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Adrian Bird - One of the best experts on this subject based on the ideXlab platform.
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mbd2 contributes to dna methylation directed repression of the xist gene
Molecular and Cellular Biology, 2007Co-Authors: Helen Barr, Brian Hendrich, Andrea Hermann, Jennifer Berger, Hsinhao Tsai, Karen Adie, Anna Prokhortchouk, Adrian BirdAbstract:Transcription of the Xist gene triggers X chromosome inactivation in cis and is therefore silenced on the X chromosome that remains active. DNA methylation contributes to this silencing, but the mechanism is unknown. As methylated DNA binding proteins (MBPs) are potential mediators of gene silencing by DNA methylation, we asked whether MBP-deficient cell lines could maintain Xist repression. The absence of Mbd2 caused significant low-level reactivation of Xist, but silencing was restored by exogenous Mbd2. In contrast, deficiencies of Mbd1, MeCP2, and Kaiso had no detectable effect, indicating that MBPs are not functionally redundant at this locus. Xist repression in Mbd2-null cells was hypersensitive to the histone deacetylase inhibitor trichostatin A and to depletion of the DNA methyltransferase Dnmt1. These synergies implicate Mbd2 as a mediator of the DNA methylation signal at this locus. The presence of redundant mechanisms to enforce repression at Xist and other loci is compatible with the hypothesis that “stacking” of imperfect repressive tendencies may be an evolutionary strategy to ensure leakproof gene silencing.
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fas associated death domain protein interacts with methyl cpg binding domain protein 4 a potential link between genome surveillance and apoptosis
Proceedings of the National Academy of Sciences of the United States of America, 2003Co-Authors: Robert A. Screaton, Adrian Bird, Stephan Kiessling, Owen J. Sansom, Catherine B. Millar, Kathryn Maddison, Alan Richard Clarke, Steven M. FrischAbstract:Fas-associated death domain protein (FADD) is an adaptor protein bridging death receptors with initiator caspases. Thus, its function and localization are assumed to be cytoplasmic, although the localization of endogenous FADD has not been reported. Surprisingly, the data presented here demonstrate that FADD is mainly nuclear in several adherent cell lines. Its accumulation in the nucleus and export to the cytoplasm required the phosphorylation site Ser-194, which was also required for its interaction with the nucleocytoplasmic shuttling protein exportin-5. Within the nucleus, FADD interacted with the methyl-CpG binding domain protein 4 (MBD4), which excises thymine from GT mismatches in methylated regions of chromatin. The MBD4-interacting mismatch repair factor MLH1 was also found in a complex with FADD. The FADD–MBD4 interaction involved the death effector domain of FADD and a region of MBD4 adjacent to the glycosylase domain. The FADD-binding region of MBD4 was downstream of a frameshift mutation that occurs in a significant fraction of human colorectal carcinomas. Consistent with the idea that MBD4 can signal to an apoptotic effector, MBD4 regulated DNA damage-, Fas ligand-, and cell detachment-induced apoptosis. The nuclear localization of FADD and its interaction with a genome surveillance/DNA repair protein that can regulate apoptosis suggests a novel function of FADD distinct from direct participation in death receptor signaling complexes.
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mbd2 is a transcriptional repressor belonging to the mecp1 histone deacetylase complex
Nature Genetics, 1999Co-Authors: Huckhui Ng, Brian Hendrich, Colin A Johnson, Bryan M Turner, Hediye Erdjumentbromage, Paul Tempst, Yi Zhang, Adrian BirdAbstract:Mammalian DNA is methylated at many CpG dinucleotides. The biological consequences of methylation are mediated by a family of methyl-CpG binding proteins1,2,3,4. The best characterized family member is MeCP2, a transcriptional repressor that recruits histone deacetylases5,6,7. Our report concerns MBD2, which can bind methylated DNA in vivo and in vitro 4 and has been reported to actively demethylate DNA (ref. 8). As DNA methylation causes gene silencing, the MBD2 demethylase is a candidate transcriptional activator. Using specific antibodies, however, we find here that MBD2 in HeLa cells is associated with histone deacetylase (HDAC) in the MeCP1 repressor complex1,9. An affinity-purified HDAC1 corepressor complex10,11 also contains MBD2, suggesting that MeCP1 corresponds to a fraction of this complex. Exogenous MBD2 represses transcription in a transient assay, and repression can be relieved by the deacetylase inhibitor trichostatin A (TSA; ref. 12). In our hands, MBD2 does not demethylate DNA. Our data suggest that HeLa cells, which lack the known methylation-dependent repressor MeCP2, use an alternative pathway involving MBD2 to silence methylated genes.
