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DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell 2020; 77:310-323.e7. [DOI: 10.1016/j.molcel.2019.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
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2
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Lane AB, Giménez-Abián JF, Clarke DJ. A novel chromatin tether domain controls topoisomerase IIα dynamics and mitotic chromosome formation. ACTA ACUST UNITED AC 2014; 203:471-86. [PMID: 24217621 PMCID: PMC3824022 DOI: 10.1083/jcb.201303045] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The dynamics of topoisomerase IIα binding to DNA and histones are important for successful mitosis and are regulated by a novel chromatin tether (ChT) domain in topoisomerase IIα. DNA topoisomerase IIα (Topo IIα) is the target of an important class of anticancer drugs, but tumor cells can become resistant by reducing the association of the enzyme with chromosomes. Here we describe a critical mechanism of chromatin recruitment and exchange that relies on a novel chromatin tether (ChT) domain and mediates interaction with histone H3 and DNA. We show that the ChT domain controls the residence time of Topo IIα on chromatin in mitosis and is necessary for the formation of mitotic chromosomes. Our data suggest that the dynamics of Topo IIα on chromosomes are important for successful mitosis and implicate histone tail posttranslational modifications in regulating Topo IIα.
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Affiliation(s)
- Andrew B Lane
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
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3
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The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells. Cell Rep 2013; 3:2142-54. [PMID: 23746450 DOI: 10.1016/j.celrep.2013.05.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 02/19/2013] [Accepted: 05/03/2013] [Indexed: 12/27/2022] Open
Abstract
Human cells contain five canonical, replication-dependent somatic histone H1 subtypes (H1.1, H1.2, H1.3, H1.4, and H1.5). Although they are key chromatin components, the genomic distribution of the H1 subtypes is still unknown, and their role in chromatin processes has thus far remained elusive. Here, we map the genomic localization of all somatic replication-dependent H1 subtypes in human lung fibroblasts using an integrative DNA adenine methyltransferase identification (DamID) analysis. We find in general that H1.2 to H1.5 are depleted from CpG-dense regions and active regulatory regions. H1.1 shows a DamID binding profile distinct from the other subtypes, suggesting a unique function. H1 subtypes can mark specific domains and repressive regions, pointing toward a role for H1 in three-dimensional genome organization. Our work integrates H1 subtypes into the epigenome maps of human cells and provides a valuable resource to refine our understanding of the significance of H1 and its heterogeneity in the control of genome function.
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Mellén M, Ayata P, Dewell S, Kriaucionis S, Heintz N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 2013; 151:1417-30. [PMID: 23260135 DOI: 10.1016/j.cell.2012.11.022] [Citation(s) in RCA: 707] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 10/05/2012] [Accepted: 11/15/2012] [Indexed: 12/13/2022]
Abstract
The high level of 5-hydroxymethylcytosine (5hmC) present in neuronal genomes suggests that mechanisms interpreting 5hmC in the CNS may differ from those present in embryonic stem cells. Here, we present quantitative, genome-wide analysis of 5hmC, 5-methylcytosine (5mC), and gene expression in differentiated CNS cell types in vivo. We report that 5hmC is enriched in active genes and that, surprisingly, strong depletion of 5mC is observed over these regions. The contribution of these epigenetic marks to gene expression depends critically on cell type. We identify methyl-CpG-binding protein 2 (MeCP2) as the major 5hmC-binding protein in the brain and demonstrate that MeCP2 binds 5hmC- and 5mC-containing DNA with similar high affinities. The Rett-syndrome-causing mutation R133C preferentially inhibits 5hmC binding. These findings support a model in which 5hmC and MeCP2 constitute a cell-specific epigenetic mechanism for regulation of chromatin structure and gene expression.
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Affiliation(s)
- Marian Mellén
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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5
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Gilbert N, Thomson I, Boyle S, Allan J, Ramsahoye B, Bickmore WA. DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction. ACTA ACUST UNITED AC 2007; 177:401-11. [PMID: 17485486 PMCID: PMC2064831 DOI: 10.1083/jcb.200607133] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation has been implicated in chromatin condensation and nuclear organization, especially at sites of constitutive heterochromatin. How this is mediated has not been clear. In this study, using mutant mouse embryonic stem cells completely lacking in DNA methylation, we show that DNA methylation affects nuclear organization and nucleosome structure but not chromatin compaction. In the absence of DNA methylation, there is increased nuclear clustering of pericentric heterochromatin and extensive changes in primary chromatin structure. Global levels of histone H3 methylation and acetylation are altered, and there is a decrease in the mobility of linker histones. However, the compaction of both bulk chromatin and heterochromatin, as assayed by nuclease digestion and sucrose gradient sedimentation, is unaltered by the loss of DNA methylation. This study shows how the complete loss of a major epigenetic mark can have an impact on unexpected levels of chromatin structure and nuclear organization and provides evidence for a novel link between DNA methylation and linker histones in the regulation of chromatin structure.
