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Journal articles on the topic 'MBD3'

Author: Grafiati

Published: 4 June 2021

Last updated: 27 April 2022

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1

Hendrich, Brian, and Adrian Bird. "Identification and Characterization of a Family of Mammalian Methyl-CpG Binding Proteins." Molecular and Cellular Biology 18, no. 11 (November 1, 1998): 6538–47. http://dx.doi.org/10.1128/mcb.18.11.6538.

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ABSTRACT Methylation at the DNA sequence 5′-CpG is required for mouse development. MeCP2 and MBD1 (formerly PCM1) are two known proteins that bind specifically to methylated DNA via a related amino acid motif and that can repress transcription. We describe here three novel human and mouse proteins (MBD2, MBD3, and MBD4) that contain the methyl-CpG binding domain. MBD2 and MBD4 bind specifically to methylated DNA in vitro. Expression of MBD2 and MBD4 tagged with green fluorescent protein in mouse cells shows that both proteins colocalize with foci of heavily methylated satellite DNA. Localization is disrupted in cells that have greatly reduced levels of CpG methylation. MBD3 does not bind methylated DNA in vivo or in vitro. MBD1, MBD2, MBD3, and MBD4 are expressed in somatic tissues, but MBD1 and MBD2 expression is reduced or absent in embryonic stem cells which are known to be deficient in MeCP1 activity. The data demonstrate that MBD2 and MBD4 bind specifically to methyl-CpG in vitro and in vivo and are therefore likely to be mediators of the biological consequences of the methylation signal.

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Cramer, Jason M., J. Neel Scarsdale, Ninad M. Walavalkar, William A. Buchwald, Gordon D. Ginder, and David C. Williams. "Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA." Journal of Biological Chemistry 289, no. 3 (December 4, 2013): 1294–302. http://dx.doi.org/10.1074/jbc.m113.512236.

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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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3

Jiang, Chun-Ling, Seung-Gi Jin, and Gerd P. Pfeifer. "MBD3L1 Is a Transcriptional Repressor That Interacts with Methyl-CpG-binding Protein 2 (MBD2) and Components of the NuRD Complex." Journal of Biological Chemistry 279, no. 50 (September 28, 2004): 52456–64. http://dx.doi.org/10.1074/jbc.m409149200.

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Methyl-CpG-binding domain proteins 2 and 3 (MBD2 and MBD3) are transcriptional repressors that contain methyl-CpG binding domains and are components of a CpG-methylated DNA binding complex named MeCP1. Methyl-CpG-binding protein 3-like 1 (MBD3L1) is a protein with substantial homology to MBD2 and MBD3, but it lacks the methyl-CpG binding domain. MBD3L1 interacts with MBD2 and MBD3in vitroand in yeast two-hybrid assays. Gel shift experiments with a CpG-methylated DNA probe indicate that recombinant MBD3L1 can supershift an MBD2-methylated DNA complex.In vivo, MBD3L1 associates with and colocalizes with MBD2 but not with MBD3 and is recruited to 5-methylcytosine-rich pericentromeric heterochromatin in mouse cells. In glutathioneS-transferase pull-down assays MBD3L1 is found associated with several known components of the MeCP1·NuRD complex, including HDAC1, HDAC2, MTA2, MBD2, RbAp46, and RbAp48, but MBD3 is not found in the MBD3L1-bound fraction. MBD3L1 enhances transcriptional repression of methylated DNA by MBD2. The data are consistent with a role of MBD3L1 as a methylation-dependent transcriptional repressor that may interchange with MBD3 as an MBD2-interacting component of the NuRD complex. MBD3L1 knockout mice were created and were found to be viable and fertile, indicating that MBD3L1 may not be essential or there is functional redundancy (through MBD3) in this pathway. Overall, this study reveals additional complexities in the mechanisms of transcriptional repression by the MBD family proteins.

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4

Krasteva, M., Y. Koycheva, T. Taseva, and S. Simeonova. "Changes in the Expression of DNA Methylation Related Genes in Leukocytes of Persons with Alcohol and Drug Dependence." Acta Medica Bulgarica 47, no. 4 (November 1, 2020): 11–17. http://dx.doi.org/10.2478/amb-2020-0039.

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AbstractBackground and objectives. Though numerous studies have shown that the dysregulation of the epigenetic control is involved in disease manifestation, limited data is available on the transcriptional activity of DNA methylation related genes in alcohol and drug addiction. With regard to this, in this study we analyzed the expression levels of genes involved in DNA methylation, including DNMT1, DNMT3a, MeCP2, MBD1, MBD2, MBD3 and MBD4, in blood samples of alcohol and drug dependent persons in comparison to healthy abstainers.Methods. The study included 51 participants: 16 persons with alcohol dependence, 17 persons with drug dependence and 18 clinically healthy controls. To detect the relative mRNA expression levels of the studied genes, Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis was applied.Results. Of the seven studied genes, four showed altered expression. MeCP2 and MBD1 were downregulated in the alcohol dependent group (FC = 0.805, p = 0.015 and FC = 0.846, p = 0.034, respectively), while DNMT1 and MBD4 were upregulated in the group with drug dependence (FC = 1.262, p = 0.001 and FC = 1.249, p = 0.005, respectively). No statistically significant changes in the relative mRNA expression were found for DNMT3a, MBD2 and MBD3 genes.Conclusions. Our results are indicative for a role of DNA methylation related genes in alcohol and drug addiction mediated through changes in their transcriptional activity. Studies in this direction will enable better understanding of the underlying mechanisms of addictions supporting the development of more effective therapeutic strategies.

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Gu, Peili, Damien Le Menuet, Arthur C. K. Chung, and Austin J. Cooney. "Differential Recruitment of Methylated CpG Binding Domains by the Orphan Receptor GCNF Initiates the Repression and Silencing of Oct4 Expression." Molecular and Cellular Biology 26, no. 24 (October 9, 2006): 9471–83. http://dx.doi.org/10.1128/mcb.00898-06.

