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The HP1-p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells. Nat Struct Mol Biol 2009; 15:972-9. [PMID: 19172751 DOI: 10.1038/nsmb.1470] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The heterochromatin protein 1 (HP1)-rich heterochromatin domains next to centromeres are crucial for chromosome segregation during mitosis. This mitotic function requires their faithful reproduction during the preceding S phase, a process whose mechanism and regulation are current puzzles. Here we show that p150, a subunit of chromatin assembly factor 1, has a key role in the replication of pericentric heterochromatin and S-phase progression in mouse cells, independently of its known function in histone deposition. By a combination of depletion and complementation assays in vivo, we link this unique function of p150 to its ability to interact with HP1. Absence of this functional interaction triggers S-phase arrest at the time of replication of pericentromeric heterochromatin, without eliciting known DNA-based checkpoint pathways. Notably, in cells lacking the histone methylases Suv39h, in which pericentric domains do not show HP1 accumulation, p150 is dispensable for S-phase progression.
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53
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Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information. Trends Cell Biol 2008; 19:29-41. [PMID: 19027300 DOI: 10.1016/j.tcb.2008.10.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/22/2008] [Accepted: 10/23/2008] [Indexed: 12/18/2022]
Abstract
Understanding the basic mechanisms underlying chromatin dynamics during DNA replication in eukaryotic cells is of fundamental importance. Beyond DNA compaction, chromatin organization represents a means to regulate genome function. Thus, the inheritance and maintenance of the DNA sequence, along with its organization into chromatin, is central for eukaryotic life. To orchestrate DNA replication in the context of chromatin is a challenge, both in terms of accessibility to the compact structures and maintenance of chromatin organization. To meet the challenge of maintenance, cells have evolved efficient nucleosome dynamics involving assembly pathways and chromatin maturation mechanisms that restore chromatin organization in the wake of DNA replication. In this review, we describe our current knowledge concerning how these pathways operate at the nucleosomal level and highlight the key players, such as histone chaperones, chromatin remodelers or modifiers, involved in the process of chromatin duplication. Major advances have been made recently concerning de novo nucleosome assembly and our understanding of its coordination with recycling of parental histones is progressing. Insights into the transmission of chromatin-based information during replication have important implications in the field of epigenetics to fully comprehend how the epigenetic landscape might, or at times might not, be stably maintained in the face of dramatic changes in chromatin structure.
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54
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The role of the epigenetic signal, DNA methylation, in gene regulation during erythroid development. Curr Top Dev Biol 2008; 82:85-116. [PMID: 18282518 DOI: 10.1016/s0070-2153(07)00004-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The sequence complexity of the known vertebrate genomes alone is insufficient to account for the diversity between individuals of a species. Although our knowledge of vertebrate biology has evolved substantially with the growing compilation of sequenced genomes, understanding the temporal and spatial regulation of genes remains fundamental to fully exploiting this information. The importance of epigenetic factors in gene regulation was first hypothesized decades ago when biologists posited that methylation of DNA could heritably alter gene expression [Holliday and Pugh, 1975. Science 187(4173), 226-232; Riggs, 1975. Cytogenet. and Cell Genet.14(1), 9-25; Scarano et al., 1967. Proc. Natl. Acad. Sci. USA 57(5), 1394-1400)]. It was subsequently shown that vertebrate DNA methylation, almost exclusively at the 5' position of cytosine in the dinucleotide CpG, played a role in a number of processes including embryonic development, genetic imprinting, cell differentiation, and tumorigenesis. At the time of this writing, a large and growing list of genes is known to exhibit DNA methylation-dependent regulation, and we understand in some detail the mechanisms employed by cells in using methylation as a regulatory modality. In this context, we revisit one of the original systems in which the role of DNA methylation in vertebrate gene regulation during development was described and studied: erythroid cells. We briefly review the recent advances in our understanding of DNA methylation and, in particular, its regulatory role in red blood cells during differentiation and development. We also address DNA methylation as a component of erythroid chromatin architecture, and the interdependence of CpG methylation and histone modification.
