Relevant bibliographies by topics / MBD3

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Academic literature on the topic 'MBD3'

Author: Grafiati
Published: 4 June 2021
Last updated: 27 April 2022

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Journal articles on the topic "MBD3"

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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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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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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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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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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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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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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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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Dissertations / Theses on the topic "MBD3"

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Laget, Sophie. "Les protéines humaines MBD4, MBD5 et MBD6, et la régulation épigénétique des gènes." Paris 11, 2010. http://www.theses.fr/2010PA112148.

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Les protéines humaines se liant à l’ADN méthylé par un domaine MBD sont des éléments clefs de la chromatine. Elles peuvent se localiser à l'hétérochromatine méthylée, et, en synergie avec d'autres composants de la chromatine, réprimer l'expression des gènes. Des mutations de MeCP2, la première protéine à domaine MBD découverte, causent un trouble neurologique humain sévère. La première partie de mon travail de doctorat était d’initier la caractérisation de deux protéines humaines à domaine MBD, MBD5 et MBD6. Comme MBD5 a récemment été associée au retard mental, il était important de clarifier si elle se lie l'ADN vraiment à l’ADN méthylé. Bien qu’elles colocalisent avec l’hétérochromatine dans les cellules de culture, les protéines n’interagissent pas avec l’ADN méthylé in vitro. Elles pourraient cependant contribuer à la formation ou la fonction de l'hétérochromatine. La deuxième partie de mon travail porte sur l'étude de MBD4, une protéine impliquée dans la réparation de l'ADN, et mutée dans plusieurs types de cancer. Nous avons constaté que MBD4 interagit directement avec la méthyltransférase de l’ADN DNMT1. Nous étudions actuellement les cibles de MBD4 à l'échelle du génome humain. Ce travail pourrait éclairer le rôle fonctionnel de MBD4 dans la régulation épigénétique des gènes et le cancer
Human methyl-CpG Binding Domain (MBD) proteins are key chromatin components. They can localize to methylated heterochromatin, and, in synergy with other chromatin components, repress gene expression. Mutations in MeCP2, the first MBD protein discovered, can cause a severe human neurological disorder. The first part of my graduate work was to initiate the characterization of two human MBD proteins, MBD5 and MBD6. As MBD5 was recently reported a possible cause of mental retardation, it was important to clarify if they really bind methylated DNA. Although they colocalize with heterochromatin in cultured cells, the proteins do not interact with methylated DNA in vitro. They could however contribute to the formation or function of heterochromatin. The study of MBD4, a protein involved in DNA repair, and mutated in several types of cancer, was the second part of my work. We found that MBD4 could interact directly with DNA methyltransferase 1 (DNMT1). We are currently studying genome-wide MBD4 targets. This work could illuminate the functional role of MBD4 in epigenetic gene regulation and cancer
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Signolet, Jason George. "Control of self-renewal and pluripotency by the Mbd3/NuRD complex." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648774.

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Brown, Shelley. "The role of MBD3 and the cell cycle in the regulation of the epigenome." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=19259.