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ABSTRACT The pluripotent factor Oct4 is a key transcription factor that maintains embryonic stem (ES) cell self-renewal and is down-regulated upon the differentiation of ES cells and silenced in somatic cells. A combination of cis elements, transcription factors, and epigenetic modifications, such as DNA methylation, are involved in the regulation of Oct4 gene expression. Here we show that the orphan nuclear receptor GCNF initiates Oct4 repression and DNA methylation by the differential recruitment of MBD (methylated CpG binding domain) factors to the promoter. Compared with wild-type ES cells and gastrulating embryos, Oct4 repression is lost and its proximal promoter is significantly hypomethylated in RA-differentiated GCNF−/− ES cells. The Oct4 gene is reexpressed in some somatic cells of GCNF−/− embryos, showing that it has not been properly silenced coincident with reduced DNA methylation of its promoter. Efforts to characterize mediators of GCNF's repressive function and DNA methylation of the Oct4 promoter identified methyl-DNA binding proteins, MBD3 and MBD2, as GCNF-interacting factors. In P19 and ES cells, upon differentiation, endogenous GCNF binds to the Oct4 proximal promoter and differentially recruits MBD3 and MBD2. In differentiated GCNF−/− ES cells, recruitment of MBD3 and MBD2 to the Oct4 promoter is lost, and repression of Oct4 expression and DNA methylation fails to occur. RNA interference-mediated knockdown of MBD3 and/or MBD2 expression results in reduced Oct4 repression in differentiated P19 and ES cells. Repression of Oct4 expression and recruitment of MBD3 are maintained in de novo DNA methylation-deficient ES cells (Dnmt3A/3B-null cells), while MBD2 recruitment is lost. Thus, recruitment of MBD3 and MBD2 by GCNF links two events, gene-specific repression and DNA methylation, which occur differentially at the Oct4 promoter. GCNF initiates the repression and epigenetic modification of Oct4 gene during ES cell differentiation.

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6

Le Guezennec, Xavier, Michiel Vermeulen, Arie B. Brinkman, Wieteke A. M. Hoeijmakers, Adrian Cohen, Edwin Lasonder, and Hendrik G. Stunnenberg. "MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties." Molecular and Cellular Biology 26, no. 3 (February 1, 2006): 843–51. http://dx.doi.org/10.1128/mcb.26.3.843-851.2006.

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ABSTRACT The human genome contains a number of methyl CpG binding proteins that translate DNA methylation into a physiological response. To gain insight into the function of MBD2 and MBD3, we first applied protein tagging and mass spectrometry. We show that MBD2 and MBD3 assemble into mutually exclusive distinct Mi-2/NuRD-like complexes, called MBD2/NuRD and MBD3/NuRD. We identified DOC-1, a putative tumor suppressor, as a novel core subunit of MBD2/NuRD as well as MBD3/NuRD. PRMT5 and its cofactor MEP50 were identified as specific MBD2/NuRD interactors. PRMT5 stably and specifically associates with and methylates the RG-rich N terminus of MBD2. Chromatin immunoprecipitation experiments revealed that PRMT5 and MBD2 are recruited to CpG islands in a methylation-dependent manner in vivo and that H4R3, a substrate of PRMT, is methylated at these loci. Our data show that MBD2/NuRD and MBD3/NuRD are distinct protein complexes with different biochemical and functional properties.

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7

Hendrich, Brian, Catherine Abbott, Heather McQueen, Doreen Chambers, Sally Cross, and Adrian Bird. "Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and Mbd4 genes." Mammalian Genome 10, no. 9 (September 1, 1999): 906–12. http://dx.doi.org/10.1007/s003359901112.

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8

Kolar, Satya Sree N., Hasna Baidouri, Samuel Hanlon, and Alison M. McDermott. "Protective Role of Murine β-Defensins 3 and 4 and Cathelin-Related Antimicrobial Peptide in Fusarium solani Keratitis." Infection and Immunity 81, no. 8 (May 13, 2013): 2669–77. http://dx.doi.org/10.1128/iai.00179-13.

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ABSTRACTAntimicrobial peptides (AMPs), such as β-defensins and cathelicidins, are essential components of innate and adaptive immunity owing to their extensive multifunctional activities. However, their role in fungal infectionin vivoremains elusive. In this study, we investigated the protective effect of murine β-defensin 3 (mBD3), mBD4, and the cathelicidin cathelin-related antimicrobial peptide (CRAMP) in a murine model ofFusarium solanikeratitis. C57BL/6 mice showed significant corneal disease 1 and 3 days after infection, which was accompanied by enhanced expression of β-defensins and CRAMP. Disease severity was significantly improved 7 days after infection, at which time AMP expression was returning to baseline. Mice deficient in mBD3 (genetic knockout), mBD4 (short interfering RNA knockdown), or CRAMP (genetic knockout) exhibited enhanced disease severity and progression, increased neutrophil recruitment, and delayed pathogen elimination compared to controls. Taken together, these data suggest a vital role for AMPs in defense againstF. solanikeratitis, a potentially blinding corneal disease.

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9

Williams, David C., Merlin Nithya Gnanapragasam, Heather D. Webb, J. Neel Scarsdale, and Gordon D. Ginder. "Targeting a Methyl Cytosine-Binding Protein Complex to Augment Fetal/Embryonic Globin Expression." Blood 114, no. 22 (November 20, 2009): 974. http://dx.doi.org/10.1182/blood.v114.22.974.974.