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55
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Glinsky GV. Stem cell origin of death-from-cancer phenotypes of human prostate and breast cancers. ACTA ACUST UNITED AC 2007; 3:79-93. [PMID: 17873385 DOI: 10.1007/s12015-007-0011-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 12/01/2022]
Abstract
In clinical terms, all human cancers diagnosed in individuals can be divided in two major categories: malignant tumors that will be cured with the existing cancer therapies and tumors that have therapy-resistant phenotypes and will return after initial treatment as incurable metastatic disease. These tumors manifesting clinically lethal death-from-cancer phenotypes represent the most formidable challenge of experimental, translational, and clinical cancer research. Clinical genomics data demonstrate that gene expression signatures associated with the "stemness" state of a cell are informative as molecular predictors of cancer therapy outcome and can help to identify cancer patients with therapy-resistant tumors. Here, we present experimental and clinical evidence in support of the BMI1 pathway rule indicating a genetic link between the stemness state and therapy-resistant death-from-cancer phenotypes. Our analysis demonstrates that therapy-resistant and therapy-responsive cancer phenotypes manifest distinct patterns of association with stemness/differentiation pathways, suggesting that therapy-resistant and therapy-responsive tumors develop within genetically distinct stemness/differentiation programs. These differences can be exploited for development of prognostic and therapy selection genetic tests utilizing a microarray-based cancer therapy outcome predictor algorithm. One of the major regulatory pathways manifesting distinct patterns of association with therapy-resistant and therapy-responsive cancer phenotypes is the Polycomb group proteins chromatin silencing pathway.
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Affiliation(s)
- Gennadi V Glinsky
- Translational & Functional Genomics Laboratory, Ordway Cancer Center, Ordway Research Institute, Albany, NY 12208, USA.
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56
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Song Y, He F, Xie G, Guo X, Xu Y, Chen Y, Liang X, Stagljar I, Egli D, Ma J, Jiao R. CAF-1 is essential for Drosophila development and involved in the maintenance of epigenetic memory. Dev Biol 2007; 311:213-22. [DOI: 10.1016/j.ydbio.2007.08.039] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 08/14/2007] [Accepted: 08/21/2007] [Indexed: 02/01/2023]
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57
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Abstract
Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic landscape may be stably maintained even in the face of dramatic changes in chromatin structure.
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Affiliation(s)
- Anja Groth
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR 218 CNRS/Institut Curie, 26 rue d'Ulm, 75248 Paris, Cedex 5, France
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58
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Exner V, Taranto P, Schönrock N, Gruissem W, Hennig L. Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development. Development 2006; 133:4163-72. [PMID: 17021044 DOI: 10.1242/dev.02599] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromatin assembly factor CAF-1 facilitates the formation of nucleosomes on newly replicated DNA in vitro. However, the role of CAF-1 in development is poorly understood because mutants are not available in most multicellular model organisms. Biochemical evidence suggests that FASCIATA1, FASCIATA2 and MSI1 form CAF-1 in Arabidopsis thaliana. Because fasciata mutants are viable, CAF-1 is not essential for cell division in plants. Arabidopsis CAF-1 mutants have defects in shoot apical meristems; in addition, CAF-1 is required to establish seedling architecture, leaf size and trichome differentiation. CAF-1 is needed to restrict branching of trichomes on rosette leaves. Increased trichome branching in CAF-1 mutants is not strictly correlated with increased nuclear DNA content. In addition, fas2 glabra3 double mutants show an additive genetic interaction, demonstrating that CAF-1 acts genetically parallel to the GLABRA3-containing, endoreduplication-coupled trichome branching pathway. However, CAF-1 is often needed to restrict endoreduplication, because seedlings of most CAF-1 mutants have increased ploidy. Notably, in the Landsberg erecta background, loss of CAF-1 does not affect ploidy, demonstrating that loss of CAF-1 can be compensated in some Arabidopsis accessions. These results reveal that the functions of FAS1, FAS2 and MSI1 are not restricted to meristems, but are also needed to control genome replication at multiple steps of development.