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DNA methylation patterns were thought to be stable and unchanging throughout life. However more evidence has emerged suggesting that the DNA methylation pattern is dynamic, subject to changes in response to physiological and environmental cues. Thus, it is crucial to understand when these changes occur and how the DNA methylation pattern can be manipulated. This thesis focuses on alterations in the DNA methylation pattern during the cell cycle both globally and at a specific promoter, as well as how the methylated DNA binding domain protein MBD3 is involved in regulating these changes. During the cell cycle, the levels of DNA methylation are highest during S phase, and drop after DNA replication during G0/G1. These changes in DNA methylation are not occurring at repetitive sequences, but rather at specific sequences throughout the genome, as determined using a CpG island microarray. Conversely, the DNA methylation pattern of the ribosomal RNA (rRNA) promoter follows an opposite pattern, with decreased levels of DNA methylation at G1/S and S phase, with the levels increasing as the cell progresses through the cell cycle. These changes at the rRNA promoter correlate with other epigenetic changes, including histone acetylation and transcription factor binding, indicating a coordinated epigenetic change regulated with the different stages of the cell cycle. We further determined how the DNA methylation pattern of the rRNA promoter is regulated, and found a critical role for the methylated DNA binding domain protein MBD3. MBD3 was found to bind to unmethylated rRNA promoters, together with the transcription factor Upstream Binding Factor (UBF). Manipulating the levels of MBD3 expression resulted in a change in the levels of DNA meth
Le patron de méthylation de l'ADN est connu pour être stable et fixes durant toute la vie. Cependant, plusieurs évidences suggèrent que le patron de méthylation de l'ADN soit dynamique, sujet aux changements en réponse à des stimuli physiologiques et environnementaux. Ainsi, il est crucial de comprendre quand ces changements se produisent et comment le patron de méthylation d'ADN peut être manipulé. Cette thèse se concentre sur les changements dans le patron de méthylation de l'ADN pendant le cycle cellulaire, à l'échelle globale et au niveau de promoteurs spécifiques, et également sur le mécanisme par lequel la protéine MBD3, qui contient un domaine de liaison à l'ADN méthylé, module ces changements. Pendant le cycle cellulaire, les niveaux de méthylation de l'ADN sont plus élevés pendant la phase de S, et chute par la suite après la réplication de l'ADN lors de la phase G0/G1. Ces changements de méthylation de l'ADN ne se produisent pas dans des séquen-ces répétitives, mais plutôt dans des séquences spécifiques dans tout le génome, tel que déterminé par microarray des îlots CpG. Réciproquement, le patron de méthylation du promoteur de l'ARN ribosomal (ARNr) suit un modèle opposé, avec un bas niveau de méthylation de l'ADN en phase G1/S et S, qui augmente progressivement pendant le cycle cellulaire. Ces changements dans le promoteur de l'ARNr corrèlent avec d'autres changements épigénétiques, y compris l'acétylation des histones et la liaison de facteurs de transcription, indiquant un changement épigénétique coordonné régulé avec les différentes étapes du cycle cellulaires. Nous avons de plus déterminé comment le patron de méthylation du promoteur de l'ARNr est régulé
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Tabaroni, Rachel. "Etude structurale du complexe de remodelage de la chromatine NuRD et sa sous-unité MBD3 liée à l'ADN." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAJ094.

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La régulation de la transcription est un processus dynamique faisant intervenir le recrutement de complexes protéiques impliqués dans le remodelage de la chromatine. Parmi eux, mon travail s’est focalisé sur le complexe NuRD (Nucleosome Remodeling and histone Deacetylation) et sa sous-unité de liaison à l’ADN CpG MBD3. Pour cela une approche de biologie structurale intégrative combinant la préparation biochimique, la caractérisation biophysique et l’étude structurale par cryo-EM et cristallographie aux rayons-X a été mise en place. Les caractérisations biophysiques de MBD3 ont permis de mettre en évidence son interaction avec un ADN non-modifié CpG et des cristaux diffractant jusqu’à 3.9 Å ont été obtenu. De plus la région désordonnée en aval du domaine de liaison a été identifiée et son impact dans la formation de complexe caractérisé. Des cristaux pour les différentes constructions en complexe avec l’ADN ont été obtenus et sont actuellement optimisés. Enfin l’optimisation de la purification et la préparation du complexe, ont permis la visualisation du complexe NuRD et mettent en avant pour la première fois une organisation en domaines du complexe
Transcription regulation of chromatin is a very dynamic process regulated through the recruitment of chromatin-remodeling complexes. My work focuses on NuRD for Nucleosome remodeling and histones deacetylation complex a 1 MDa multi-subunit protein complex and its subunit MBD3 a CpG-binding protein and more precisely on an integrated biology approach of this molecular assembly and its interaction with DNA. It combines biochemical preparation, biophysical characterization, single particle cryo-eletron microscopy and x-ray crystallography. Biophysical analysis show that MBD domain of MBD3 interacts with unmodified CpG DNA, a crystal diffracting up to 3.9 Å were obtained. Moreover a C-terminal intrinsically disordered region of MBD3 were identified and despite is inherent disorder seems to increase the binding affinity of MBD3 for DNA. Crystals were obtained for both constructs in complex with DNA and are currently optimized.Cryo-EM study of NuRD complex allows us to develop and optimized purification and grids preparation for the visualization of the complex. The present results reveal a domain organization of the complex never identify before
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Cramer, Jason. "EVOLUTION AND DIVERGENCE OF THE STRUCTURAL AND PHYSICAL PROPERTIES OF DNA BINDING BY METHYL-CYTOSINE BINDING DOMAIN FAMILY MEMBERS 2 AND 3." VCU Scholars Compass, 2014. http://scholarscompass.vcu.edu/etd/3517.