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Affiliation(s)
- Nick Gilbert
- Medical Research Council Human Genetics Unit, Edinburgh, Scotland, UK
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6
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Lavi T, Isakov E, Harony H, Fisher O, Siman-Tov R, Ankri S. Sensing DNA methylation in the protozoan parasite Entamoeba histolytica. Mol Microbiol 2006; 62:1373-86. [PMID: 17059565 DOI: 10.1111/j.1365-2958.2006.05464.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the protozoan parasite Entamoeba histolytica, 5-methylcytosine (m5C) was found predominantly in repetitive elements. Its formation is catalysed by Ehmeth, a DNA methyltransferase that belongs to the Dnmt2 subfamily. Here we describe a 32 kDa nuclear protein that binds in vitro with higher affinity to the methylated form of a DNA encoding a reverse transcriptase of an autonomous non-long-terminal repeat retrotransposon (RT LINE) compared with the non-methylated RT LINE. This protein, named E. histolytica-methylated LINE binding protein (EhMLBP), was purified from E. histolytica nuclear lysate, identified by mass spectrometry, and its corresponding gene was cloned. EhMLBP corresponds to a gene of unknown function that shares strong homology with putative proteins present in Entamoeba dispar and Entamoeba invadens. In contrast, the homology dropped dramatically when non-Entamoebidae sequences were considered and only a weak sequence identity was found with Trypanosoma and several prokaryotic histone H1. Recombinant EhMLBP showed the same binding preference for methylated RT LINE as the endogenous EhMLBP. Deletion mapping analysis localized the DNA binding region at the C-terminal part of the protein. This region is sufficient to assure the binding to methylated RT LINE with high affinity. Western blot and immunofluorescence microscopy, using an antibody raised against EhMLBP, showed that it has a nuclear localization. Chromatin immunoprecipitation (ChIP) confirmed that EhMLBP interacts with RT LINE in vivo. Finally, we showed that EhMLBP can also bind rDNA episome, a DNA that is methylated in the parasite. This suggests that EhMLBP may serve as a sensor of methylated repetitive DNA. This is the first report of a DNA-methylated binding activity in protozoa.
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Affiliation(s)
- Tal Lavi
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Israel
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7
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Folco HD, Freitag M, Ramón A, Temporini ED, Alvarez ME, García I, Scazzocchio C, Selker EU, Rosa AL. Histone H1 Is required for proper regulation of pyruvate decarboxylase gene expression in Neurospora crassa. EUKARYOTIC CELL 2003; 2:341-50. [PMID: 12684383 PMCID: PMC154839 DOI: 10.1128/ec.2.2.341-350.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 12/20/2002] [Indexed: 11/20/2022]
Abstract
We show that Neurospora crassa has a single histone H1 gene, hH1, which encodes a typical linker histone with highly basic N- and C-terminal tails and a central globular domain. A green fluorescent protein-tagged histone H1 chimeric protein was localized exclusively to nuclei. Mutation of hH1 by repeat-induced point mutation (RIP) did not result in detectable defects in morphology, DNA methylation, mutagen sensitivity, DNA repair, fertility, RIP, chromosome pairing, or chromosome segregation. Nevertheless, hH1 mutants had mycelial elongation rates that were lower than normal on all tested carbon sources. This slow linear growth phenotype, however, was less evident on medium containing ethanol. The pyruvate decarboxylase gene, cfp, was abnormally derepressed in hH1 mutants on ethanol-containing medium. This derepression was also found when an ectopically integrated fusion of the cfp gene promoter to the reporter gene hph was analyzed. Thus, Neurospora histone H1 is required for the proper regulation of cfp, a gene with a key role in the respiratory-fermentative pathway.
