Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs

Wu, Zhibin; Chen, Sizhuo; Zhou, Mengqi; Jia, Lingbo; Li, Zhenhua; Zhang, Xiyou; Min, Jinrong; Liu, Ke

doi:10.1016/j.jmb.2021.167404

Cited by 8 publications

(11 citation statements)

References 50 publications

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“…The canonical MBDs bind to mCG and TG DNA by the conserved base-specific interactions between arginine residues and guanine base of mCG/TG dinucleotide, as well as electrostatic interactions with the negatively charged backbone phosphate of dsDNA [ 18 , 19 , 20 , 21 , 22 , 23 , 32 , 33 ]. Notwithstanding, sequence alignment revealed that R760 and R781, corresponding R166 and R188 of human MBD2, are conserved in the TAM domain of BAZ2B ( Figure 1 B).…”

Section: Resultsmentioning

confidence: 99%

“…Thus, we speculate that these structural features might restrain R760 to point to the mCG dinucleotide, and also hamper the R760 to specifically bind to mCG dinucleotide as the R166 of MBD2 does ( Figure 4 C). Besides the arginine fingers, the loop connecting β1 and β2, and the α1 of MBD2 make contact with the sugar-phosphate backbone, which recently has been shown to be crucial for DNA binding [ 23 ]. However, there is a short loop between the β1 and β2 of the BAZ2B TAM domain, and it fails to form interaction with the DNA backbone (Figures 1 B and 4 D).…”

Section: Resultsmentioning

confidence: 99%

“…In addition to the epigenetic reader domains PHD and BRD, BAZ2B also has a TAM domain with a C-terminal additional BAZ-specific moiety compared to the canonical MBD (Figures 1 A and 1B). The canonical MBDs, such as those of MeCP2 and MBD1-4, have been characterized as the mCpG and TpG binders [ 18 , 19 , 20 , 21 , 22 , 23 ]. For the TAM domain, we have recently demonstrated the structural basis for the recognition of dsDNA by the TAM domain of BAZ2A, which showed that the BAZ2A TAM domain recognizes dsDNA without methylation preference [ 24 , 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

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Crystal structure of the BAZ2B TAM domain

Feng

Chen²,

Zhou³

et al. 2022

Heliyon

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Crystal structure of the BAZ2B TAM domain

Feng

Chen²,

Zhou³

et al. 2022

Heliyon

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“…The binding activity and specificity have not been established for AtMBD3, 9, 10, 12, and 13 ( Ito et al, 2003 ; Scebba et al, 2003 ; Grafi et al, 2007 ). Recently, it was demonstrated that AtMBD6 and AtMBD7 are actually readers for methylated DNA ( Wu et al, 2022 ). AtMBD5 and AtMBD6, which are closely related and may have redundant functions ( Berg et al, 2003 ), are recruited to chromatin by recognition of CG methylation to redundantly repress a subset of genes and transposons ( Ichino et al, 2021 ), or participate in the formation of HDAC complexes to modulate the chromatin structure and gene transcription ( Zemach et al, 2005 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Characterization of the Methyl CpG Binding Domain-Containing Proteins in Watermelon and Functional Analysis of Their Roles in Disease Resistance Through Ectopic Overexpression in Arabidopsis thaliana

Liang

Li²,

Wen³

et al. 2022

Front. Plant Sci.

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Methyl-CPG-Binding Domain (MBD) proteins play important roles in plant growth, development, and stress responses. The present study characterized the MBD families in watermelon and other cucurbit plants regarding the gene numbers and structures, phylogenetic and syntenic relationships, evolution events, and conserved domain organization of the MBD proteins. The watermelon ClMBD proteins were found to be localized in nucleus, and ClMBD2 and ClMBD3 interacted with ClIDM2 and ClIDM3. ClMBD2 bound to DNA harboring methylated CG sites but not to DNA with methylated CHG and CHH sites in vitro. The ClMBD genes exhibited distinct expression patterns in watermelon plants after SA and MeJA treatment and after infection by fungal pathogens Fusarium oxysporum f.sp. niveum and Didymella bryoniae. Overexpression of ClMBD2, ClMBD3, or ClMBD5 in Arabidopsis resulted in attenuated resistance against Botrytis cinerea, accompanied by down-regulated expression of AtPDF1.2 and increased accumulation of H2O2 upon B. cinerea infection. Overexpression of ClMBD1 and ClMBD2 led to down-regulated expression of AtPR1 and decreased resistance while overexpression of ClMBD5 resulted in up-regulated expression of AtPR1 and increased resistance against Pseudomonas syringae pv. tomato DC3000. Transcriptome analysis revealed that overexpression of ClMBD2 in Arabidopsis up-regulated the expression of a small set of genes that negatively regulate Arabidopsis immunity. These data suggest the importance of some ClMBD genes in plant immunity and provide the possibility to improve plant immunity through modification of specific ClMBD genes.

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“…MBD1, MBD2, and MBD4 form a monophyletic group (Supplementary Fig. 1a), and all three proteins contain the conserved MBD domain 8,[12][13][14][16][17][18] (Supplementary Fig. 1b).…”

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confidence: 99%

MBD2 couples DNA methylation to Transposable Elements silencing during male gametogenesis

Wang,

Ichino

et al. 2023

Preprint

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DNA methylation is an essential component of transposable element (TE) silencing, yet the mechanism by which methylation causes transcriptional repression remains poorly understood1–5. Here we study theArabidopsis thalianaMethyl-CpG Binding Domain (MBD) proteins MBD1, MBD2, and MBD4, and show that MBD2 acts as a transposable element (TE) repressor during male gametogenesis. MBD2 bound chromatin regions containing high levels of CG methylation, and MBD2 was capable of silencing theFWAgene when tethered to its promoter. MBD2 loss caused TE activation in the vegetative cell (VC) of mature pollen without affecting DNA methylation levels, demonstrating that MBD2-mediated silencing acts strictly downstream of DNA methylation. Loss of silencing inmbd2became more significant in thembd5 mbd6oradcp1mutant backgrounds, as well as in plants with chemically induced genome-wide DNA demethylation, suggesting that MBD2 acts redundantly with other silencing pathways to safeguard TEs from activation. Overall, our study identifies MBD2 as a novel methyl reader that acts downstream of DNA methylation to silence TEs during male gametogenesis.

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Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs

Cited by 8 publications

References 50 publications

Crystal structure of the BAZ2B TAM domain

Crystal structure of the BAZ2B TAM domain

Genome-Wide Characterization of the Methyl CpG Binding Domain-Containing Proteins in Watermelon and Functional Analysis of Their Roles in Disease Resistance Through Ectopic Overexpression in Arabidopsis thaliana

MBD2 couples DNA methylation to Transposable Elements silencing during male gametogenesis

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