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The studies presented in this dissertation, Evolution And Divergence Of The Structural And Physical Properties Of DNA Binding By Methyl-Cytosine Binding Domain Family Members 2 And 3, pertain primarily to two key epigenetic regulators involved with the biological interpretation of methylated DNA marks. We provide insights into the emergence and evolution of the MBD2 and MBD3 and how those molecular entities influence heritable changes in gene activity. We further provide details regarding the mystery surrounding MBD3 function and the MBD2-mediated capacity of primitive animals to carry out methylation-specific epigenetic mechanisms. In chapter two, we describe the DNA binding properties of MBD2 and MBD3. This study provides information regarding previously unidentified MBD3 binding properties and potential biological function. In chapter three, we show that sponges demonstrate a MBD2-mediated capacity for binding methylated DNA sites, recruit NuRD components in vitro, and knockdown of MBD2 in the freshwater desmosponge, Ephydatia muelleri, promotes an abnormal growth phenotype.
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Ee, Ly-Sha. "Regulation of Pluripotency and Differentiation by Chromatin Remodeling Factors." eScholarship@UMMS, 2017. https://escholarship.umassmed.edu/gsbs_diss/921.

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Central to the control of virtually all cellular activity is the regulation of gene expression. In eukaryotes, this regulation is greatly influenced by chromatin structure, which is itself regulated by numerous chromatin-remodeling complexes. These are typically large protein complexes with interchangeable subunits that allow for highly specialized functions in different cell types. Moreover, additional specificity can be gained through complexes formed from different subunit isoforms. Histone modifications also regulate chromatin by recruiting remodeling complexes to particular genomic regions. In this thesis we characterize MBD3C, an isoform of the Nucleosome Remodeling and Deacetylase (NuRD) complex subunit MBD3. MBD3 is essential for pluripotency and development, but MBD3C appears to be expressed only in embryonic stem cells (ESCs), and whether it forms a distinct NuRD complex, how its expression is regulated, and its precise function(s) remain unknown. We show that MBD3C forms a complete NuRD complex that functions redundantly with the other MBD3 isoforms in ESC gene regulation. Furthermore, MBD3C binds the SET/MLL complex subunit WDR5 through a conserved motif within its unique N-terminal region, and this interaction is necessary for the regulation of >2,000 ESC genes. Together, these findings indicate that ESCs can utilize isoforms of the same protein to achieve similar functions through diverse mechanisms. The second part of this thesis focuses on the role of the histone modification H3.3K56ac in pluripotency and differentiation. Although H3K56ac is well-studied in yeast, in mammalian cells it is far less abundant and its functions are largely unknown. Our data indicate that the H3.3K56R mutant is largely normal for ESC maintenance and loss of pluripotency markers during differentiation, but H3.3K56ac is necessary for proper lineage commitment. Ongoing studies will characterize the H3.3K56Q phospho-mimetic mutant during differentiation, and examine H3.3K56ac function at lineage-specific genes.
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Ee, Ly-Sha. "Regulation of Pluripotency and Differentiation by Chromatin Remodeling Factors." eScholarship@UMMS, 2008. http://escholarship.umassmed.edu/gsbs_diss/921.