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Affiliation(s)
- H Diego Folco
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, 5016 Córdoba, Argentina
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8
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Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H. Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 2002; 277:37741-6. [PMID: 12124387 DOI: 10.1074/jbc.m204050200] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
When maize seedlings were exposed to cold stress, a genome-wide demethylation occurred in root tissues. Screening of genomic DNA identified one particular fragment that was demethylated during chilling. This 1.8-kb fragment, designated ZmMI1, contained part of the coding region of a putative protein and part of a retrotransposon-like sequence. ZmMI1 was transcribed only under cold stress. Direct methylation mapping revealed that hypomethylated regions spanning 150 bases alternated with hypermethylated regions spanning 50 bases. Analysis of nuclear DNA digested with micrococcal nuclease indicated that these regions corresponded to nucleosome cores and linkers, respectively. Cold stress induced severe demethylation in core regions but left linker regions relatively intact. Thus, methylation and demethylation were periodic in nucleosomes. The following biological significance is conceivable. First, because DNA methylation in nucleosomes induces alteration of gene expression by changing chromatin structures, vast demethylation may serve as a common switch for many genes that are simultaneously controlled upon environmental cues. Second, because artificial demethylation induces heritable changes in plant phenotype (Sano, H., Kamada, I., Youssefian, S., Katsumi, M., and Wabilko, H. (1990) Mol. Gen. Genet. 220, 441-447), altered DNA methylation may result in epigenetic inheritance, in which gene expression is modified without changing the nucleotide sequence.
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Affiliation(s)
- Nicolas Steward
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Nara 630-0101, Japan
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9
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Paulsen M, Ferguson-Smith AC. DNA methylation in genomic imprinting, development, and disease. J Pathol 2001; 195:97-110. [PMID: 11568896 DOI: 10.1002/path.890] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Changes in DNA methylation profiles are common features of development and in a number of human diseases, such as cancer and imprinting disorders like Beckwith-Wiedemann and Prader-Willi/Angelman syndromes. This suggests that DNA methylation is required for proper gene regulation during development and in differentiated tissues and has clinical relevance. DNA methylation is also involved in X-chromosome inactivation and the allele-specific silencing of imprinted genes. This review describes possible mechanisms by which DNA methylation can regulate gene expression, using imprinted genes as examples. The molecular basis of methylation-mediated gene regulation is related to changes in chromatin structure and appears to be similar for both imprinted and biallelically expressed genes.
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Affiliation(s)
- M Paulsen
- University of Cambridge, Department of Anatomy, Cambridge CB2 3DY, UK
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Akhmanova A, Verkerk T, Langeveld A, Grosveld F, Galjart N. Characterisation of transcriptionally active and inactive chromatin domains in neurons. J Cell Sci 2000; 113 Pt 24:4463-74. [PMID: 11082040 DOI: 10.1242/jcs.113.24.4463] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tandemly organised ribosomal DNA (rDNA) repeats are transcribed by a dedicated RNA polymerase in a specialised nuclear compartment, the nucleolus. There appears to be an intimate link between the maintenance of nucleolar structure and the presence of heterochromatic chromatin domains. This is particularly evident in many large neurons, where a single nucleolus is present, which is separated from the remainder of the nucleus by a characteristic shell of heterochromatin. Using a combined fluorescence in situ hybridisation and immunocytochemistry approach, we have analysed the molecular composition of this highly organised neuronal chromatin, to investigate its functional significance. We find that clusters of inactive, methylated rDNA repeats are present inside large neuronal nucleoli, which are often attached to the shell of heterochromatic DNA. Surprisingly, the methylated DNA-binding protein MeCP2, which is abundantly present in the centromeric and perinucleolar heterochromatin, does not associate significantly with the methylated rDNA repeats, whereas histone H1 does overlap partially with these clusters. Histone H1 also defines other, centromere-associated chromatin subdomains, together with the mammalian Polycomb group factor Eed. These data indicate that neuronal, perinucleolar heterochromatin consists of several classes of inactive DNA, that are linked to a fraction of the inactive rDNA repeats. These distinct chromatin domains may serve to regulate RNA transcription and processing efficiently and to protect rDNA repeats against unwanted silencing and/or homologous recombination events.