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Abstract Abstract 974 The vertebrate β-type globin genes were among the first genes shown to be regulated, at least in part, by DNA methylation. The mechanism of transcriptional repression by DNA methylation is chiefly through binding of methyl cytosine binding domain (MBD) proteins and their associated co-repressor complexes. The chicken homolog to an MBD2 containing NuRD co-repressor complex (MeCPC) has previously been purified from primary erythroid cells and characterized as binding to the methylated ρ-globin promoter in erythroid cells of adult chickens in which the gene is silent [Kransdorf et al. Blood 2006; 108:2836-45]. Knockdown of MBD2 by siRNA in MEL cells stably transfected with a methylated ρ-globin gene construct leads to a greater than 10-fold increase in ρ-globin gene expression. Likewise, knockout of MBD2 results in a ∼20 fold upregulation of the human gamma globin gene in adult erythroid cells of βYAC transgenic mice [Rupon et al. PNAS 2006; 103:6617-22]. These observations suggest that disruption of the interaction of MBD2 with its co-repressor complex in adult erythropoiesis would increase fetal hemoglobin expression; a therapeutically beneficial effect for both sickle cell anemia and β-thalassemia. This possibility is further supported by the observation that DNA methylation inhibitors such as 5-azacitidine can increase the expression of γ-globin in patients. Based on these studies, we have pursued structural analysis of the interaction between MBD2 and other components from the MeCPC. We have shown that the individual coiled coil regions from MBD2 and a subunit of the NuRD complex, p66α, form a stable heterodimeric complex. Solving the structure of this coiled coil complex by NMR reveals that the interaction involves a combination of hydrophobic and ionic interactions typical of coiled coil complexes as well as a unique charge interaction involving a pair of highly conserved glutamates residues from p66α and arginine residues from MBD2. The key residues involved in binding are conserved across species, between p66α and p66β homologs, as well as between MBD2, MBD3, and the MBD3L1-L5 homologs. We have shown that the p66α coiled coil can stably bind to MBD3 in solution, indicating that similar tertiary interactions are involved in forming both MBD2 and MBD3 containing NuRD complexes. In order to explore this interaction as a potential therapeutic target, we hypothesized that over-expressing the p66α coiled coil region in tissue culture would disrupt the formation of a normal MeCPC and thereby block the function of MBD2. As predicted, expressing this region in both avian (MEL-ρ) and human (CID-βYAC) tissue culture models of globin gene regulation in adult erythroid cells induces embryonic and fetal β-type globin gene expression, respectively. Furthermore, knock-down of p66α induces fetal/embryonic globin gene expression to a similar degree as knock-down of MBD2. These studies suggest a model in which the p66α coiled peptide can bind MBD2 and block recruitment of native p66α to the NuRD complex, thereby acting in a dominant-negative manner to disrupt MBD2 function. We propose that a peptidomimetic of the p66α coiled coil region could be used therapeutically to augment fetal hemoglobin expression. Disclosures: No relevant conflicts of interest to declare.

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10

Brown, Shelley E., and Moshe Szyf. "Epigenetic Programming of the rRNA Promoter by MBD3." Molecular and Cellular Biology 27, no. 13 (April 23, 2007): 4938–52. http://dx.doi.org/10.1128/mcb.01880-06.

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ABSTRACT Within the human genome there are hundreds of copies of the rRNA gene, but only a fraction of these genes are active. Silencing through epigenetics has been extensively studied; however, it is essential to understand how active rRNA genes are maintained. Here, we propose a role for the methyl-CpG binding domain protein MBD3 in epigenetically maintaining active rRNA promoters. We show that MBD3 is localized to the nucleolus, colocalizes with upstream binding factor, and binds to unmethylated rRNA promoters. Knockdown of MBD3 by small interfering RNA results in increased methylation of the rRNA promoter coupled with a decrease in RNA polymerase I binding and pre-rRNA transcription. Conversely, overexpression of MBD3 results in decreased methylation of the rRNA promoter. Additionally, overexpression of MBD3 induces demethylation of nonreplicating plasmids containing the rRNA promoter. We demonstrate that this demethylation occurs following the overexpression of MBD3 and its increased interaction with the methylated rRNA promoter. This is the first demonstration that MBD3 is involved in inducing and maintaining the demethylated state of a specific promoter.

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Pontes, Thaís Brilhante, Elizabeth Suchi Chen, Carolina Oliveira Gigek, Danielle Queiroz Calcagno, Fernanda Wisnieski, Mariana Ferreira Leal, Samia Demachki, et al. "Reduced mRNA expression levels of MBD2 and MBD3 in gastric carcinogenesis." Tumor Biology 35, no. 4 (December 13, 2013): 3447–53. http://dx.doi.org/10.1007/s13277-013-1455-y.

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12

Loughran, Stephen J., Federico Comoglio, Fiona K. Hamey, Alice Giustacchini, Youssef Errami, Eleanor Earp, Berthold Göttgens, et al. "Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program." Journal of Experimental Medicine 214, no. 10 (September 12, 2017): 3085–104. http://dx.doi.org/10.1084/jem.20161827.

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Differentiation of lineage-committed cells from multipotent progenitors requires the establishment of accessible chromatin at lineage-specific transcriptional enhancers and promoters, which is mediated by pioneer transcription factors that recruit activating chromatin remodeling complexes. Here we show that the Mbd3/nucleosome remodeling and deacetylation (NuRD) chromatin remodeling complex opposes this transcriptional pioneering during B cell programming of multipotent lymphoid progenitors by restricting chromatin accessibility at B cell enhancers and promoters. Mbd3/NuRD-deficient lymphoid progenitors therefore prematurely activate a B cell transcriptional program and are biased toward overproduction of pro–B cells at the expense of T cell progenitors. The striking reduction in early thymic T cell progenitors results in compensatory hyperproliferation of immature thymocytes and development of T cell lymphoma. Our results reveal that Mbd3/NuRD can regulate multilineage differentiation by constraining the activation of dormant lineage-specific enhancers and promoters. In this way, Mbd3/NuRD protects the multipotency of lymphoid progenitors, preventing B cell–programming transcription factors from prematurely enacting lineage commitment. Mbd3/NuRD therefore controls the fate of lymphoid progenitors, ensuring appropriate production of lineage-committed progeny and suppressing tumor formation.