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Affiliation(s)
- Vivien Exner
- Institute of Plant Sciences and Basel-Zurich Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
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59
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Houlard M, Berlivet S, Probst AV, Quivy JP, Héry P, Almouzni G, Gérard M. CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells. PLoS Genet 2006; 2:e181. [PMID: 17083276 PMCID: PMC1630711 DOI: 10.1371/journal.pgen.0020181] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 09/11/2006] [Indexed: 01/08/2023] Open
Abstract
During mammalian development, chromatin dynamics and epigenetic marking are important for genome reprogramming. Recent data suggest an important role for the chromatin assembly machinery in this process. To analyze the role of chromatin assembly factor 1 (CAF-1) during pre-implantation development, we generated a mouse line carrying a targeted mutation in the gene encoding its large subunit, p150CAF-1. Loss of p150CAF-1 in homozygous mutants leads to developmental arrest at the 16-cell stage. Absence of p150CAF-1 in these embryos results in severe alterations in the nuclear organization of constitutive heterochromatin. We provide evidence that in wild-type embryos, heterochromatin domains are extensively reorganized between the two-cell and blastocyst stages. In p150CAF-1 mutant 16-cell stage embryos, the altered organization of heterochromatin displays similarities to the structure of heterochromatin in two- to four-cell stage wild-type embryos, suggesting that CAF-1 is required for the maturation of heterochromatin during preimplantation development. In embryonic stem cells, depletion of p150CAF-1 using RNA interference results in the mislocalization, loss of clustering, and decondensation of pericentric heterochromatin domains. Furthermore, loss of CAF-1 in these cells results in the alteration of epigenetic histone methylation marks at the level of pericentric heterochromatin. These alterations of heterochromatin are not found in p150CAF-1-depleted mouse embryonic fibroblasts, which are cells that are already lineage committed, suggesting that CAF-1 is specifically required for heterochromatin organization in pluripotent embryonic cells. Our findings underline the role of the chromatin assembly machinery in controlling the spatial organization and epigenetic marking of the genome in early embryos and embryonic stem cells.
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Affiliation(s)
- Martin Houlard
- Epigenetic Regulation and Cancer Group, Service de Biologie Moléculaire Systémique, Département de Biologie Joliot-Curie, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique, CEA Saclay, Gif-sur-Yvette, France
- Section de Recherche, Institut Curie, UMR218 du Centre National de la Recherche Scientifique, Paris, France
| | - Soizik Berlivet
- Epigenetic Regulation and Cancer Group, Service de Biologie Moléculaire Systémique, Département de Biologie Joliot-Curie, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique, CEA Saclay, Gif-sur-Yvette, France
| | - Aline V Probst
- Section de Recherche, Institut Curie, UMR218 du Centre National de la Recherche Scientifique, Paris, France
| | - Jean-Pierre Quivy
- Section de Recherche, Institut Curie, UMR218 du Centre National de la Recherche Scientifique, Paris, France
| | - Patrick Héry
- Epigenetic Regulation and Cancer Group, Service de Biologie Moléculaire Systémique, Département de Biologie Joliot-Curie, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique, CEA Saclay, Gif-sur-Yvette, France
| | - Geneviève Almouzni
- Section de Recherche, Institut Curie, UMR218 du Centre National de la Recherche Scientifique, Paris, France
| | - Matthieu Gérard
- Epigenetic Regulation and Cancer Group, Service de Biologie Moléculaire Systémique, Département de Biologie Joliot-Curie, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique, CEA Saclay, Gif-sur-Yvette, France
- * To whom correspondence should be addressed. E-mail:
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Uchimura Y, Ichimura T, Uwada J, Tachibana T, Sugahara S, Nakao M, Saitoh H. Involvement of SUMO modification in MBD1- and MCAF1-mediated heterochromatin formation. J Biol Chem 2006; 281:23180-90. [PMID: 16757475 DOI: 10.1074/jbc.m602280200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Small ubiquitin-related modifiers, SUMO-2/3 and SUMO-1, are involved in gene regulation and nuclear structures. However, little is known about the roles of SUMO, in heterochromatin formation of mammalian cells. Here we demonstrate that SUMOs directly interact with human MCAF1, which forms complexes with either the methyl-CpG-binding protein MBD1 or SETDB1, which trimethylates histone H3 at lysine 9 (H3-K9) in the presence of MCAF1. Modification of MBD1 with either SUMO-2/3 or SUMO-1 facilitated the interaction between MBD1 and MCAF1, suggesting that SUMOylation links the methylation of DNA and histones. In a cultured human cell line, SUMOs were localized in MBD1- and MCAF1-containing heterochromatin regions that were enriched in trimethyl-H3-K9 and the heterochromatin proteins HP1beta and HP1gamma. Specific knockdown of either SUMO-2/3 or SUMO-1 induced dissociation of MCAF1, trimethyl-H3-K9, and the HP1 proteins from the MBD1-containing heterochromatin foci, suggesting a requirement for SUMOs for heterochromatin assembly. These findings provide insights into the roles of SUMOylation in the regulation of heterochromatin formation and gene silencing.