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Affiliation(s)
- A Akhmanova
- MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, Rotterdam, The Netherlands
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11
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Zlatanova J, Caiafa P, Van Holde K. Linker histone binding and displacement: versatile mechanism for transcriptional regulation. FASEB J 2000; 14:1697-704. [PMID: 10973918 DOI: 10.1096/fj.99-0869rev] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In recent years, the connection between chromatin structure and its transcriptional activity has attracted considerable experimental effort. The post-translational modifications to both the core histones and the linker histones are finely tuned through interactions with transcriptional regulators and change chromatin structure in a way to allow transcription to occur. Here we review evidence for the involvement of linker histones in transcriptional regulation and suggest a scenario in which the reversible and controllable binding/displacement of proteins of this class to the nucleosome entry/exit point determine the accessibility of the nucleosomal DNA to the transcriptional machinery.
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Affiliation(s)
- J Zlatanova
- Biochip Technology Center, Argonne National Laboratory, Argonne, Illinois 60439-4833, USA.
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12
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El-Osta A, Wolffe AP. DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease. Gene Expr 2000; 9:63-75. [PMID: 11097425 PMCID: PMC5964960 DOI: 10.3727/000000001783992731] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA methylation is a major determinant in the epigenetic silencing of genes. The mechanisms underlying the targeting of DNA methylation and the subsequent repression of transcription are relevant to human development and disease, as well as for attempts at somatic gene therapy. The success of transgenic technologies in plants and animals is also compromised by DNA methylation-dependent silencing pathways. Recent biochemical experiments provide a mechanistic foundation for understanding the influence of DNA methylation on transcription. The DNA methyltransferase Dnmt1, and several methyl-CpG binding proteins, MeCP2, MBD2, and MBD3, all associate with histone deacetylase. These observations firmly connect DNA methylation with chromatin modifications. They also provide new pathways for the potential targeting of DNA methylation to repressive chromatin as well as the assembly of repressive chromatin on methylated DNA. Here we discuss the implications of the methylation-acetylation connection for human cancers and the developmental syndromes Fragile X and Rett, which involve a mistargeting of DNA methylation-dependent repression.
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Affiliation(s)
- Assam El-Osta
- Laboratory of Molecular Embryology, National Institute of Child Heath and Human Development, NIH, Bethesda, MD 20892-5431
| | - Alan P. Wolffe
- Laboratory of Molecular Embryology, National Institute of Child Heath and Human Development, NIH, Bethesda, MD 20892-5431
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13
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Barra JL, Rhounim L, Rossignol JL, Faugeron G. Histone H1 is dispensable for methylation-associated gene silencing in Ascobolus immersus and essential for long life span. Mol Cell Biol 2000; 20:61-9. [PMID: 10594009 PMCID: PMC85047 DOI: 10.1128/mcb.20.1.61-69.2000] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/1999] [Accepted: 09/28/1999] [Indexed: 11/20/2022] Open
Abstract
A gene encoding a protein that shows sequence similarity with the histone H1 family only was cloned in Ascobolus immersus. The deduced peptide sequence presents the characteristic three-domain structure of metazoan linker histones, with a central globular region, an N-terminal tail, and a long positively charged C-terminal tail. By constructing an artificial duplication of this gene, named H1, it was possible to methylate and silence it by the MIP (methylation induced premeiotically) process. This resulted in the complete loss of the Ascobolus H1 histone. Mutant strains lacking H1 displayed normal methylation-associated gene silencing, underwent MIP, and showed the same methylation-associated chromatin modifications as did wild-type strains. However, they displayed an increased accessibility of micrococcal nuclease to chromatin, whether DNA was methylated or not, and exhibited a hypermethylation of the methylated genome compartment. These features are taken to imply that Ascobolus H1 histone is a ubiquitous component of chromatin which plays no role in methylation-associated gene silencing. Mutant strains lacking histone H1 reproduced normally through sexual crosses and displayed normal early vegetative growth. However, between 6 and 13 days after germination, they abruptly and consistently stopped growing, indicating that Ascobolus H1 histone is necessary for long life span. This constitutes the first observation of a physiologically important phenotype associated with the loss of H1.