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Verma, Rakesh, Zifeng Mai, Mina Xu, Lin Zhang, Kavita Dhodapkar, and Madhav V. Dhodapkar. "Identification of a Cereblon-Independent Protein Degradation Pathway in Residual Myeloma Cells Treated with Immunomodulatory Drugs." Blood 126, no. 23 (December 3, 2015): 913. http://dx.doi.org/10.1182/blood.v126.23.913.913.

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Abstract Recent studies have shown that binding of immune modulatory drugs (IMiDs)R lenalidomide and pomalidomide (Pom) to the CRBN-CRL4 E3 ubiquitin ligase complex leads to degradation of IKZF1 and IKZF3, which in turn mediates anti-proliferative effects on myeloma cells and enhance IL2 expression by T cells. However as the drug-induced IKZF1 degradation is proteasome-mediated, this mechanism does not explain the apparent paradox that IMiDs mediate synergistic anti-myeloma effects with proteasome inhibitors in the clinic. In order to better understand how MM cells may resist potent IMiDs such as Pom, we examined the clonogenic growth properties of residual MM cells following Pom exposure. Surprisingly, residual MM cell lines and primary MM cells following Pom exposure exhibit paradoxically enhanced clonogenic growth in culture. Human MM cells persisting after Pom exposure also exhibit greater capacity for growth in vivo. Enhanced clonogenic growth was associated with increased expression of embryonal stem cell genes such as SOX2 and RNAi-mediated inhibition of SOX2 abrogated Pom-induced enrichment of clonogenic potential. We hypothesized that as with CBRN/IKZF1-mediated effects, the induction of ES/pluripotency genes in Pom-exposed cells may be related to degradation of repressors of gene transcription. Recent studies have identified MBD3 as a critical component of the pluripotency repressor complex. Pom-exposure led to ubiquitin and proteasome-mediated degradation of MBD3 and RNAi-mediated inhibition of MBD3 led to induction of pluripotency genes by MM cells. As expected, loss of CRBN abrogates the capacity of Pom to mediate degradation of IKZF1. Surprisingly, Pom-mediated degradation of MBD3, enrichment of ES genes and enhancement of clonogenic growth was independent of CRBN as it was observed in MM1s-R10R cells with genomic loss of CRBN, and was not impacted by RNAi-mediated inhibition of CRBN. RNAi-mediated inhibition of IKZF1 also does not lead to enrichment of ES genes and does not phenocopy the effects of MBD3 depletion. Residual MM cells in patients (n=2) treated with Pom also revealed marked depletion of MBD3 protein as well as enrichment of ES gene transcripts. Taken together, these data identify a CRBN/IKZF1-independent pathway for Pom-induced depletion of MBD3 and enrichment of pluripotency genes. Pre-exposure to proteasome inhibitor MG132 abrogated Pom-mediated loss of MBD3 and enrichment of ES genes. Similar results were obtained following treatment with Trichostatin A (TSA) and Romidepsin (FK228), which also inhibited Pom-induced depletion of MBD3. Therefore concurrent therapy of IMiDs with proteasome or HDAC inhibitors may mediate synergistic anti-tumor effects by abrogating adverse effects of Pom exposure on clonogenic growth of residual cells. In order to further dissect the underlying mechanism of Pom-induced degradation of MBD3 in MM cells, we hypothesized engagement of another E3 ligase complex other than CRBN. We show that Pom-induced degradation of MBD3 depends on TRIM27/29 E3 ligase complex, known to be overexpressed in MM plasma cells. Accordingly, RNAi-mediated downregulation of TRIM27/29 inhibits Pom-induced MBD3 depletion and enrichment of clonogenic growth. In summary, these data identify a novel CRBN-independent, TRIM27/29 E3 ligase-dependent pathway for degradation of MDB3 engaged by Pomalidomide, which contributes to the biology of residual MM cells via enrichment of ES genes following exposure to these drugs in vitro/in vivo and provides a novel mechanism for observed synergy with proteasome and HDAC inhibitors. Targeting these pathways may be essential to enhance the therapeutic potential of IMiDs and minimize residual disease in MM. Disclosures No relevant conflicts of interest to declare.

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Banzon, Virryan, Tatiana Kousnetzova, Maria Hankewych, Kenneth Peterson, Joseph DeSimone, and Donald Lavelle. "RNAi Targeting MBD2 Increases γ-Globin Expression in a CID-Dependent Human β-YAC Murine Fetal Bone Marrow Cell Line." Blood 110, no. 11 (November 16, 2007): 1769. http://dx.doi.org/10.1182/blood.v110.11.1769.1769.