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Central to the control of virtually all cellular activity is the regulation of gene expression. In eukaryotes, this regulation is greatly influenced by chromatin structure, which is itself regulated by numerous chromatin-remodeling complexes. These are typically large protein complexes with interchangeable subunits that allow for highly specialized functions in different cell types. Moreover, additional specificity can be gained through complexes formed from different subunit isoforms. Histone modifications also regulate chromatin by recruiting remodeling complexes to particular genomic regions. In this thesis we characterize MBD3C, an isoform of the Nucleosome Remodeling and Deacetylase (NuRD) complex subunit MBD3. MBD3 is essential for pluripotency and development, but MBD3C appears to be expressed only in embryonic stem cells (ESCs), and whether it forms a distinct NuRD complex, how its expression is regulated, and its precise function(s) remain unknown. We show that MBD3C forms a complete NuRD complex that functions redundantly with the other MBD3 isoforms in ESC gene regulation. Furthermore, MBD3C binds the SET/MLL complex subunit WDR5 through a conserved motif within its unique N-terminal region, and this interaction is necessary for the regulation of >2,000 ESC genes. Together, these findings indicate that ESCs can utilize isoforms of the same protein to achieve similar functions through diverse mechanisms. The second part of this thesis focuses on the role of the histone modification H3.3K56ac in pluripotency and differentiation. Although H3K56ac is well-studied in yeast, in mammalian cells it is far less abundant and its functions are largely unknown. Our data indicate that the H3.3K56R mutant is largely normal for ESC maintenance and loss of pluripotency markers during differentiation, but H3.3K56ac is necessary for proper lineage commitment. Ongoing studies will characterize the H3.3K56Q phospho-mimetic mutant during differentiation, and examine H3.3K56ac function at lineage-specific genes.
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Lyst, Matthew James. "Biochemical analysis of MBD1." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3931.

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Methylation of cytosines within CpG dinucleotides is a feature of vertebrate DNA. The precise role of DNA methylation is unknown to date, although it has been implicated in several processes relating to transcriptional regulation. One approach to study DNA methylation is the characterization of proteins that bind specifically to methylated DNA. One such family of proteins is the methyl-CpG binding domain (MBD) containing family and MBD1 is a member of this family. MBD1 is implicated in transcriptional repression and various mechanisms by which it might bring about gene silencing have been proposed. These are mainly based on studies reporting interactions between MBD1 and various proteins that regulate chromatin structure. Also MBD1 function can be modified by PIAS proteins, which stimulate its conjugation to SUMO (small ubiquitinlike modifier).The original aim of this work was to address two questions about MBD1: (1) Does MBD1 form part of a stable complex with other factors, and if so, what are the identities of the other components? Purification of MBD1 revealed the presence of no stably bound interacting proteins. However, some evidence indicates MBD1 may interact with itself and form dimers, a finding which impacts on many aspects of the function of MBD1. Also a proteomics screen for transient interaction partners identified candidate binding partners for MBD1 and the related protein MeCP2, which may throw light on the function of these proteins. (2) Are there any activities which regulate MBD1 function by the removal of SUMO from this protein? No activities capable of removing SUMO from native MBD1 were found but it was demonstrated that this modification leads to the destabilization of MBD1 in vitro. The relevance of this finding in vivo is yet to be determined.
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Morey, Ramonell Lluís. "Chromatin alterations imposed by the oncogenic transcription factor PML-RAR." Doctoral thesis, Universitat Pompeu Fabra, 2008. http://hdl.handle.net/10803/7138.

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En mamíferos, así como en plantas, mutaciones en AND helicasas/ATPasas del la família SNF2, no solo afectan a la estructura de la cromatina, sino que también afectan al patrón global de la metilación del ADN. Sugiriendo una relación funcional entre la estructura de la cromatina y la epigenética. El complejo NuRD, el cual posee una ATPasa de la familía SNF2, está relacionado con la represión de la transcripción y en el remodelamiento de la cromatina. Nuestro laboratorio demostró que la proteína leucémica PML-RARα reprime la transcripción de sus genes diana por el reclutamiento de DNMTs y el complejo PRC2. En esta tesis, demostramos una relación directa del complejo NuRD en la represión génica y en los cambios epigenéticos en la leucemia promielocítica aguda (APL). Mostramos que PML-RARα se une y recluta NuRD a sus genes diana, incluyendo el gen supresor de tumores RAR2, facilitando que el complejo de Polycomb se reclute y metile la lisina 27 de la histona H3. Tratamiento con Acido Retinóico (RA), el qual se utiliza en pacientes, reduce la ocupación de NuRD en células leucémicas. Eliminando NuRD no solo provoca que las histonas no se deacetilen y que la cromatina no se compacte, sino que también provoca que tanto la metilación del ADN y de las histonas no se produzca, así como la represión génica del gen RAR2, favoreciendo la diferenciación celular. Nuestros resultados caracterizan un nuevo papel del complejo NuRD en el establecimiento de los patrones epigenéticos en APL, demostrando una relación esencial entre la estructura de la cromatina y epigenética durante el desarrollo de la leucemia, pudiéndose aplicar a la terapia de esta enfermedad.
In mammals, as in plants, mutations in SNF2-like DNA helicases/ATPases were shown to affect not only chromatin structure but also global methylation patterns, suggesting a potential functional link between chromatin structure and epigentic marks. The SNF2-like containing NuRD complex is involved in gene transcriptional repression and chromatin remodeling. We have previously shown that the leukemogenic protein PMLRARα represses target genes through recruitment of DNMTs and Polycomb complex. In this thesis, we demonstrate a direct role of the NuRD complex in aberrant gene repression and transmission of epigenetic repressive marks in acute promyelocytic leucemia (APL). We show that PML-RARα binds and recruits NuRD to target genes, including to the tumor-suppressor gene RAR2. In turn, the NuRD complex facilitates Polycomb binding and histone methylation at lysine 27. Retinoic acid treatment reduced the promoter occupancy of the NuRD complex. Knock-down of the NuRD complex in leukemic cells not only prevented histone deacetylation and chromatin compaction, but also impaired DNA and histone methylation as well as stable silencing, thus favoring cellular differentiation. These results unveil an important role for NuRD in the establishment of altered epigenetic marks in APL, demonstrating an essential link between chromatin structure and epigenetics in leukemogenesis that could be exploited for therapeutic intervention.
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MacDougall, Eilidh Fiona. "Functional analysis of the DNA repair protein MBD4." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/12502.