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Affiliation(s)
- Yasuhiro Uchimura
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
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61
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Schönrock N, Exner V, Probst A, Gruissem W, Hennig L. Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana. J Biol Chem 2006; 281:9560-8. [PMID: 16452472 DOI: 10.1074/jbc.m513426200] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Duplication of chromatin following DNA replication requires spatial reorganization of chromatin domains assisted by chromatin assembly factor CAF-1. Here, we tested the genomic consequences of CAF-1 loss and the function of chromatin assembly factor CAF-1 in heterochromatin formation. Genes located in heterochromatic regions are usually silent, and we found that this transcriptional repression persists in the absence of CAF-1 in Arabidopsis. However, using microarrays we observed that genes that are active during late S-phase, when heterochromatin is duplicated, were up-regulated in CAF-1 mutants. Arabidopsis CAF-1 mutants also have reduced cytological heterochromatin content; however, DNA methylation of pericentromeric repeats was normal, demonstrating that CAF-1 is not required for maintenance of DNA methylation. Instead, hypomethylation of the genome, which has only mild effects on the development of wild-type plants, completely arrested development of CAF-1 mutants. These results suggest that CAF-1 functions in heterochromatin formation. CAF-1 and DNA methylation, which is also needed for heterochromatin formation, have partially redundant functions that are essential for cell proliferation. Interestingly, transcriptional repression and heterochromatin compaction can be genetically separated, and CAF-1 is required only for the complete compaction of heterochromatin but not to maintain transcriptional repression of heterochromatic genes.
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Affiliation(s)
- Nicole Schönrock
- Institute of Plant Sciences, ETH Zurich and Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland
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62
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DNA methylation and cancer-associated genetic instability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2006; 570:363-92. [PMID: 18727508 DOI: 10.1007/1-4020-3764-3_13] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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63
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Datta J, Majumder S, Bai S, Ghoshal K, Kutay H, Smith DS, Crabb JW, Jacob ST. Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells. Cancer Res 2005; 65:10891-900. [PMID: 16322236 PMCID: PMC2241737 DOI: 10.1158/0008-5472.can-05-1455] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Dnmt3a and Dnmt3b are de novo DNA methyltransferases that also act as transcriptional repressors independent of methyltransferase activity. To elucidate the underlying mechanism of transcriptional repression, Dnmt3a was purified from mouse lymphosarcoma cells (P1798) by extensive fractionation on five different chromatographic matrices followed by glycerol density gradient centrifugation. Liquid chromatography electrospray tandem mass spectrometry analysis of Dnmt3a-associated polypeptides identified the methyl CpG binding protein Mbd3, histone deacetylase 1(Hdac1), and components of Brg1 complex (Brg1, Baf155, and Baf57) in the purified preparation. Association of Dnmt3a with Mbd3 and Brg1 was confirmed by coimmunoprecipitation and coimmunolocalization studies. Glutathione S-transferase pulldown assay showed that the NH2-terminal ATRX homology domain of Dnmt3a interacts with the methyl CpG binding domain of Mbd3 and with both bromo and ATPase domains of Brg1. Chromatin immunoprecipitation assay revealed that all three proteins are associated with transcriptionally silent methylated metallothionein (MT-I) promoter in the mouse lymphosarcoma cells. To understand the functional significance of their association with the promoter, their role on the MT-I promoter activity was analyzed by transient transfection assay. The results showed that Mbd3 and Dnmt3a specifically inhibited the methylated promoter, and the catalytic activity of Dnmt3a was dispensable for the suppression. In contrast, the wild-type but not the ATPase-inactive mutant of Brg1 suppressed MT-I promoter irrespective of its methylation status, implicating involvement of ATP-dependent chromatin remodeling in the process. Coexpression of two of the three interacting proteins at a time augmented their repressor function. This study shows physical and functional interaction of Dnmt3a with components of nucleosome remodeling machinery.
