A novel protein complex that regulates active DNA demethylation in Arabidopsis

Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression.The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1000 s of genomic regions in Arabidopsis.How ROS1 is regulated and targeted to specific genomic regions is not well understood.Here,we report the discovery of an Arabidopsis protein complex that contains ROS1,regulates ROS1 gene expression,and likely targets the ROS1 protein to specific genomic regions.ROS1 physically interacts with a WD40 domain protein(RWD40),which in turn interacts with a methyl-DNA binding protein(RMB1)as well as with a zinc finger and homeobox domain protein(RHD1).RMB1 binds to DNA that is methylated in any sequence context,and this binding is necessary for its function in vivo.Loss-of-function mutations in RWD40,RMB1,or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1.Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter,plants mutated in RWD40,RMB1,or RHD1 show increased ROS1 expression.Importantly,ROS1 binding to the ROS1 promoter requires RWD40,RMB1,and RHD1,suggesting that this complex dictates ROS1 targeting to this locus.Our results demonstrate that ROS1 forms a protein complex with RWD40,RMB1,and RHD1,and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.

The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis

DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.