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The methylation of cytosine plays a fundamental role in mediating transcriptional repression. However, 5-methylcytosine can undergo spontaneous hydrolytic delamination to form thymine. It the resulting T:G mismatch is replicated prior to being repaired, a C:G to T:A transition mutation will be present in one of the two daughter DNA molecules. Methyl-CpG-binding domain protein 4 (MBD4) is a DNA glycosylase that can excise thymine from mismatches with guanine, and that acts preferentially on T:G mismatches within CpG dinucleotides in vitro. In order to test the hypothesis that MBD4 repairs the product of 5-methylcytosine delamination in vivo, MBD4-deficient mice were crossed onto the Big Blue genetic background. This background enables the frequency and spectrum of in vivo mutations in a bacteriophage lambda cII transgene to be determined. As predicted, Mbd4-/- mice have a significantly increased frequency of C:G to T:A mutation sat CpG dinucleotides. T:G mismatch-specific thymine DNA glycosine (TDG) can also attempt to excise thymine from T:G mismatches within CpG dinucleotides in vitro. In an attempt to determine the relative contributions of MBD4 and TDG to the repair of 5-methylcytosine delamination-induced T:G mismatches in vivo, the mutation frequencies and spectra in cell lines lacking MBD4 and/or TDG were measured. An additional line of research focused on potential mechanisms by which the DNA repair activity of MBD4 may be regulated. A novel protein has previously been shown to interact with MBD4 in a yeast two-hybrid screen that used MBD4 as the bait protein. This interaction was further characterised by mapping of the interaction domains using the yeast two-hybrid assay, and by immunocytochemistry. Finally, it was also shown that MBD4 may be post-translationally modified by sumoylation.
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Books on the topic "MBD3"

1

Salomon, Fred. Praxisbuch Ethik in der Notfallmedizin: Orientierungshilfen für kritische Entscheidungen. Berlin: MWV Medizinisch Wissenschaftliche Verlagsgesellschaft, 2015.

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Tikkanen, Märta. Sofia vuxen med sitt MBD. 2nd ed. [Stockholm]: Forum, 1998.

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Virtanen, Timo. Parenting stress and coping among mothers with MBD children. Rovaniemi: University of Lapland, 1991.

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Hyperactivity, the so-called attention-deficit disorder, and the group of MBD syndromes. Cresskill, N.J: Creative Therapeutics, 1987.

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Agency, United States Minority Business Development. QA: Answers to questions about MBDA's business assistance to minority entrepreneurs : MBDA-assisted entrepreneurship provides jobs, economic growth. [Washington, D.C.]: U.S. Dept. of Commerce, Minority Business Development Agency, 1993.

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QA: Answers to questions about MBDA's business assistance to minority entrepreneurs : MBDA-assisted entrepreneurship provides jobs, economic growth. [Washington, D.C.]: U.S. Dept. of Commerce, Minority Business Development Agency, 1993.