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Abstract Increased fetal hemoglobin (HbF) can alleviate the symptoms and increase the life span of patients with sickle cell disease. The development of new methods to increase HbF in patients has been hampered by the lack of cell line models. Recently a new murine fetal bone marrow (FBM) cell line containing the human β-globin gene locus in the context of a yeast artificial chromosome (βYAC) whose growth is dependent on the chemical inducer of dimerization (CID) AP20187 (Ariad Pharmaceuticals) was described (Blau et al, J Biol Chem280: 36642, 2005). The DNA methyltransferase (DNMTase) inhibitor 5-azacytidine increased γ-globin gene expression in this cell line suggesting that it is a good model system for studying the mechanism of DNA methylation in γ-globin gene silencing. To investigate the role of methylated DNA binding proteins in γ-globin silencing, we transduced this cell line with retrovirus vectors expressing shRNA targeting the methylated DNA binding proteins MBD2 and MBD3. Transduced pools were selected for puromycin resistance and the effect on expression of the target gene and γ-globin determined by real time PCR using the ΔΔCT method. Single cell clones were isolated by limited dilution platings for further analysis. No difference in γ-globin expression was observed between clones derived from the parental cell line and cells transduced with a nonsilencing control vector. MBD3 expression was decreased 70–85% but γ-globin expression was not affected in the selected pool or in 12 clones following transduction wth a vector targeting MBD3. In 2 selected pools transduced with an shRNA vector targeting MBD2, MBD2 expression was decreased 60 and 82% and γ-globin expression increased 3.7 fold and 4.76 fold. Mean expression of γ-globin was 3.83 fold higher in 14 clones that showed >90% decrease in MBD2 mRNA compared to 11 clonal isolates derived from cells transduced with the non-silencing control vector (p<.05). In three clones that showed the greatest induction of γ-globin, the fold change (mean +SD) of ε-, γ-, and β-globin expression was 3.98±1.75, 11.29±4.27 and 1.90±1.34, respectively, demonstrating that MBD2 knockdown increased both ε- and γ-globin expression. The level of MBD2 protein in these clones and in two additional clones that showed >90% decrease in MBD2 mRNA but no induction of γ-globin expression were compared by Western blot analysis. MBD2 was decreased >90% in all clones compared to the parental line. Decreased MBD2 levels were therefore not associated with increased γ-globin expression in all clones. We then compared shRNA-mediated MBD2 knockdown with the DNMTase inhibitor decitabine for effects on ε- and γ-globin expression. Expression of ε-globin was increased 76.0±6.1 fold, γ-globin 131±10.2 fold, and β-globin 3.6±0.38 fold following treatment with decitabine (1 × 10−6 M; 48 hours; n=3). We conclude that decreased expression of MBD2 following transduction of the CID-dependent mouse FBM βYAC cell line with an shRNA vector targeting MBD2 is associated with increased γ-globin expression, confirming previous results of analysis of βYAC-MBD2 knockout mice (Rupon et al, PNAS103: 6617, 2006). However, the increase in γ-globin expression was approximately 10 fold greater following decitabine treatment than was achieved with shRNA-mediated MBD2 knockdown.

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Gong, Zihua, Marc Brackertz, and Rainer Renkawitz. "SUMO Modification Enhances p66-Mediated Transcriptional Repression of the Mi-2/NuRD Complex." Molecular and Cellular Biology 26, no. 12 (June 15, 2006): 4519–28. http://dx.doi.org/10.1128/mcb.00409-06.

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ABSTRACT Human p66α and p66β are two potent transcriptional repressors that interact with the methyl-CpG-binding domain proteins MBD2 and MBD3. An analysis of the molecular mechanisms mediating repression resulted in the identification of two major repression domains in p66α and one in p66β. Both p66α and p66β are SUMO-modified in vivo: p66α at two sites (Lys-30 and Lys-487) and p66β at one site (Lys-33). Expression of SUMO1 enhanced the transcriptional repression activity of Gal-p66α and Gal-p66β. Mutation of the SUMO modification sites or using a SUMO1 mutant or a dominant negative Ubc9 ligase resulted in a significant decrease of the transcriptional repression of p66α and p66β. The Mi-2/NuRD components MBD3, RbAp46, RbAp48, and HDAC1 were found to bind to both p66α and p66β in vivo. Most of the interactions were not affected by the SUMO site mutations in p66α or p66β, with two exceptions. HDAC1 binding to p66α was lost in the case of a p66αK30R mutant, and RbAp46 binding was reduced in the case of a p66βK33R mutant. These results suggest that interactions within the Mi-2/NuRD complex as well as optimal repression are mediated by SUMOylation.

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Battistini, Federica, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, and Modesto Orozco. "The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function." PLOS Computational Biology 17, no. 11 (November 8, 2021): e1009547. http://dx.doi.org/10.1371/journal.pcbi.1009547.

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We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

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Li, Chuanyin, Wenli Lu, Liguang Yang, Zhengwei Li, Xiaoyi Zhou, Rong Guo, Junqi Wang, et al. "MKRN3 regulates the epigenetic switch of mammalian puberty via ubiquitination of MBD3." National Science Review 7, no. 3 (February 14, 2020): 671–85. http://dx.doi.org/10.1093/nsr/nwaa023.

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Abstract Central precocious puberty (CPP) refers to a human syndrome of early puberty initiation with characteristic increase in hypothalamic production and release of gonadotropin-releasing hormone (GnRH). Previously, loss-of-function mutations in human MKRN3, encoding a putative E3 ubiquitin ligase, were found to contribute to about 30% of cases of familial CPP. MKRN3 was thereby suggested to serve as a ‘brake’ of mammalian puberty onset, but the underlying mechanisms remain as yet unknown. Here, we report that genetic ablation of Mkrn3 did accelerate mouse puberty onset with increased production of hypothalamic GnRH1. MKRN3 interacts with and ubiquitinates MBD3, which epigenetically silences GNRH1 through disrupting the MBD3 binding to the GNRH1 promoter and recruitment of DNA demethylase TET2. Our findings have thus delineated a molecular mechanism through which the MKRN3–MBD3 axis controls the epigenetic switch in the onset of mammalian puberty.

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Hendrich, B. "Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development." Genes & Development 15, no. 6 (March 15, 2001): 710–23. http://dx.doi.org/10.1101/gad.194101.

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Jaffer, Sajjida, Pollyanna Goh, Mahnaz Abbasian, and Amit C. Nathwani. "Mbd3 Promotes Reprogramming of Primary Human Fibroblasts." International Journal of Stem Cells 11, no. 2 (November 30, 2018): 235–41. http://dx.doi.org/10.15283/ijsc18036.