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Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and MBD4 genes.
Mammalian genome : official journal of the International Mammalian Genome Society, 1999Co-Authors: Brian Hendrich, Catherine M. Abbott, Heather A. Mcqueen, Doreen M. Chambers, Sally H. Cross, Adrian BirdAbstract:DNA methylation is essential for murine development and is implicated in the control of gene expression. MeCP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of mammalian, nuclear proteins related by the presence in each of an amino acid motif called the methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MeCP2, MBD1 and MBD2 can also repress transcription. We describe the genomic structure and chromosomal localization of the human and murine Mbd1, Mbd2, Mbd3, and MBD4 genes. We find that the highly similar MBD2 and MBD3 proteins are encoded by genes that map to different chromosomes in humans and mice but show a similar genomic structure. The Mbd1 and Mbd2 genes, in contrast, map together to murine and human Chromosomes (Chrs)18. The Mbd3 and MBD4 genes map to murine Chrs 10 and 6, respectively, while the human MBD3 and MBD4 genes map to Chrs 19 and 3, respectively.
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identification and characterization of a family of mammalian methyl cpg binding proteins
Molecular and Cellular Biology, 1998Co-Authors: Brian Hendrich, Adrian BirdAbstract: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. DNA methylation is the major modification of eukaryote genomes. In vertebrates, this occurs predominantly at position 5 of cytosines when followed by guanosine (CpG). DNA methylation can repress transcription and for this reason has been implicated in stable alterations of gene expression in development (3). Whereas the genomes of certain invertebrates appear to contain “compartments” of either mostly methylated or mostly unmethylated DNA (43), the somatic genomes of vertebrates are globally methylated, with the exception of socalled CpG islands (6). CpG islands are GC-rich regions of DNA, stretching for an average of about 1 kb, which are coincident with the promoters of approximately 60% of human RNA polymerase II-transcribed genes (1). Methylation of CpG islands and subsequent silencing of associated transcription units have been found to occur in genes located on the inactive X chromosome (39), genes silenced by genomic imprinting (36, 38), and genes silenced in transformed cell lines and tumors (2, 8, 16, 18, 40). DNA methylation is known to play an essential role in mammalian development because mice lacking a functional gene encoding the maintenance DNA methyltransferase (DNMT) are developmentally retarded and die at midgestation (29). In contrast to the situation in somatic cells, undifferentiated embryonic stem (ES) cells lacking a functional DNMT gene apparently grow normally despite containing approximately 5% of the wild-type DNA
Mitsuyoshi Nakao - One of the best experts on this subject based on the ideXlab platform.