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United States. Minority Business Development Agency. QA: Answers to questions about MBDA's business assistance to minority entrepreneurs : MBDA-assisted entrepreneurship provides jobs, economic growth. [Washington, D.C.]: U.S. Dept. of Commerce, Minority Business Development Agency, 1993.

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Report on the risk assessment of MBDB in the framework of the joint action on new synthetic drugs. Luxembourg: Office for Official Publications of the European Communities, 1999.

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International Seminar on Mineral Business Development (2004 Nagpur, India). International Seminar on Mineral Business Development: January 16-17, 2004, Nagpur, India : proceedings MBD 2004. Edited by Rajau K. S and Indian Bureau of Mines. [Nagpur: Mineral Information and Development Centre, 2004.

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Agency, United States Minority Business Development. Minority Business Development Centers (MBDC) Program: Competitive application kit (to be used for awards beginning October 1, 1991, or later). [Washington, D.C.?]: U.S. Dept. of Commerce, [Minority Business Development Agency, 1993.

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Book chapters on the topic "MBD3"

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Mirtalebi, Mohsen. "MBD and Requirements Model." In Embedded Systems Architecture for Agile Development, 183–205. Berkeley, CA: Apress, 2017. http://dx.doi.org/10.1007/978-1-4842-3051-0_8.

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Vo, Victoria T., and Stuart M. Sprague. "ESKD Complications: CKD-MBD." In Applied Peritoneal Dialysis, 211–31. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-70897-9_17.

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Di Giacomo, Giulio, Fabrizio Donati, Carlo Perisano, Michele Attilio Rosa, and Giulio Maccauro. "Infections After Surgery for MBD." In Management of Bone Metastases, 183–89. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-73485-9_18.

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Di Biagio, C., P. Piccirilli, F. Batino, S. Capoleoni, F. Giammarino, M. Ronchi, D. Vitelli, and A. E. Guida. "MBDA Extendible C2 Weapon System in Collaboration Environment." In Proceedings of 4th International Conference in Software Engineering for Defence Applications, 215–29. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27896-4_18.

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Aberg, Karolina A., Robin F. Chan, Linying Xie, Andrey A. Shabalin, and Edwin J. C. G. van den Oord. "Methyl-CpG-Binding Domain Sequencing: MBD-seq." In Methods in Molecular Biology, 171–89. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7481-8_10.

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Makita, Kiyoshi. "Problems in Nomenclature and Classification of MBD." In Child and Adolescent Psychiatry, Mental Retardation, and Geriatric Psychiatry, 11–16. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4615-9367-6_3.

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Dittmar, Anke, and Peter Forbrig. "An Exploration of Perspective Changes within MBD." In Human-Computer Interaction. New Trends, 806–15. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02574-7_90.

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Ureña-Torres, Pablo A., Jordi Bover, and Martine Cohen-Solal. "Relation Between PTH and Biochemical Markers of MBD." In Parathyroid Glands in Chronic Kidney Disease, 103–16. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-43769-5_7.

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Leow, Kheng Song, and Rahul Lohan. "Malignant Bile Duct Obstruction (MBDO): Obstruction Solutions for Liver and Gallbladder." In Interventional Radiology in Palliative Care, 243–57. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-65463-4_23.

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Kuhlmann, Martin K. "Dialysis in the Older Adult: Management of CKD–MBD." In Dialysis in Older Adults, 109–21. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-3320-4_10.

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Conference papers on the topic "MBD3"

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Shimbo, Takashi, Christopher Lavender, Sara A. Grimm, Makiko I. Doi, Telmo Henriques, Kimberly R. Cannady, Kevin J. Murphy, et al. "Abstract 2862: MBD3 regulates chromatin accessibility at active promoters." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2862.

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Shimbo, Takashi, Ying Du, Sara Grimm, Archana Dhasarathy, Deepak Mav, Ruchir Shah, Huidong Shi, and Paul A. Wade. "Abstract B63: MBD3 accumulates at promoters and enhancers of active genes." In Abstracts: AACR Special Conference on Chromatin and Epigenetics in Cancer - June 19-22, 2013; Atlanta, GA. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.cec13-b63.