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Moon, Byoung-San, Hyung-Mun Yun, Wen-Hsuan Chang, Bradford H. Steele, Mingyang Cai, Si Ho Choi, and Wange Lu. "Smek promotes corticogenesis through regulating Mbd3’s stability and Mbd3/NuRD complex recruitment to genes associated with neurogenesis." PLOS Biology 15, no. 5 (May 3, 2017): e2001220. http://dx.doi.org/10.1371/journal.pbio.2001220.

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21

Chatterjee, Shankha Subhra, Mayukh Biswas, Liberalis Debraj Boila, Sayan Chakraborty, Sayantani Sinha, Debasis Banerjee, and Amitava Sengupta. "UTX and MBD3 Epistasis Regulates Rac Gtpase Activation and Sensitizes Human Acute Myeloid Leukemia Cells to Dock Inhibition." Blood 132, Supplement 1 (November 29, 2018): 3880. http://dx.doi.org/10.1182/blood-2018-99-113843.

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Abstract Transcriptional plasticity is an evolving phenomenon in cancer biology. Mutational profiling alone may not suffice to dissect transcriptional dependency and underlying epigenetic vulnerabilities in tumorigenesis. Histone 3 lysine 27 (H3K27) demethylases (UTX, UTY and JMJD3) critically regulate transcriptional architecture. Recently it has been demonstrated that Utx (Kdm6a) plays tumor suppressor role in myeloid leukemogenesis through noncatalytic activity (Gozdecka M, et al., Nat Genet, 2018). Conditional (Mx1-Cre) deletion of Utx caused development of acute myeloid leukemia (AML) in ~ 60% of the mice; wherein, only Utx-/-, but not Utx+/-, aged (22 months) mice presented with AML. Paradoxically, previous report suggested that Utx conditional (Vav1-Cre) knock out male/female mice did not develop leukemia over 18 months (Tian, L., et al., Blood, 2015). In our recent report we have identified that expression of UTX is significantly increased in human primary AML, and pharmacological inhibition of H3K27 demethylase catalytic activity attenuated survival of AML cells (Boila L.D. et al,. Exp Hematol, 2017). Therefore the contribution of UTX in AML pathogenesis remains context dependent, and probably contentious, and warrants further investigations. ATP-dependent chromatin remodelers have been implicated in AML pathobiology (Chatterjee S.S., et al., Mol Cancer Res, 2018). We reported that loss of MBD3, a scaffold of NuRD chromatin remodeler, in human primary AML cells associates with nucleation of leukemic NuRD (Biswas M et al., Blood, 2017). Loss of Mbd3(Vav1-Cre) has been shown to disrupt NuRD complex integrity and causes T-cell lymphoma, suggesting tissue-specific function of NuRD (Loughran, S.J., et al., J Exp Med, 2017). Interestingly, in our present study we have identified for the first time that endogenous UTX, but not JMJD3, reversibly co-immunoprecipitates with NuRD in AML cells. These findings led us to test the hypothesis whether UTX would participate with NuRD in AML. ChIP-seq analysis in AML blasts using antibodies against UTX and CHD4 (intact ATPase component of leukemic NuRD) along with H3K27ac identified the co-localized genes. ChIP-qPCR, transcriptome, pathway analysis (P<0.001) performed in paired AML, and MBD3loss of function experiments suggested an enrichment of Dedicator of Cytokinesis (DOCK) transcripts as bona fide effectors of UTX and NuRD in AML. DOCK proteins are conserved atypical guanine nucleotide exchange factors (GEFs) for Rho GTPase activation, regulating cell motility and invasion. Earlier we had shown that small GTPases regulate myeloid leukemia cell engraftment, survival in vivo (Sengupta A et al., Blood, 2010). DOCK1 upregulation is associated with a poor prognosis in AML (Hwei, L.S., Blood, 2016). TCGA cross-cancer analysis showed that UTX is maximally expressed, whereas MBD3 is downregulated in AML among all cancer types. Consistent with this observation, DOCK expression was significantly (P<0.001) increased in MBD3loUTXhi AML cohort compared to MBD3hiUTXlo AML. Importantly, MBD3loUTXhi patients have relatively poor survival compared to MBD3hiUTXhi individuals, indicating that a combination of high UTX and low MBD3 expression could be a marker of poor prognosis in AML. Mechanistically, MBD3 deficiency caused loss of HDAC1 occupancy with a corresponding increase in UTX, CBP and H3K27ac on target DOCK loci leading to de-repression of gene expression. In agreement with this finding, loss of MBD3 resulted in ~ 2-fold increase in active Rac GTP and promoted AML cell migration to CXCL12. Interestingly, UTX silencing opposed DOCK expression, Rac activation and reversed hyper-migratory phenotype of MBD3-deficient AML cells. Together, these data account for UTX and MBD3 epistasis in regulating DOCK-Rac signalling in AML. Finally, treatment with DOCK inhibitor CPYPP dramatically inhibited survival of AML cells while having minimal effect on the survival of normal CD34+ cells. In unison, our findings highlight UTX as a putative oncogene in conjunction with leukemic NuRDand posit DOCK proteins as an important target of UTX-NuRD axis in human AML cells. To conclude, we provide evidence for MBD3-deficient NuRD in leukemia pathobiology, and inform a novel epistasis between UTX and NuRD towards maintenance of oncogenic gene expression in AML, and rationalize DOCK inhibition as a novel therapeutic modality for precision medicine in AML. Disclosures No relevant conflicts of interest to declare.

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22

Li, Ruizhi, Qihua He, Shuo Han, Mingzhi Zhang, Jinwen Liu, Ming Su, Shiruo Wei, Xuan Wang, and Li Shen. "MBD3 inhibits formation of liver cancer stem cells." Oncotarget 8, no. 4 (November 22, 2016): 6067–78. http://dx.doi.org/10.18632/oncotarget.13496.