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transcriptional repression and heterochromatin formation by mbd1 and mcaf am family proteins
Journal of Biological Chemistry, 2005Co-Authors: Takaya Ichimura, Naoyuki Fujita, Sugiko Watanabe, Yasuo Sakamoto, Takahiro Aoto, Mitsuyoshi NakaoAbstract:Abstract DNA methylation cooperates with methylation at lysine 9 of histone H3 (H3-K9), a modified histone molecule that is targeted by heterochromatin protein 1, to form a transcriptionally silent chromatin. Methyl CpG-binding protein MBD1 recognizes methylated CpG dinucleotide and recruits H3-K9 methyltransferases such as SETDB1 to genomic regions. Here we show that MBD1-containing chromatin-associated factor (MCAF) 1, also known as the human homologue of murine ATFa-associated modulator (AM), is required for transcriptional repression and heterochromatin formation by MBD1, together with the involvement of SETDB1. Moreover, the amino acid sequence of MCAF1 shows similarity to a number of sequences of the MCAF/AM-related proteins, resulting in the identification of a new member of the protein family, termed MCAF2. Immunoprecipitation and in vitro binding analyses reveal that both MCAF proteins interact with MBD1, SETDB1, and Sp1 via two evolutionarily conserved distinct domains. Furthermore, MCAF1 enhances transcriptional repression by MBD1 together with SETDB1, and exogenous expression of MCAF2 partly compensates for the repressive activity in MCAF1 knockdown HeLa cells. The expression of MBD1 mutant, which lacks interaction with MCAF proteins, perturbs heterochromatin protein 1-enriched heterochromatin formation at the MBD1-containing chromosomal loci. These data suggest that MBD1·MCAF1·SETDB1 complex facilitates the formation of heterochromatic domains, emphasizing the role of MCAF/AM family proteins in epigenetic control.
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Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression
The Journal of biological chemistry, 2003Co-Authors: Naoyuki Fujita, Sugiko Watanabe, Takaya Ichimura, Shu Tsuruzoe, Yoichi Shinkai, Makoto Tachibana, Tsutomu Chiba, Mitsuyoshi NakaoAbstract:Cytosine methylation and posttranslational modifications of the amino termini of the core histones in the nucleosome provide epigenetic codes for genome regulation. In the nucleus, not only is the DNA methylated, but the methylated DNA is also interpreted by methyl-CpG binding domain (MBD) proteins. MBD1 possesses an MBD involved in mediating DNA methylation-dependent transcriptional repression. The MBD of MBD1 binds a symmetrically methylated CpG sequence, but the precise roles of this domain have not been investigated. In addition, little is understood about the state of histone modifications within MBD1-containing heterochromatin on methylated gene promoters. Here we show that histone H3 methylase Suv39h1 and the methyl lysine-binding protein HP1 directly interact with MBD of MBD1 in vitro and in cells. Suv39h1 was found to enhance MBD1-mediated transcriptional repression via MBD but not via the C-terminal transcriptional repression domain of MBD1. Furthermore, MBD1 links to histone deacetylases through Suv39h1, resulting in methylation and deacetylation of histones for gene inactivation. These data indicate that MBD1 may tether the Suv39h1-HP1 complex to methylated DNA regions, suggesting the presence of a pathway from DNA methylation to the modifications of histones for epigenetic gene regulation.
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Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.
Cell, 2001Co-Authors: Izuru Ohki, Naoyuki Fujita, Mitsuyoshi Nakao, Nobuya Shimotake, Jun-goo Jee, Takahisa Ikegami, Masahiro ShirakawaAbstract:In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA. DNA binding causes a loop in MBD1 to fold into a major and novel DNA binding interface. Recognition of the methyl groups and CG sequence at the methylation site is due to five highly conserved residues that form a hydrophobic patch. The structure indicates how MBD may access nucleosomal DNA without encountering steric interference from core histones, and provides a basis to interpret mutations linked to Rett syndrome in MeCP2.