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Affiliation(s)
- J L Barra
- Institut Jacques Monod, UMR 7592, CNRS/Université Paris 7/Université Paris 6, 75251 Paris Cedex 05, France
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14
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Abstract
Interleukin-2 (IL-2) is a growth and differentiation factor critical for clonal T cell expansion and function. Produced exclusively in T cells, IL-2 transcription and synthesis occurs only after appropriate cellular activation via the clonotypic antigen-receptor and co-stimulatory molecules. IL-2 gene expression is initiated by the cooperative binding of different transcription factors and is predominantly controlled at the transcriptional level. Recently, it has been demonstrated that IL-2 transcriptional activity is normally confined to a single, randomly chosen allele. This monoallelic expression of a non-receptor gene product encoded at a non-imprinted, autosomal locus represents an unusual regulatory mode. Although the molecular mechanisms operational for IL-2 transcription have yet to be defined, allele-specific expression of the IL-2 locus constitutes an important expansion to the concept of stochastic gene expression.
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Affiliation(s)
- G A Holländer
- Pediatric Immunology Department of Research and The Children's University Hospital, Hebelstrasse 20, 4031 Basel, Switzerland.
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15
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Jones PL, Wolffe AP. Relationships between chromatin organization and DNA methylation in determining gene expression. Semin Cancer Biol 1999; 9:339-47. [PMID: 10547342 DOI: 10.1006/scbi.1999.0134] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromatin is the natural substrate for the control of gene expression. Chromatin contains DNA, the transcriptional machinery and structural proteins such as histones. Recent advances demonstrate that transcriptional activity of a gene is largely controlled by the packaging of the template within chromatin. The covalent modification of chromatin provides an attractive mechanism for establishing and maintaining stable states of gene activity. DNA methylation and histone acetylation alter the nucleosomal infrastructure to repress or activate transcription. These covalent modifications have causal roles in both promoter-specific events and the global control of chromosomal activity. DNA methylation and histone acetylation have a major impact in both oncogenic transformation and normal development.
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Affiliation(s)
- P L Jones
- Laboratory of Molecular Embryology, Nat'l Inst. of Child Health and Human Development, NIH, Bldg. 18T, Rm. 106, Bethesda, MD 20892-5431, USA
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Chandler SP, Guschin D, Landsberger N, Wolffe AP. The methyl-CpG binding transcriptional repressor MeCP2 stably associates with nucleosomal DNA. Biochemistry 1999; 38:7008-18. [PMID: 10353812 DOI: 10.1021/bi990224y] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the interactions of the methyl-CpG binding transcriptional repressor MeCP2 with nucleosomal DNA. We find that MeCP2 forms discrete complexes with nucleosomal DNA associating with methyl-CpGs exposed in the major groove via the methyl-CpG-binding domain (MBD). In addition to the MBD, the carboxyl-terminal segment of MeCP2 facilitates binding both to naked DNA and to the nucleosome core. These observations provide a molecular mechanism by which MeCP2 can gain access to chromatin in order to target corepressor complexes that further modify chromatin structure.
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Affiliation(s)
- S P Chandler
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892-5431, USA
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17
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Sengupta PK, Smith BD. Methylation in the initiation region of the first exon suppresses collagen pro-alpha2(I) gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1443:75-89. [PMID: 9838053 DOI: 10.1016/s0167-4781(98)00188-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Our previous studies demonstrated that the collagen alpha2(I) gene is hypermethylated in the promoter/first exon region after chemical transformation and the alpha2(I) promoter/first exon is sensitive to methylation in transfection studies. In this paper, we demonstrate that a minimum collagen promoter containing the preinitiation region (-41 to +54) driving luciferase reporter gene was inactivated by DNA methylation as judged by transfection assays. All the methylation sites within the preinitiation region were located in the first exon, not in the promoter. Methylation of the promoter construct inhibited transcription as determined by an in vitro assay, only if proteins were extracted from nuclei using 500 mM NaCl. Gel mobility shift analysis suggested that methylation within the first exon decreased the formation of the largest preinitiation complex while increasing the formation of faster migrating protein-DNA complexes. Competition gel mobility shift analysis indicated that the faster migrating protein-DNA complex could be competed by a smaller initiator probe which did not contain TATA binding region. A protein-DNA complex with increased affinity to methylated sequences was detected using the initiator probe, which contained two methylation sites and no TATA sequence (-25 to 30) suggesting that a separate repressor complex binds to the methylated sequences. Mutations at the methylation sites (+7, +23) in the first exon also increased the protein-DNA complex formation in gel shift analysis and inhibited collagen alpha2(I) transcription as judged by transient transfection and in vitro transcription assays. Therefore, these methylation sites in the preinitiation region are important for transcription of alpha2(I) gene and the protein responsible for the repression of transcription is extractable using high salt nuclear extracts.