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23

Brown, Shelley E., and Moshe Szyf. "Epigenetic Programming of the rRNA Promoter by MBD3." Molecular and Cellular Biology 28, no. 3 (February 1, 2008): 1195. http://dx.doi.org/10.1128/mcb.02037-07.

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24

Günther, Katharina, Mareike Rust, Joerg Leers, Thomas Boettger, Maren Scharfe, Michael Jarek, Marek Bartkuhn, and Rainer Renkawitz. "Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences." Nucleic Acids Research 41, no. 5 (January 29, 2013): 3010–21. http://dx.doi.org/10.1093/nar/gkt035.

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25

Zaccak, Michael, Zena Qasem, Lada Gevorkyan-Airapetov, and Sharon Ruthstein. "An EPR Study on the Interaction between the Cu(I) Metal Binding Domains of ATP7B and the Atox1 Metallochaperone." International Journal of Molecular Sciences 21, no. 15 (August 2, 2020): 5536. http://dx.doi.org/10.3390/ijms21155536.

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Copper’s essentiality and toxicity mean it requires a sophisticated regulation system for its acquisition, cellular distribution and excretion, which until now has remained elusive. Herein, we applied continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) spectroscopy in solution to resolve the copper trafficking mechanism in humans, by considering the route travelled by Cu(I) from the metallochaperone Atox1 to the metal binding domains of ATP7B. Our study revealed that Cu(I) is most likely mediated by the binding of the Atox1 monomer to metal binding domain 1 (MBD1) and MBD4 of ATP7B in the final part of its extraction pathway, while the other MBDs mediate this interaction and participate in copper transfer between the various MBDs to the ATP7B membrane domain. This research also proposes that MBD1-3 and MBD4-6 act as two independent units.

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Brumbaugh, Justin, and Konrad Hochedlinger. "Removing Reprogramming Roadblocks: Mbd3 Depletion Allows Deterministic iPSC Generation." Cell Stem Cell 13, no. 4 (October 2013): 379–81. http://dx.doi.org/10.1016/j.stem.2013.09.012.

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27

Zhang, Lei, Yongchao Zheng, Yuanqing Sun, Ying Zhang, Jia yan, Zhifeng Chen, and Hong Jiang. "MiR‐134‐Mbd3 axis regulates the induction of pluripotency." Journal of Cellular and Molecular Medicine 20, no. 6 (February 29, 2016): 1150–58. http://dx.doi.org/10.1111/jcmm.12805.

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28

Cui, Jie, Biao Duan, Xuyang Zhao, Yan Chen, Shixun Sun, Wenjie Deng, Yujie Zhang, Jun Du, Yongchang Chen, and Luo Gu. "MBD3 mediates epigenetic regulation on EPAS1 promoter in cancer." Tumor Biology 37, no. 10 (July 27, 2016): 13455–67. http://dx.doi.org/10.1007/s13277-016-5237-1.

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29

Wang, Xingwang, Junsong Shi, Gengyuan Cai, Enqin Zheng, Dewu Liu, Zhenfang Wu, and Zicong Li. "Overexpression of MBD3 Improves Reprogramming of Cloned Pig Embryos." Cellular Reprogramming 21, no. 5 (October 1, 2019): 221–28. http://dx.doi.org/10.1089/cell.2019.0008.

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30

Li, Wanyi, Yan Feng, Yu Kuang, Wei Zeng, Yuan Yang, Hong Li, Zhonghua Jiang, and Mingyuan Li. "Construction of Eukaryotic Expression Vector with mBD1-mBD3 Fusion Genes and Exploring Its Activity against Influenza A Virus." Viruses 6, no. 3 (March 13, 2014): 1237–52. http://dx.doi.org/10.3390/v6031237.

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31

Brackertz, Marc, Joern Boeke, Ru Zhang, and Rainer Renkawitz. "Two Highly Related p66 Proteins Comprise a New Family of Potent Transcriptional Repressors Interacting with MBD2 and MBD3." Journal of Biological Chemistry 277, no. 43 (August 14, 2002): 40958–66. http://dx.doi.org/10.1074/jbc.m207467200.

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32

Jin, Seung-Gi, Chun-Ling Jiang, Tibor Rauch, Hongwei Li, and Gerd P. Pfeifer. "MBD3L2 Interacts with MBD3 and Components of the NuRD Complex and Can Oppose MBD2-MeCP1-mediated Methylation Silencing." Journal of Biological Chemistry 280, no. 13 (January 27, 2005): 12700–12709. http://dx.doi.org/10.1074/jbc.m413492200.

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33

Yu, Xiaofei, Alexander Azzo, Stephanie M. Bilinovich, Xia Li, Mikhail Dozmorov, Ryo Kurita, Yukio Nakamura, David C. Williams, and Gordon D. Ginder. "Disruption of the MBD2-NuRD complex but not MBD3-NuRD induces high level HbF expression in human adult erythroid cells." Haematologica 104, no. 12 (April 19, 2019): 2361–71. http://dx.doi.org/10.3324/haematol.2018.210963.

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34

Cui, Yi, Jian Li, Ling Weng, Sara E. Wirbisky, Jennifer L. Freeman, Jingping Liu, Qing Liu, Xianrui Yuan, and Joseph Irudayaraj. "Regulatory landscape and clinical implication of MBD3 in human malignant glioma." Oncotarget 7, no. 49 (November 7, 2016): 81698–714. http://dx.doi.org/10.18632/oncotarget.13173.

