A Histone Acetyltransferase Regulates Active DNA Demethylation in
            <i>Arabidopsis</i>

Qian, Weiqiang; Miki, Daisuke; Zhang, Heng; Liu, Yunhua; Zhang, Xi; Tang, Kai; Kan, Yunchao; La, Honggui; Li, Xiaojie; Li, Shaofang; Zhu, Xiaohong; Shi, Xiaobing; Zhang, Kangling; Pontes, Olga; Chen, Xuemei; Liu, Renyi; Gong, Zhizhong; Zhu, Jian Kang

doi:10.1126/science.1219416

Cited by 213 publications

(332 citation statements)

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“…Therefore, components involved in DNA demethylation are often referred to as antisilencing factors (3). In Arabidopsis, dysfunction of the 5-mC DNA glycosylase/demethylase ROS1 enhances the transcriptional silencing of some transgenes, endogenous genes, and TEs due to DNA hypermethylation (14,16,19). RNAi of ROS1 orthologs in cotton and tomato also reduce the expression of several genes due to promoter DNA hypermethylation (29,35).…”

Section: Discussionmentioning

confidence: 99%

“…Most of these genomic regions are in TEs or intergenic regions. Only a small number of genes are hypermethylated and silenced in Arabidopsis ros1 mutants, and the mutants do not show dramatic phenotypes in growth or development (7,14,19,21). Like ROS1 in Arabidopsis (20), SlDML2 in tomato preferentially targets highly methylated TEs and intergenic regions near genes (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Enzymes and regulators involved in active DNA demethylation are also known as antisilencing factors because of their function in preventing DNA hypermethylation and in therefore restraining transcriptional gene silencing (3,14). In sldml2-1, there are 29,764 hyper-DMRs relative to the WT, and 47.3% (14,074) of them are located within 1 kb of 12,902 genes.…”

Section: Sldml2-mediated Dna Demethylation Also Has Silencing Functionsmentioning

confidence: 99%

“…Expression of some transgenes, endogenous genes, and transposable elements (TEs) is reduced in ros1 mutants because of DNA hypermethylation (14,16,18,19). In Arabidopsis, ROS1 preferentially targets TEs (20).…”

mentioning

confidence: 99%

“…Because the ROS1 family of enzymes function in the first step of the DNA demethylation pathway, their targeting to specific genomic sequences determines the patterns of DNA methylation removal. Recent studies revealed a histone acetyltransferase complex that regulates DNA demethylation by facilitating the targeting of ROS1 (14)(15)(16)(17).…”

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confidence: 99%

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Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

Lang

YiHai

Tang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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DNA methylation is a conserved epigenetic mark important for genome integrity, development, and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5-mC DNA glycosylases/lyases (i.e., DNA demethylases). Recent reports suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlDML2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes. These genes included not only hundreds of ripening-induced genes but also many ripening-repressed genes. Our results show that SlDML2 is critical for tomato fruit ripening and suggest that active DNA demethylation is required for both the activation of ripeninginduced genes and the inhibition of ripening-repressed genes.DNA demethylase | 5-mC DNA glycosylase | DNA methylation | epigenetic regulation | gene silencing D NA methylation is a conserved epigenetic modification that is generally associated with inactive transcription in plants and mammals. As such, DNA methylation plays important roles in many biological processes, such as genome stability, gene imprinting, development, and response to the environment (1-3). In contrast to mammals, in which DNA methylation predominantly occurs at cytosines in the symmetric CG sequence context, plants commonly have methylation in the asymmetrical CHH sequence context (H = A, C, or T), as well as in the symmetrical CG and CHG contexts (1, 2). In plants, cytosines in all sequence contexts can be de novo methylated through the well-known RNA-directed DNA methylation pathway (RdDM), in which 24-nt siRNAs guide the DNA methyltransferase domains rearranged methyltransferase 2 (DRM2) to methylate target loci (4). DNA methylation can be maintained during replication; mCG and mCHG are maintained by the DNA methyltransferases DNA methyltransferase 1 (MET1) and chromomethylase 3 (CMT3), respectively, whereas mCHH is maintained by CMT2 and RdDM (4, 5).Cytosine methylation levels are dynamically regulated by DNA methylation and demethylation reactions (3, 6). DNA methylation can be lost either because of failure in maintaining methylation after replication (i.e., passive DNA demethylation) or because of active removal by enzymes (i.e., active DNA demethylation). Previous studies have identified and characterized several enzymes important for active DNA demethylation in Arabidopsis (7-11). The ROS1 family of bifunctional 5-methylcytosine DNA glycosylases/lyases, often referred to as DNA demethylases, initiate active DNA demethylation by removing the methylcytosine base from the DNA backbone, resulting in a single nucleotide gap that can be filled with an unmethylated cytosine through a base excision repair pathway (7,8,12,13). Several enzymes acting downstream of ROS1, such as the 3′ DNA phosphatase ZDP, AP endonuclease-like protein APE1L, and DNA ligase I (AtLIG1), have also been identified ...

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