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Affiliation(s)
- Jhrana Datta
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
| | - Sarmila Majumder
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
| | - Shoumei Bai
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
| | - Kalpana Ghoshal
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
| | - Huban Kutay
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
| | - David Spencer Smith
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
| | - John W. Crabb
- Cole Eye Institute and Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Samson T. Jacob
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio
- Department of Internal Medicine, Ohio State University, Columbus, Ohio
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64
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Wallace JA, Orr-Weaver TL. Replication of heterochromatin: insights into mechanisms of epigenetic inheritance. Chromosoma 2005; 114:389-402. [PMID: 16220346 DOI: 10.1007/s00412-005-0024-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 08/13/2005] [Accepted: 08/15/2005] [Indexed: 12/20/2022]
Abstract
Heterochromatin is composed of tightly condensed chromatin in which the histones are deacetylated and methylated, and specific nonhistone proteins are bound. Additionally, in vertebrates and plants, the DNA within heterochromatin is methylated. As the heterochromatic state is stably inherited, replication of heterochromatin requires not only duplication of the DNA but also a reinstallment of the appropriate protein and DNA modifications. Thus replication of heterochromatin provides a framework for understanding mechanisms of epigenetic inheritance. In recent studies, roles have been identified for replication factors in reinstating heterochromatin, particularly functions for origin recognition complex, proliferating cell nuclear antigen, and chromatin-assembly factor 1 in recruiting the heterochromatin binding protein HP1, a histone methyltransferase, a DNA methyltransferase, and a chromatin remodeling complex. Potential mechanistic links between these factors are discussed. In some cells, replication of the heterochromatin is blocked, and in Drosophila this inhibition is mediated by a chromatin binding protein SuUR.
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65
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Santoro R, De Lucia F. Many players, one goal: how chromatin states are inherited during cell division. Biochem Cell Biol 2005; 83:332-43. [PMID: 15959559 DOI: 10.1139/o05-021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Replication of genomic material is a process that requires not only high fidelity in the duplication of DNA sequences but also inheritance of the chromatin states. In the last few years enormous effort has been put into elucidating the mechanisms involved in the correct propagation of chromatin states. From all these studies it emerges that an epigenetic network is at the base of this process. A coordinated interplay between histone modifications and histone variants, DNA methylation, RNA components, ATP-dependent chromatin remodeling, and histone-specific assembly factors regulates establishment of the replication timing program, initiation of replication, and propagation of chromatin domains. The aim of this review is to examine, in light of recent findings, how so many players can be coordinated with each other to achieve the same goal, a correct inheritance of the chromatin state.
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Affiliation(s)
- Raffaella Santoro
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany.
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66
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Salozhin SV, Prokhorchuk EB, Georgiev GP. Methylation of DNA — One of the Major Epigenetic Markers. BIOCHEMISTRY (MOSCOW) 2005; 70:525-32. [PMID: 15948706 DOI: 10.1007/s10541-005-0146-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Regulation of gene expression is a complex process. It includes a great number of steps from control of mRNA synthesis to posttranslational modification of proteins. Epigenetic events play essential roles in regulation of transcription. In this review, we concentrate on methylation of DNA as one of the important epigenetic marks. It is well known that DNA methylation is associated with closed chromatin state and, therefore, repressed, inactive genes. Here we describe major processes that depend on DNA methylation: imprinting, X-inactivation, and oncogenesis. Also we describe a number of known methyl-DNA-binding proteins and links between methylation of DNA and higher-order chromatin structure.
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Affiliation(s)
- S V Salozhin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.
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67
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Ichimura T, Watanabe S, Sakamoto Y, Aoto T, Fujita N, Nakao M. Transcriptional repression and heterochromatin formation by MBD1 and MCAF/AM family proteins. J Biol Chem 2005; 280:13928-35. [PMID: 15691849 DOI: 10.1074/jbc.m413654200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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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Affiliation(s)
- Takaya Ichimura
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
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68
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Danam RP, Howell SR, Brent TP, Harris LC. Epigenetic regulation of O6-methylguanine-DNA methyltransferase gene expression by histone acetylation and methyl-CpG binding proteins. Mol Cancer Ther 2005. [DOI: 10.1158/1535-7163.61.4.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Transcriptional silencing of the DNA repair gene, O6-methylguanine-DNA methyltransferase (MGMT) in a proportion of transformed cell lines is associated with methylated CpG hotspots in the MGMT 5′ flank. The goal of the study was to evaluate the mechanism by which CpG methylation of theMGMT promoter region influenced silencing of the gene. Analysis of histone acetylation status in two regions of the promoter using chromatin immunoprecipitation assay showed that a higher level of histone acetylation was associated with expression in three MGMT-expressing cell lines (HeLa CCL2, HT29, and Raji) compared with three MGMT-silenced cell lines (HeLa S3, BE, and TK6). To determine how the modulation of CpG methylation and histone acetylation influenced MGMT expression, we exposed the cells to 5-aza-2′deoxycytidine (5-Aza-dC), inhibitor of DNA methylation, which strongly up-regulated MGMT expression in three MGMT-silenced cell lines whereas trichostatin A, inhibitor of histone deacetylase, weakly induced MGMT. However, combined treatment with 5-Aza-dC and trichostatin A significantly up-regulated MGMT RNA expression to a greater extent than in cells treated with either agent alone suggesting that histone deacetylation plays a role in MGMT silencing but that CpG methylation has a dominant effect. Consistent with enhanced MGMT expression, 5-Aza-dC increased the association of acetylated histone H3 and H4 bound to the MGMT promoter. Chromatin immunoprecipitation analysis of methyl-CpG binding domain containing proteins detected a greater amount of MeCP2, MBD1, and CAF-1 bound to the MGMT promoter in MGMT-silenced cells. Our findings implicate specific MBD proteins in methylation-mediated transcriptional silencing of MGMT.
