ArticleThe Journal of biological chemistry2014
Probing the dynamic distribution of bound states for methylcytosine-binding domains on DNA.
Article in The Journal of biological chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 65 citations in OpenAlex.
- Exploring the bistable equilibrium of methylated CpG DNA recognition by the MBD2 protein.Nucleic acids research · 2026Article
- Gene regulatory mechanisms downstream of DNA methylation.Nature reviews. Genetics · 2026Review
- Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.Molecular & cellular proteomics : MCP · 2026Article
- Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.bioRxiv : the preprint server for biology · 2026Article
- Uncovering the Molecular Interactions Underlying MBD2 and MBD3 Phase Separation.The journal of physical chemistry. B · 2025Article
- Targeting redox-sensitive MBD2-NuRD condensate in cancer cells.Nature cell biology · 2025Article
- Article
- Mechanistic model for epigenetic maintenance by methyl-CpG-binding domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Analysis of the complex between MBD2 and the histone deacetylase core of NuRD reveals key interactions critical for gene silencing.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- MBD2a-NuRD binds to the methylated γ-globin gene promoter and uniquely forms a complex required for silencing of HbF expression.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Computational discovery of novel inhibitory candidates targeting versatile transcriptional repressor MBD2.Journal of molecular modeling · 2022Article
- Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination.Protein science : a publication of the Protein Society · 2022Article
- Epigenetic remodelling of Fxyd1 promoters in developing heart and brain tissues.Scientific reports · 2022Article
- Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 fromACS omega · 2022Article
- Unique protein interaction networks define the chromatin remodelling module of the NuRD complex.The FEBS journal · 2022Article
- CRISPR-Cas9 to induce fetal hemoglobin for the treatment of sickle cell disease.Molecular therapy. Methods & clinical development · 2021Review
- The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.PLoS computational biology · 2021Article
- Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders.Neurochemistry international · 2021Article
- MBD2 and EZH2 regulate the expression of SFRP1 without affecting its methylation status in a colorectal cancer cell line.Experimental and therapeutic medicine · 2020Article
- The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture.Cell reports · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Although highly homologous to other methylcytosine-binding domain (MBD) proteins, MBD3 does not selectively bind methylated DNA, and thus the functional role of MBD3 remains in question. To explore the structural basis of its binding properties and potential function, we characterized the solution structure and binding distribution of the MBD3 MBD on hydroxymethylated, methylated, and unmethylated DNA. The overall fold of this domain is very similar to other MBDs, yet a key loop involved in DNA binding is more disordered than previously observed. Specific recognition of methylated DNA constrains the structure of this loop and results in large chemical shift changes in NMR spectra. Based on these spectral changes, we show that MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated cytosine-guanosine dinucleotides (CpGs), yet does not distinguish between hydroxymethylated and unmethylated sites. Measuring residual dipolar couplings for the different bound states clearly shows that the MBD3 structure does not change between methylation-specific and nonspecific binding modes. Furthermore, residual dipolar couplings measured for MBD3 bound to methylated DNA can be described by a linear combination of those for the methylation and nonspecific binding modes, confirming the preferential localization to methylated sites. The highly homologous MBD2 protein shows similar but much stronger localization to methylated as well as unmethylated CpGs. Together, these data establish the structural basis for the relative distribution of MBD2 and MBD3 on genomic DNA and their observed occupancy at active and inactive CpG-rich promoters.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.