The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

Tang, Kai; Lang, Zhaobo; Zhang, Heng; Zhu, Jian‐Kang

doi:10.1038/nplants.2016.169

Cited by 149 publications

(148 citation statements)

References 45 publications

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“…As shown in Fig. 2A and consistent with features of AtROS1 targets in Arabidopsis (20), DNA hypermethylation in sldml2 mutant fruits occurred in all three sequence contexts: mCG, mCHG, and mCHH. To confirm the function of SlDML2 in DNA demethylation, we examined DNA methylation levels of the other mutant allele of SlDML2, sldml2-2, and found that the identified SlDML2 targets in sldml2-1 have similar increases in mCG, mCHG, and mCHH levels in sldml2-2 at 60 dpa compared with the WT at 60 dpa (Fig.…”

Section: Resultssupporting

confidence: 84%

“…These results suggest that, during fruit ripening, SlDML2 may have a function similar to that of AtROS1 in preventing gene silencing by demethylating nearby TEs or highly methylated intergenic regions. However, in contrast to AtROS1, which targets TEs in both euchromatic and heterochromatic regions (20), SlDML2 preferentially targets TEs in euchromatic regions. Boxplots showing DNA methylation levels at combined sldml2-1 hyper-DMRs in WT-46dpa, WT60dpa, two biological replicates of sldml2-1-46dpa, and two biological replicates of sldml2-2-60dpa.…”

Section: Resultsmentioning

confidence: 86%

“…3B). However, in contrast to AtROS1 targets that are concentrated around pericentromeric regions (20), sldml2 hyper-DMRs aggregate in chromosomal arms (Fig. 3B).…”

Section: Resultsmentioning

confidence: 95%

“…In Arabidopsis, ROS1 preferentially targets TEs (20). Among the simulated genomic regions in tomato, 66.1% are in TEs, 22.5% in intergenic regions (IGs), and 11.4% in genic regions.…”

Section: Resultsmentioning

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). When ROS1-targeted TEs are located in the promoter regions of genes, ROS1 can protect gene expression by demethylating the adjacent TEs.…”

mentioning

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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394

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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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Section: Resultssupporting

confidence: 84%

Section: Resultsmentioning

confidence: 86%

“…3B). However, in contrast to AtROS1 targets that are concentrated around pericentromeric regions (20), sldml2 hyper-DMRs aggregate in chromosomal arms (Fig. 3B).…”

Section: Resultsmentioning

confidence: 95%

“…In Arabidopsis, ROS1 preferentially targets TEs (20). Among the simulated genomic regions in tomato, 66.1% are in TEs, 22.5% in intergenic regions (IGs), and 11.4% in genic regions.…”

Section: Resultsmentioning

confidence: 99%

mentioning

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.

Self Cite

394

409

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Snapshot of epigenetic regulation in legumes

et al. 2020

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In the current context of food security and increase in plant protein demand, legumes have an important role in facing challenges of climate change. With the recent improvement of sequencing technologies and the emergence of new knowledge related to plant epigenetic regulation in response to developmental and environmental changes, legume epigenetics is an emerging field with high potential for improving legume crop productivity and adaptability. The objective of this review is to provide a snapshot of epigenetic studies in different legume species. We have summarized the state‐of‐the‐art regarding legume epigenetic regulation controlling or participating in developmental aspects such as nodule, flower, and seed development and related to biotic and abiotic stresses. This extensive view of the different studies on legume epigenetics provides a baseline for identifying common and distinct mechanisms, and key players in epigenetic regulation from those of model species, such Arabidopsis, and highlights the impact that a better understanding of these mechanisms in legumes could have in order to improve plant productivity and adaptability.

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Flocculation potential regulation to achieve the improved thermal‐mechanical performance for CB/GO reinforced NR nanocomposites

Chen,

Tian,

Chen

et al. 2024

Polymer Composites

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With the rapid development of modern transportation systems, optimizing the relationship between structure and performance to obtain natural rubber‐based nanocomposites with excellent comprehensive performance is still worth to investigation. Herein, the regulation of flocculation potential through different flocculants selection on the thermomechanical properties for carbon black/graphene oxide reinforced natural rubber (CB/GO/NR) nanocomposites were investigated based on the compression electric double layer theory. The results showed that formic acid owned the highest zeta potential with comparison of sodium chloride (NaCl), calcium chloride (CaCl2), and aluminum chloride (AlCl3). Meanwhile, as the content was 8 wt%, tensile strength, tearing strength and thermal conductivity could achieve to 27.64 MPa, 56.89 N/mm, and 1.05 W m−1 K−1, respectively. While the heat generation after compression fatigue dropped to 10.1°C. These findings reveal that the highest zeta potential of formic acid could promote the improvement of flocculation degree between GO and NR latex and significantly enhanced the thermomechanical properties of CB/GO/NR nanocomposites due to the larger flocculation potential difference. Therefore, this study not only provides important theoretical insights for preparing high‐performance NR‐based nanocomposites, but also highlights the crucial role of high zeta potential flocculants in optimizing the composite performance. More importantly, the findings offer the creative insights for preparation of the excellent comprehensive NR nanocomposites for the practical industry application.Highlights The effect of flocculation degree on the properties of CB/GO/NR composites was studied. Formic acid was benefit to the flocculation and could promote the surface interaction. CB/GO/NR composites possessed the improved thermal and mechanical properties.

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The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

Cited by 149 publications

References 45 publications

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

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

Snapshot of epigenetic regulation in legumes

Flocculation potential regulation to achieve the improved thermal‐mechanical performance for CB/GO reinforced NR nanocomposites

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