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METHYLATION-MEDIATED TRANSCRIPTIONAL SILENCING IN EUCHROMATIN BY METHYL-CPG BINDING PROTEIN MBD1 ISOFORMS
Molecular and cellular biology, 1999Co-Authors: Naoyuki Fujita, Tsutomu Chiba, Shin-ichiro Takebayashi, Katsuzumi Okumura, Shinichi Kudo, Hideyuki Saya, Mitsuyoshi NakaoAbstract:DNA methylation of promoter-associated CpG islands is involved in the transcriptional repression of vertebrate genes. To investigate the mechanisms underlying gene inactivation by DNA methylation, we characterized a human MBD1 protein, one of the components of MeCP1, which possesses a methyl-CpG binding domain (MBD) and cysteine-rich (CXXC) domains. Four novel MBD1 isoforms (MBD1v1, MBD1v2, MBD1v3, and MBD1v4) were identified by the reverse transcription-PCR method. We found that these transcripts were alternatively spliced in the region of CXXC domains and the C terminus. Green fluorescent protein-fused MBD1 was localized to multiple foci on the human genome, mostly in the euchromatin regions, and particularly concentrated in the pericentromeric region of chromosome 1. Both the MBD sequence and genome methylation were required for proper localization of the MBD1 protein. We further investigated whether MBD1 isoforms are responsible for transcriptional repression of human genes. A bacterially expressed MBD1 protein bound preferentially to methylated DNA fragments containing CpG islands from the tumor suppressor genes p16, VHL, and E-cadherin and from an imprinted SNRPN gene. All MBD1 isoforms inhibited promoter activities of these genes via methylation. Interestingly, MBD1 isoforms v1 and v2 containing three CXXC domains also suppressed unmethylated promoter activities in mammalian cells. These effects were further manifested in Drosophila melanogaster cells, which lack genome methylation. Sp1-activated transcription of methylated p16 and SNRPN promoters was inhibited by all of the MBD1 isoforms, whereas the isoforms v1 and v2 reduced Sp1-activated transcription from unmethylated promoters as well. These findings suggested that the MBD1 isoforms have different roles in methylation-mediated transcriptional silencing in euchromatin.
Pernilla Wittung-stafshede - One of the best experts on this subject based on the ideXlab platform.
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Copper relay path through the N-terminus of Wilson disease protein, ATP7B.
Metallomics, 2019Co-Authors: Kumaravel Ponnandai Shanmugavel, Pernilla Wittung-stafshedeAbstract:In human cells, copper (Cu) ions are transported by the cytoplasmic Cu chaperone Atox1 to the Wilson disease protein (ATP7B) in the Golgi for loading of Cu-dependent enzymes. ATP7B is a membrane-spanning protein which, in contrast to non-mammalian homologs, has six cytoplasmic metal-binding domains (MBDs). To address the reason for multiple MBDs, we introduced strategic mutations in which one, two or three MBDs had been blocked for Cu binding via cysteine-to-serine mutations (but all six MBDs are present in all) in a yeast system that probes Cu flow through Atox1 and ATP7B. The results, combined with earlier work, support a mechanistic model in which MBD1-3 forms a regulatory unit of ATP7B Cu transport. Cu delivery via Atox1 to this unit, followed by loading of Cu in MBD3, promotes release of inhibitory interactions. Whereas the Cu site in MBD4 can be mutated without a large effect, an intact Cu site in either MBD5 or MBD6 is required for Cu transport. All MBDs, expressed as single-domain proteins, can replace Atox1 and deliver Cu to full-length ATP7B. However, only MBD6 can deliver Cu to truncated ATP7B where all six MBDs are removed, suggesting a docking role for this structural unit.
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Disease-causing point-mutations in metal-binding domains of Wilson disease protein decrease stability and increase structural dynamics
BioMetals, 2017Co-Authors: Ranjeet Kumar, Candan Ariöz, Niklas Bosaeus, Yaozong Li, Sandra Rocha, Pernilla Wittung-stafshedeAbstract:After cellular uptake, Copper (Cu) ions are transferred from the chaperone Atox1 to the Wilson disease protein (ATP7B) for incorporation into Cu-dependent enzymes in the secretory pathway. Human ATP7B is a large multi-domain membrane-spanning protein which, in contrast to homologues in other organisms, has six similar cytoplasmic metal-binding domains (MBDs). The reason for multiple MBDs is proposed to be indirect modulation of enzymatic activity and it is thus intriguing that point mutations in MBDs can promote Wilson disease. We here investigated, in vitro and in silico, the biophysical consequences of clinically-observed Wilson disease mutations, G85V in MBD1 and G591D in MBD6, incorporated in domain 4. Because G85 and G591 correspond to a conserved Gly found in all MBDs, we introduced the mutations in the well-characterized MBD4. We found the mutations to dramatically reduce the MBD4 thermal stability, shifting the midpoint temperature of unfolding by more than 20 °C. In contrast to wild type MBD4 and MBD4D, MBD4V adopted a misfolded structure with a large β-sheet content at high temperatures. Molecular dynamic simulations demonstrated that the mutations increased backbone fluctuations that extended throughout the domain. Our findings imply that reduced stability and enhanced dynamics of MBD1 or MBD6 is the origin of ATP7B dysfunction in Wilson disease patients with the G85V or G591D mutation.