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Affiliation(s)
- P K Sengupta
- Department of Biochemistry, Boston University School of Medicine, 715 Albany St., Boston, MA 02118, USA
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18
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Kass SU, Wolffe AP. DNA methylation, nucleosomes and the inheritance of chromatin structure and function. NOVARTIS FOUNDATION SYMPOSIUM 1998; 214:22-35; discussion 36-50. [PMID: 9601010 DOI: 10.1002/9780470515501.ch3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The replication of the genome during S phase is a crucial period for the establishment and maintenance of programmes of differential gene activity. Existing chromosomal structures are disrupted during replication and reassembled on both daughter chromatids. The capacity to reassemble a particular chromatin structure with defined functional properties reflects the commitment of a cell type to a particular state of determination. The core and linker histones and their modifications, enzymes that modify the histones, DNA methylation and proteins that recognize methylated DNA within chromatin may all play independent or interrelated roles in defining the functional properties of chromatin. Pre-existing protein-DNA interactions and DNA methylation in a parental chromosome will influence the structure and function of daughter chromosomes generating an epigenetic imprint. In this chapter we consider the events occurring at the eukaryotic replication fork, their consequences for pre-existing chromosomal structures and how an epigenetic imprint might be maintained.
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Affiliation(s)
- S U Kass
- Department of Experimental Molecular Biology
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19
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Abstract
The regulation of eukaryotic gene expression is a complicated process involving the interaction of a large number of transacting factors with specific cis-regulatory elements. DNA methylation plays a role in this scheme by acting in cis to modulate protein-DNA interactions. Several lines of evidence indicate that methylation serves to silence transcription, mainly through indirect mechanisms involving the assembly of repressive nucleoprotein complexes. DNA demethylation is mostly an active enzymatic process, controlled by cis regulatory elements which provide binding sites for trans demethylation factors. In the immune system DNA methylation plays multiple roles, such as regulating both gene expression and gene rearrangement
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Affiliation(s)
- Y Bergman
- The Hubert H. Humphrey Center for Experimental Medicine and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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20
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Abstract
It is now generally accepted that the presence of 5-methylcytosine (5mC) in human DNA has both a genetic and an epigenetic effect on cellular development, differentiation and transformation. First, 5mC is more unstable than its unmethylated counterpart cytosine. Hydrolytic deamination of 5mC leads to a G/T mismatch and subsequently, if unrepaired, to a C-->T transition mutation. Sites of DNA methylation are mutational hotspots in many human tumors. Second, DNA methylation of promoter regions is often correlated with the down regulation of the corresponding gene. Both of these effects have fundamental consequences for basic functions of the cell like cellular differentiation, the development of cancer and possibly other diseases, and on the evolutionary process. Recent hypotheses also propose a role for methylation in the process of aging. In this review we will describe recent findings and hypotheses about the function of 5mC in DNA with the focus on its involvement in human carcinogenesis.
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Affiliation(s)
- C Schmutte
- Thomas Jefferson University, Kimmel Cancer Center, Philadelphia, PA 19107, USA
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Schwarz S, Hess D, Jost JP. The methylated DNA binding protein-2-H1 (MDBP-2-H1) consists of histone H1 subtypes which are truncated at the C-terminus. Nucleic Acids Res 1997; 25:5052-6. [PMID: 9396815 PMCID: PMC147137 DOI: 10.1093/nar/25.24.5052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The methylated DNA binding protein-2-H1 (MDBP-2-H1), present in rooster liver, is a member of the histone H1 family which inhibits transcription by binding selectively to methylated promoters. Here we have determined the primary structure of MDBP-2-H1. A comparison between histone H1 and MDBP-2-H1 was achieved by analyzing reversed phase HPLC-purified and V8-digested proteins by mass spectrometry and/or microsequencing. In rooster liver the most abundant histone H1 subtypes are H1 01 and H1 11L. Similarly, MDBP-2-H1 contains the same subtypes of histone H1. The histone H1 subtype H1 01 in MDBP-2-H1 has 150 amino acids, whereas the full-size histone H1 01 is 218 amino acids. The difference in mass between the two proteins is explained by C-terminal truncation of histone H1 01.