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Aijaz, Javeria, Justin Sperlazza, and Gordon D. Ginder. "Abstract 721: CHD4 mediates genotoxic sensitivity and tumor initiation of AML cells through both MBD2-NuRD and MBD3-NuRD co-repressor complexes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-721.

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Aijaz, Javeria, Justin Sperlazza, and Gordon D. Ginder. "Abstract 721: CHD4 mediates genotoxic sensitivity and tumor initiation of AML cells through both MBD2-NuRD and MBD3-NuRD co-repressor complexes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-721.

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Shimbo, Takashi, Ying Du, Sara A. Grimm, Archana Dhasarathy, Deepak Mav, Ruchir R. Shah, Huidong Shi, and Paul A. Wade. "Abstract 405: Mbd3 localizes at promoters, gene bodies and enhancers of active genes." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-405.

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Ranjan, Alok, Surajit Sinha, Reed Ayabe, Michael Wach, Samantha Ruff, Shreya Gupta, James McDonald, Kirsten Remmert, Imani Alexander, and Jonathan Hernandez. "Abstract C44: MBD3 stabilizes MYC, leading to metastatic outgrowth of pancreatic cancer in the liver." In Abstracts: AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; September 6-9, 2019; Boston, MA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.panca19-c44.

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Tan, Xun, Xingyu Chen, Guowei Zhang, Jishiyu Ding, and Xuguang Lan. "MBDF-Net." In MM '21: ACM Multimedia Conference. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3475721.3484311.

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Brent, Michael R., and Xiaopeng Tao. "Chinese text segmentation with MBDP-1." In the 39th Annual Meeting. Morristown, NJ, USA: Association for Computational Linguistics, 2001. http://dx.doi.org/10.3115/1073012.1073025.

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"MBD/MOMPES 2006 Committees." In Joint Meeting of the Fourth Workshop on Model-Based Development Computer-Based Systems and the Third International Workshop on Model-Based Methodologies for Pervasive and Embedded Software. IEEE, 2006. http://dx.doi.org/10.1109/mbd-mompes.2006.15.

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"MB3 session: Analog 1." In 2010 IEEE International SOC Conference (SOCC). IEEE, 2010. http://dx.doi.org/10.1109/socc.2010.5784708.

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Reports on the topic "MBD3"

1

Aldridge, Chris D. Mobile biometric device (MBD) technology :. Office of Scientific and Technical Information (OSTI), June 2013. http://dx.doi.org/10.2172/1089989.

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Stone, M. E. Melt Rate Improvements for MB3: Feed Preparation. Office of Scientific and Technical Information (OSTI), July 2001. http://dx.doi.org/10.2172/783014.

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Lorier, T. H. Melt Rate Improvement for DWPF MB3: Crucible Studies. Office of Scientific and Technical Information (OSTI), June 2001. http://dx.doi.org/10.2172/782044.

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Lorier, T. H. Melt Rate Improvement for DWPF MB3: Frit Preparation. Office of Scientific and Technical Information (OSTI), June 2001. http://dx.doi.org/10.2172/782045.

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Lambert, D. P. Melt Rate Improvement for DWPF MB3: Summary and Recommendations. Office of Scientific and Technical Information (OSTI), July 2001. http://dx.doi.org/10.2172/783015.

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Stone, M. E. Melt Rate Improvement for DWPF MB3: Sugar Addition Test. Office of Scientific and Technical Information (OSTI), June 2001. http://dx.doi.org/10.2172/782216.

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Stone, M. E. Melt Rate Improvement for DWPF MB3: Melt Rate Furnace Testing. Office of Scientific and Technical Information (OSTI), July 2001. http://dx.doi.org/10.2172/783821.

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Bir, G. S. User's Guide to MBC3: Multi-Blade Coordinate Transformation Code for 3-Bladed Wind Turbine. Office of Scientific and Technical Information (OSTI), September 2010. http://dx.doi.org/10.2172/989416.

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Peeler, D. K. Melt Rate Improvements for DWPF MB3: Frit Development and Model Assessment. Office of Scientific and Technical Information (OSTI), July 2001. http://dx.doi.org/10.2172/783013.

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Peeler, D. K. Melt Rate Improvement for DWPF MB3: Foaming Theory and Mitigation Techniques. Office of Scientific and Technical Information (OSTI), July 2001. http://dx.doi.org/10.2172/783820.

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