Moshe Szyf - One of the best experts on this subject based on the ideXlab platform.
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transcription onset of genes critical in liver carcinogenesis is epigenetically regulated by methylated dna binding protein mbd2
Carcinogenesis, 2013Co-Authors: Barbara Stefanska, Matthew Suderman, Ziv Machnes, Bishnu Bhattacharyya, Michael Hallett, Moshe SzyfAbstract:: We previously delineated genes whose promoters are hypomethylated and induced in hepatocellular carcinoma (HCC) patients. The purpose of this study was to establish the players that regulate these genes in liver cancer cells. We performed chromatin immunoprecipitation with methyl-CpG-binding domain protein 2 (MBD2), RNA polymerase II (RNA pol II), CCAAT/enhancer-binding protein alpha (CEBPA) antibodies and methylated DNA immunoprecipitation in HepG2 liver cancer cells treated with scrambled small interfering RNA (siRNA) and siRNA to MBD2 or CEBPA. We then hybridized DNA to microarrays spanning the entire coding sequences, introns and regulatory regions of several hundred HCC-hypomethylated genes. These analyses reveal that MBD2 binds a significant fraction of the hypomethylated genes, determines RNA pol II binding and DNA methylation state. MBD2 binding can result in promoter activation and hypomethylation or in repression. In activated target genes, MBD2 colocalizes with the transcription factor CEBPA, and MBD2 binding at these positions is reduced upon CEBPA depletion. Significant fraction of MBD2 effects on DNA methylation and transcription appears to be indirect since changes occur upon MBD2 depletion in genes where no MBD2 binding was detected. Our study delineates the rules governing the interaction of MBD2 with its targets and the consequences to RNA pol II binding and DNA methylation states. This has important implications for understanding the role of DNA methylation in cancer and targeting DNA methylation proteins in cancer therapy.
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methylated dna binding protein 2 antisense inhibitors suppress tumourigenesis of human cancer cell lines in vitro and in vivo
Carcinogenesis, 2003Co-Authors: Paul M Campbell, Veronica Bovenzi, Moshe SzyfAbstract:Methylated DNA-binding protein 2 (MBD2) has been proposed to function both as a silencer of methylated genes and as a DNA demethylase. Our previous data indicated that knockdown of MBD2 inhibited tumourigenesis of human cancer lines and MBD2-deficient mice were recently shown to be resistant to intestinal tumourigenesis. MBD2 is an attractive anticancer target since MBD2-deficient mice were previously shown to be viable and fertile and knockdown of MBD2 was reported to have no effect on cellular growth parameters of non-transformed cells. In this paper we test the hypothesis that pharmacological inhibition of MBD2 inhibits cancer growth in vivo using human tumour lines implanted in mice as a model. We develop sequence-specific antisense inhibitors of MBD2 and we show that these agents inhibit anchorage-independent growth of human lung (A549) and colorectal (HCT116) cancer cell lines in vitro and tumourigenic growth of human cancer cell xenografts in vivo. MBD2 antisense oligonucleotide does not inhibit the growth of normal and transformed cell lines and does not alter cell cycle parameters in vitro and does not exhibit overt toxicity in vivo in comparison with a scrambled control oligonucleotide, as determined by measuring body mass, blood cell parameters and liver and kidney enzymes. Our data provide a proof of principle that MBD2 is a new anticancer target and that pharmacological inhibition of MBD2 by agents such as the antisense inhibitors described in this paper is a potential new anticancer therapy, which in contrast to the vast majority of current approaches does not target normal progression of the cell cycle.