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Affiliation(s)
- Rebecca P. Danam
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherie R. Howell
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Thomas P. Brent
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Linda C. Harris
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee
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69
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Alikhani-Koopaei R, Fouladkou F, Frey FJ, Frey BM. Epigenetic regulation of 11 beta-hydroxysteroid dehydrogenase type 2 expression. J Clin Invest 2004; 114:1146-57. [PMID: 15489962 PMCID: PMC522246 DOI: 10.1172/jci21647] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The enzyme 11 beta-hydroxysteroid dehydrogenase type 2 (11 beta HSD2) is selectively expressed in aldosterone target tissues, where it confers aldosterone selectivity for the mineralocorticoid receptor by inactivating 11 beta-hydroxyglucocorticoids. Variable activity of 11 beta HSD2 is relevant for blood pressure control and hypertension. The present investigation aimed to elucidate whether an epigenetic mechanism, DNA methylation, accounts for the rigorous control of expression of the gene encoding 11 beta HSD2, HSD11B2. CpG islands covering the promoter and exon 1 of HSD11B2 were found to be densely methylated in tissues and cell lines with low expression but not those with high expression of HSD11B2. Demethylation induced by 5-aza-2'-deoxycytidine and procainamide enhanced the transcription and activity of the 11 beta HSD2 enzyme in human cells in vitro and in rats in vivo. Methylation of HSD11B2 promoter-luciferase constructs decreased transcriptional activity. Methylation of recognition sequences of transcription factors, including those for Sp1/Sp3, Arnt, and nuclear factor 1 (NF1) diminished their DNA-binding activity. Herein NF1 was identified as a strong HSD11B2 stimulatory factor. The effect of NF1 was dependent on the position of CpGs and the combination of CpGs methylated. A methylated-CpG-binding protein complex 1 transcriptional repression interacted directly with the methylated HSD11B2 promoter. These results indicate a role for DNA methylation in HSD11B2 gene repression and suggest an epigenetic mechanism affecting this gene causally linked with hypertension.
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Affiliation(s)
- Rasoul Alikhani-Koopaei
- Department of Nephrology and Hypertension, University Hospital of Berne, Berne UNK 3010, Switzerland
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Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell 2004; 15:595-605. [PMID: 15327775 DOI: 10.1016/j.molcel.2004.06.043] [Citation(s) in RCA: 309] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 05/30/2004] [Accepted: 06/17/2004] [Indexed: 01/17/2023]
Abstract
In mammals, heterochromatin is characterized by DNA methylation at CpG dinucleotides and methylation at lysine 9 of histone H3. It is currently unclear whether there is a coordinated transmission of these two epigenetic modifications through DNA replication. Here we show that the methyl-CpG binding protein MBD1 forms a stable complex with histone H3-K9 methylase SETDB1. Moreover, during DNA replication, MBD1 recruits SETDB1 to the large subunit of chromatin assembly factor CAF-1 to form an S phase-specific CAF-1/MBD1/SETDB1 complex that facilitates methylation of H3-K9 during replication-coupled chromatin assembly. In the absence of MBD1, H3-K9 methylation is lost at multiple genomic loci and results in activation of p53BP2 gene, normally repressed by MBD1 in HeLa cells. Our data suggest a model in which H3-K9 methylation by SETDB1 is dependent on MBD1 and is heritably maintained through DNA replication to support the formation of stable heterochromatin at methylated DNA.