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Affiliation(s)
- S Schwarz
- Friedrich-Miescher Institut, PO Box 2543, CH-4002 Basel, Switzerland
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22
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Abstract
DNA methylation has an essential regulatory function in mammalian development, serving to repress nontranscribed genes stably in differentiated adult somatic cells. Recent data implicate transcriptional repressors specific for methylated DNA and chromatin assembly in this global control of gene activity. The assembly of specialized nucleosomal structures on methylated DNA helps to explain the capacity of methylated DNA segments to silence transcription more effectively than conventional chromatin. Specialized nucleosomes also provide a potential molecular mechanism for the stable propagation of DNA methylation-dependent transcriptional silencing through cell division.
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Affiliation(s)
- S U Kass
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-5431, USA.
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23
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Feil R, Boyano MD, Allen ND, Kelsey G. Parental chromosome-specific chromatin conformation in the imprinted U2af1-rs1 gene in the mouse. J Biol Chem 1997; 272:20893-900. [PMID: 9252416 DOI: 10.1074/jbc.272.33.20893] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The imprinted U2af1-rs1 gene on mouse chromosome 11 is expressed exclusively from the paternal allele. We found that U2af1-rs1 resides in a chromosomal domain that displays marked differences in chromatin conformation and DNA methylation between the parental chromosomes. Chromatin conformation was assayed in brain and liver, in fetuses, and in embryonic stem cells by sensitivity to nucleases in nuclei. In all these tissues, the unmethylated paternal chromosome is sensitive to DNase-I and MspI and has two DNase-I hypersensitive sites in the 5'-untranslated region. In brain and in differentiated stem cells, which display high levels of U2af1-rs1 expression, a paternal DNase-I hypersensitive site is also readily apparent in the promoter region. On the maternal chromosome, in contrast, the entire U2af1-rs1 gene and its promoter are highly resistant to DNase-I and MspI in all tissues analyzed and are fully methylated. No differential MNase sensitivity was detected in this imprinted domain. The parental chromosome-specific DNA methylation and chromatin conformation were also present in parthenogenetic and androgenetic cells and in tissues from animals maternally or paternally disomic for chromosome 11. This demonstrates that these parental chromosome-specific epigenotypes are independently established and maintained and provides no evidence for interallelic trans-sensing and counting mechanisms in U2af1-rs1.
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Affiliation(s)
- R Feil
- Department of Development and Genetics, the Babraham Institute, Cambridge CB2 4AT, United Kingdom.
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24
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Mostoslavsky R, Bergman Y. DNA methylation: regulation of gene expression and role in the immune system. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1333:F29-50. [PMID: 9294017 DOI: 10.1016/s0304-419x(97)00010-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- R Mostoslavsky
- The Hubert H. Humphrey Center for Experimental Medicine and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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25
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Abstract
This paper will explore emerging concepts related to alternative carcinogenic mechanisms of 'non-mutagenic,' and hence epigenetic, carcinogens that may heritably alter DNA methylation without changing the underlying DNA sequence. In this review, we will touch on the basic concepts of DNA methylation, and will elaborate in greater detail on related topics including chromatin condensation, and heterochromatin spreading that is well known to induce gene silencing by position effect variegation in Drosophila and other species. Data from our model transgenic G12 cell system will be presented to support our hypothesis that certain carcinogens, such as nickel, may be carcinogenic not primarily because of their overt mutability, but rather as the result of their ability to promote DNA hypermethylation of important cancer-related genes. We will conclude with a discussion of the broader relevance of our findings and its application to other so-called 'epigenetic' carcinogens.
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Affiliation(s)
- C B Klein
- Nelson Institute of Environmental Medicine, New York University Medical Center, NY 10016, USA
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26
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Abstract
One of the mechanisms proposed to explain how CpG methylation effects gene repression invokes a DNA methylation-determined chromatin structure. Previous work implied that this DNA modification does not influence nucleosome formation in vitro, thus current models propose that certain non-histone proteins or a preferential affinity by linker histones for methylated DNA may mediate changes in chromatin structure. We have reinvestigated whether CpG methylation alters the chromatin structure of reconstitutes comprising only core histones and DNA. We find that DNA methylation prevents the histone octamer from interacting with an otherwise high affinity positioning sequence in the promoter region of the chicken adult beta-globin gene. This exclusion is attributed to methylation-determined changes in DNA structure within a triplet of CpG dinucleotides. In the affected nucleosome, this sequence motif is located 1.5 helical turns from the dyad axis and is oriented towards the histone core. These findings establish that DNA methylation does have the capacity to modulate chromatin structure directly, at its most fundamental level. Furthermore, our observations strongly suggest that a very limited number of nucleotides can make a decisive contribution to the translational positioning of nucleosomes.