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antisense mbd2 gene therapy inhibits tumorigenesis
Journal of Gene Medicine, 2002Co-Authors: Andrew Slack, Veronica Bovenzi, Pascal Bigey, M A Ivanov, Shyam Ramchandani, Sanjoy K Bhattacharya, Benjamin R Tenoever, B Lamrihi, Daniel Scherman, Moshe SzyfAbstract:Background Aberration in the pattern of DNA methylation is one of the hallmarks of cancer. We present data suggesting that dysregulation of MBD2, a recently characterized member of a novel family of methylated DNA binding proteins, is involved in tumorigenesis. Two functions were ascribed to MBD2, DNA demethylase activity and repression of methylated genes. Methods Multiple antisense expression and delivery systems, transfection, electrotransfer and adenoviral were employed to demonstrate that MBD2 is essential in tumorigenesis, both ex vivo and in vivo. Results Inhibition of MBD2 by antisense expression resulted in inhibition of anchorage-independent growth of antisense transfected cancer cells or cells infected with an adenoviral vector expressing MBD2 antisense. Xenograft tumors treated with an adenoviral vector expressing MBD2 antisense or xenografts treated with electrotransferred plasmids expressing MBD2 antisense showed reduced growth. Conclusions These results support the hypothesis that one or both of the functions described for MBD2 are critical in tumorigenesis and that MBD2 is a potential anticancer target. Copyright © 2002 John Wiley & Sons, Ltd.
Naoyuki Fujita - One of the best experts on this subject based on the ideXlab platform.
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transcriptional repression and heterochromatin formation by mbd1 and mcaf am family proteins
Journal of Biological Chemistry, 2005Co-Authors: Takaya Ichimura, Naoyuki Fujita, Sugiko Watanabe, Yasuo Sakamoto, Takahiro Aoto, Mitsuyoshi NakaoAbstract:Abstract DNA methylation cooperates with methylation at lysine 9 of histone H3 (H3-K9), a modified histone molecule that is targeted by heterochromatin protein 1, to form a transcriptionally silent chromatin. Methyl CpG-binding protein MBD1 recognizes methylated CpG dinucleotide and recruits H3-K9 methyltransferases such as SETDB1 to genomic regions. Here we show that MBD1-containing chromatin-associated factor (MCAF) 1, also known as the human homologue of murine ATFa-associated modulator (AM), is required for transcriptional repression and heterochromatin formation by MBD1, together with the involvement of SETDB1. Moreover, the amino acid sequence of MCAF1 shows similarity to a number of sequences of the MCAF/AM-related proteins, resulting in the identification of a new member of the protein family, termed MCAF2. Immunoprecipitation and in vitro binding analyses reveal that both MCAF proteins interact with MBD1, SETDB1, and Sp1 via two evolutionarily conserved distinct domains. Furthermore, MCAF1 enhances transcriptional repression by MBD1 together with SETDB1, and exogenous expression of MCAF2 partly compensates for the repressive activity in MCAF1 knockdown HeLa cells. The expression of MBD1 mutant, which lacks interaction with MCAF proteins, perturbs heterochromatin protein 1-enriched heterochromatin formation at the MBD1-containing chromosomal loci. These data suggest that MBD1·MCAF1·SETDB1 complex facilitates the formation of heterochromatic domains, emphasizing the role of MCAF/AM family proteins in epigenetic control.