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Affiliation(s)
- Shireen A Sarraf
- School of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, United Kingdom
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Abstract
During DNA replication, transcription and DNA repair in eukaryotes, the cellular machineries performing these tasks need to gain access to the DNA that is packaged into chromatin in the nucleus. Chromatin is a dynamic structure that modulates the access of regulatory factors to the genetic material. A precise coordination and organization of events in opening and closing of the chromatin is crucial to ensure that the correct spatial and temporal epigenetic code is maintained within the eukaryotic genome. This review will summarize the current knowledge of how chromatin remodeling and histone modifying complexes cooperate to break and remake chromatin during nuclear processes on the DNA template.
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72
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Jørgensen HF, Ben-Porath I, Bird AP. Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains. Mol Cell Biol 2004; 24:3387-95. [PMID: 15060159 PMCID: PMC381685 DOI: 10.1128/mcb.24.8.3387-3395.2004] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MBD1 is a vertebrate methyl-CpG binding domain protein (MBD) that can bring about repression of methylated promoter DNA sequences. Like other MBD proteins, MBD1 localizes to nuclear foci that in mice are rich in methyl-CpG. In methyl-CpG-deficient mouse cells, however, Mbd1 remains localized to heterochromatic foci whereas other MBD proteins become dispersed in the nucleus. We find that Mbd1a, a major mouse isoform, contains a CXXC domain (CXXC-3) that binds specifically to nonmethylated CpG, suggesting an explanation for methylation-independent localization. Transfection studies demonstrate that the CXXC-3 domain indeed targets nonmethylated CpG sites in vivo. Repression of nonmethylated reporter genes depends on the CXXC-3 domain, whereas repression of methylated reporters requires the MBD. Our findings indicate that MBD1 can interpret the CpG dinucleotide as a repressive signal in vivo regardless of its methylation status.
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Affiliation(s)
- Helle F Jørgensen
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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73
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Loyola A, Almouzni G. Histone chaperones, a supporting role in the limelight. ACTA ACUST UNITED AC 2004; 1677:3-11. [PMID: 15020040 DOI: 10.1016/j.bbaexp.2003.09.012] [Citation(s) in RCA: 255] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Revised: 09/25/2003] [Accepted: 09/25/2003] [Indexed: 10/26/2022]
Abstract
In eukaryotic cells, highly basic histone proteins are associated with the DNA to form the nucleosome, the fundamental unit of chromatin. Histones are closely escorted by histone chaperones from their point of synthesis up to their delivery site. We will present an overview of the histone chaperones identified to date with their various roles, in an attempt to highlight their importance in cellular metabolism. Nucleoplasmin will illustrate a role in histone storage and Nap-1, a histone translocator. CAF-1 and Hira will provide examples of distinct histone deposition factors coupled to and uncoupled from DNA synthesis, respectively, while Asf1 could act as a histone donor. We then will illustrate with two examples how histone chaperones can be associated with chromatin remodeling activities. Finally, we will discuss how the RbAp46/48 proteins, as escort factors, are part of multiple complexes with various functions. Based on these examples, we will propose a scheme in which the diverse roles of histone chaperones are integrated within an assembly line for chromatin formation and regulation. Finally, we discuss how these chaperones may have more than a supporting role in a histone metabolic pathway.
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Affiliation(s)
- Alejandra Loyola
- Institut Curie/Section de Recherche, UMR 21826, rue d'Ulm, 75231 Paris Cedex 05, France
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74
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Abstract
Heterochromatin remains condensed throughout the cell cycle, is generally transcriptionally inert and is built and maintained by groups of factors with each group member sharing a similar function. In mammals, these groups include sequence-specific transcriptional repressors, functional RNA and proteins involved in DNA and histone methylation. Heterochromatin is cemented together via interactions within and between each protein group and is maintained by the cell's replication machinery. It can be constitutive (permanent) or facultative (developmentally regulated) and be any size, from a gene promotor to a whole genome. By studying the formation of facultative heterochromatin, we have gained information about how heterochromatin is assembled. We have discovered that there are many different architectural plans for the building of heterochromatin, leading to a seemingly never-ending variety of heterochromatic loci, with each built according to a general rule.
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Affiliation(s)
- Jeffrey M Craig
- Chromosome Research Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Melbourne, Victoria 3052, Australia.
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