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35

dos Santos, Rodrigo L., Luca Tosti, Aliaksandra Radzisheuskaya, Isabel M. Caballero, Keisuke Kaji, Brian Hendrich, and José C. R. Silva. "MBD3/NuRD Facilitates Induction of Pluripotency in a Context-Dependent Manner." Cell Stem Cell 15, no. 1 (July 2014): 102–10. http://dx.doi.org/10.1016/j.stem.2014.04.019.

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36

dos Santos, Rodrigo L., Luca Tosti, Aliaksandra Radzisheuskaya, Isabel M. Caballero, Keisuke Kaji, Brian Hendrich, and José C. R. Silva. "MBD3/NuRD Facilitates Induction of Pluripotency in a Context-Dependent Manner." Cell Stem Cell 15, no. 3 (September 2014): 392. http://dx.doi.org/10.1016/j.stem.2014.08.005.

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37

Zhu, Y., D. J. Harrison, and S. A. Bader. "Genetic and epigenetic analyses of MBD3 in colon and lung cancer." British Journal of Cancer 90, no. 10 (April 13, 2004): 1972–75. http://dx.doi.org/10.1038/sj.bjc.6601776.

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38

Shimbo, Takashi, Ying Du, Sara A. Grimm, Archana Dhasarathy, Deepak Mav, Ruchir R. Shah, Huidong Shi, and Paul A. Wade. "MBD3 Localizes at Promoters, Gene Bodies and Enhancers of Active Genes." PLoS Genetics 9, no. 12 (December 26, 2013): e1004028. http://dx.doi.org/10.1371/journal.pgen.1004028.

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39

Brown, Shelley E., Matthew J. Suderman, Michael Hallett, and Moshe Szyf. "DNA demethylation induced by the methyl-CpG-binding domain protein MBD3." Gene 420, no. 2 (September 2008): 99–106. http://dx.doi.org/10.1016/j.gene.2008.05.009.

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40

Mor, Nofar, Yoach Rais, Daoud Sheban, Shani Peles, Alejandro Aguilera-Castrejon, Asaf Zviran, Dalia Elinger, et al. "Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency." Cell Stem Cell 23, no. 3 (September 2018): 412–25. http://dx.doi.org/10.1016/j.stem.2018.07.004.

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41

Iwano, Hidetomo, Masahiko Nakamura, and Shoji Tajima. "Xenopus MBD3 plays a crucial role in an early stage of development." Developmental Biology 268, no. 2 (April 2004): 416–28. http://dx.doi.org/10.1016/j.ydbio.2003.12.032.

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42

Kaji, Keisuke, Isabel Martín Caballero, Ruth MacLeod, Jennifer Nichols, Valerie A. Wilson, and Brian Hendrich. "The NuRD component Mbd3 is required for pluripotency of embryonic stem cells." Nature Cell Biology 8, no. 3 (February 5, 2006): 285–92. http://dx.doi.org/10.1038/ncb1372.

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43

Bachmann, Nadine, Sabrina Spengler, Gerhard Binder, and Thomas Eggermann. "MBD3 mutations are not responsible for ICR1 hypomethylation in Silver–Russell syndrome." European Journal of Medical Genetics 53, no. 1 (January 2010): 23–24. http://dx.doi.org/10.1016/j.ejmg.2009.12.002.

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44

Shimbo, Takashi, Motoki Takaku, and Paul A. Wade. "High-quality ChIP-seq analysis of MBD3 in human breast cancer cells." Genomics Data 7 (March 2016): 173–74. http://dx.doi.org/10.1016/j.gdata.2015.12.029.

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45

Tatematsu, Ken-ichiro, Tetsu Yamazaki, and Fuyuki Ishikawa. "MBD2-MBD3 complex binds to hemi-methylated DNA and forms a complex containing DNMT1 at the replication foci in late S phase." Genes to Cells 5, no. 8 (August 2000): 677–88. http://dx.doi.org/10.1046/j.1365-2443.2000.00359.x.

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46

Aguilera, Cristina, Kentaro Nakagawa, Rocio Sancho, Atanu Chakraborty, Brian Hendrich, and Axel Behrens. "c-Jun N-terminal phosphorylation antagonises recruitment of the Mbd3/NuRD repressor complex." Nature 469, no. 7329 (January 2011): 231–35. http://dx.doi.org/10.1038/nature09607.

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47

Reese, Kimberly J., Shu Lin, Raluca I. Verona, Richard M. Schultz, and Marisa S. Bartolomei. "Maintenance of Paternal Methylation and Repression of the Imprinted H19 Gene Requires MBD3." PLoS Genetics 3, no. 8 (August 17, 2007): e137. http://dx.doi.org/10.1371/journal.pgen.0030137.

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48

Reese, Kimberly, Shu Lin, Raluca I. Verona, Richard Schultz, and Marisa Bartolomei. "Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3." PLoS Genetics preprint, no. 2007 (2005): e137. http://dx.doi.org/10.1371/journal.pgen.0030137.eor.

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49

Yildirim, Ozlem, Ruowang Li, Jui-Hung Hung, Poshen B. Chen, Xianjun Dong, Ly-Sha Ee, Zhiping Weng, Oliver J. Rando, and Thomas G. Fazzio. "Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells." Cell 147, no. 7 (December 2011): 1498–510. http://dx.doi.org/10.1016/j.cell.2011.11.054.

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50

Jiang, Chun-Ling, Seung-Gi Jin, Dong-Hyun Lee, Zi-Jian Lan, Xueping Xu, Timothy R. O'Connor, Piroska E. Szabó, Jeffrey R. Mann, Austin J. Cooney, and Gerd P. Pfeifer. "MBD3L1 and MBD3L2, Two New Proteins Homologous to the Methyl-CpG-Binding Proteins MBD2 and MBD3: Characterization of MBD3L1 as a Testis-Specific Transcriptional Repressor." Genomics 80, no. 6 (December 2002): 621–29. http://dx.doi.org/10.1006/geno.2002.7001.

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