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Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression
The Journal of biological chemistry, 2003Co-Authors: Naoyuki Fujita, Sugiko Watanabe, Takaya Ichimura, Shu Tsuruzoe, Yoichi Shinkai, Makoto Tachibana, Tsutomu Chiba, Mitsuyoshi NakaoAbstract:Cytosine methylation and posttranslational modifications of the amino termini of the core histones in the nucleosome provide epigenetic codes for genome regulation. In the nucleus, not only is the DNA methylated, but the methylated DNA is also interpreted by methyl-CpG binding domain (MBD) proteins. MBD1 possesses an MBD involved in mediating DNA methylation-dependent transcriptional repression. The MBD of MBD1 binds a symmetrically methylated CpG sequence, but the precise roles of this domain have not been investigated. In addition, little is understood about the state of histone modifications within MBD1-containing heterochromatin on methylated gene promoters. Here we show that histone H3 methylase Suv39h1 and the methyl lysine-binding protein HP1 directly interact with MBD of MBD1 in vitro and in cells. Suv39h1 was found to enhance MBD1-mediated transcriptional repression via MBD but not via the C-terminal transcriptional repression domain of MBD1. Furthermore, MBD1 links to histone deacetylases through Suv39h1, resulting in methylation and deacetylation of histones for gene inactivation. These data indicate that MBD1 may tether the Suv39h1-HP1 complex to methylated DNA regions, suggesting the presence of a pathway from DNA methylation to the modifications of histones for epigenetic gene regulation.
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Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.
Cell, 2001Co-Authors: Izuru Ohki, Naoyuki Fujita, Mitsuyoshi Nakao, Nobuya Shimotake, Jun-goo Jee, Takahisa Ikegami, Masahiro ShirakawaAbstract:In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA. DNA binding causes a loop in MBD1 to fold into a major and novel DNA binding interface. Recognition of the methyl groups and CG sequence at the methylation site is due to five highly conserved residues that form a hydrophobic patch. The structure indicates how MBD may access nucleosomal DNA without encountering steric interference from core histones, and provides a basis to interpret mutations linked to Rett syndrome in MeCP2.
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METHYLATION-MEDIATED TRANSCRIPTIONAL SILENCING IN EUCHROMATIN BY METHYL-CPG BINDING PROTEIN MBD1 ISOFORMS
Molecular and cellular biology, 1999Co-Authors: Naoyuki Fujita, Tsutomu Chiba, Shin-ichiro Takebayashi, Katsuzumi Okumura, Shinichi Kudo, Hideyuki Saya, Mitsuyoshi NakaoAbstract:DNA methylation of promoter-associated CpG islands is involved in the transcriptional repression of vertebrate genes. To investigate the mechanisms underlying gene inactivation by DNA methylation, we characterized a human MBD1 protein, one of the components of MeCP1, which possesses a methyl-CpG binding domain (MBD) and cysteine-rich (CXXC) domains. Four novel MBD1 isoforms (MBD1v1, MBD1v2, MBD1v3, and MBD1v4) were identified by the reverse transcription-PCR method. We found that these transcripts were alternatively spliced in the region of CXXC domains and the C terminus. Green fluorescent protein-fused MBD1 was localized to multiple foci on the human genome, mostly in the euchromatin regions, and particularly concentrated in the pericentromeric region of chromosome 1. Both the MBD sequence and genome methylation were required for proper localization of the MBD1 protein. We further investigated whether MBD1 isoforms are responsible for transcriptional repression of human genes. A bacterially expressed MBD1 protein bound preferentially to methylated DNA fragments containing CpG islands from the tumor suppressor genes p16, VHL, and E-cadherin and from an imprinted SNRPN gene. All MBD1 isoforms inhibited promoter activities of these genes via methylation. Interestingly, MBD1 isoforms v1 and v2 containing three CXXC domains also suppressed unmethylated promoter activities in mammalian cells. These effects were further manifested in Drosophila melanogaster cells, which lack genome methylation. Sp1-activated transcription of methylated p16 and SNRPN promoters was inhibited by all of the MBD1 isoforms, whereas the isoforms v1 and v2 reduced Sp1-activated transcription from unmethylated promoters as well. These findings suggested that the MBD1 isoforms have different roles in methylation-mediated transcriptional silencing in euchromatin.