants carrying broadly distributed cytosine methylation and repeats, we analyzed the effect of deficiency in the DDM1 function of rice. In the rice genome, cytosine methylation and repeats distribute broadly throughout chromosomes with a weak concentration at around centromeres, and DDM1-deficiency induced not only a strong reduction of CG and CHG methylation in the pericentromeric regions but also significant decrease of CG/CHG methylation in arms of chromosomes. Unexpectedly, CHH methylation that is plainly distributes throughout rice chromosomes exhibited a marked increase at centromeres in the DDM1-deficient line. Global reduction of CHG methylation in the gene body was also observed irrespective of expression states in wild-type or the DDM1-deficient line. Our results indicate novel functions of DDM1 on cytosine methylation in centromeres and gene bodies in rice, and, together with the previously reported effects of deficiency in a DDM1-ortholog in mouse, suggest that the action of DDM1 varies depending on the nature of genome composition. |