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Affiliation(s)
- C Davey
- Department of Biochemistry, University of Edinburgh, UK
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27
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Abstract
MeCP2 is an abundant mammalian protein that binds to methylated CpG. We have found that native and recombinant MeCP2 repress transcription in vitro from methylated promoters but do not repress nonmethylated promoters. Repression is nonlinearly dependent on the local density of methylation, becoming significant at the density found in bulk vertebrate genomic DNA. Transient transfection using fusions with the GAL4 DNA binding domain identified a region of MeCP2 that is capable of long-range repression in vivo. Moreover, MeCP2 is able to displace histone H1 from preassembled chromatin that contains methyl-CpG. These properties, together with the abundance of MeCP2 and the high frequency of its 2 bp binding site, suggest a role as a global transcriptional repressor in vertebrate genomes.
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Affiliation(s)
- X Nan
- Institute of Cell and Molecular Biology, University of Edinburgh, United Kingdom
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28
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Jost JP, Bruhat A. The formation of DNA methylation patterns and the silencing of genes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 57:217-48. [PMID: 9175435 DOI: 10.1016/s0079-6603(08)60282-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J P Jost
- Friedrich Miescher Institute, Basel, Switzerland
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29
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Abstract
The past few years have seen a wider acceptance of a role for DNA methylation in cancer. This can be attributed to three developments. First, the documentation of the over-representation of mutations at CpG dinucleotides has convincingly implicated DNA methylation in the generation of oncogenic point mutations. The second important advance has been the demonstration of epigenetic silencing of tumor suppressor genes by DNA methylation. The third development has been the utilization of experimental methods to manipulate DNA methylation levels. These studies demonstrate that DNA methylation changes in cancer cells are not mere by-products of malignant transformation, but can play an instrumental role in the cancer process. It seems clear that DNA methylation plays a variety of roles in different cancer types and probably at different stages of oncogenesis. DNA methylation is intricately involved in a wide diversity of cellular processes. Likewise, it appears to exert its influence on the cancer process through a diverse array of mechanisms. It is our task not only to identify these mechanisms, but to determine their relative importance for each stage and type of cancer. Our hope then will be to translate that knowledge into clinical applications.
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Affiliation(s)
- P W Laird
- Department of Surgery, University of Southern California, School of Medicine/Norris Comprehensive Cancer Center, Los Angeles 90033, USA.
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30
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Abstract
A detailed investigation of how nucleosomes are formed and arranged on the DNA sequence is a prerequisite to understanding the molecular mechanisms of DNA-dependent processes such as transcription, replication, DNA repair, and mutagenesis. In this report we analyzed the chromatin structure of exons 5-8 of the p53 gene in human fibroblasts. We mapped at the nucleotide level the positions of DNase I and micrococcal nuclease cleavage sites in permeabilized cells. Areas of clear DNase I protection, which would be indicative of the binding of sequence-specific proteins, were not detected. Instead, the micrococcal nuclease and DNase digestion patterns suggested that this region was covered by nucleosomes and that two areas spanning exons 5 and 6 are occupied preferentially. These nucleosomes could influence DNA damage distribution, repair of certain lesions, and other aspects of the mutagenesis process in p53 sequences.
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Affiliation(s)
- S Tornaletti
- Department of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California 91010, USA
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31
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Godde JS, Kass SU, Hirst MC, Wolffe AP. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J Biol Chem 1996; 271:24325-8. [PMID: 8798682 DOI: 10.1074/jbc.271.40.24325] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Expansion and methylation of CGG repeat sequences is associated with Fragile X syndrome in humans. We have examined the consequences of CGG repeat expansion and methylation for nucleosome assembly and positioning on the Fragile X Mental Retardation gene 1 (FMR1) gene. Short unmethylated CGG repeats are not particularly favored in terms of affinity for the histone octamer or for positioning of the reconstituted nucleosome. However, upon methylation their affinity for the histone octamer increases and a highly positioned nucleosome assembles with the repeat sequences found adjacent to the nucleosomal dyad. Expansion of these CGG repeats abolishes the preferential nucleosome assembly due to methylation. Thus, the expansion and methylation of these triplet repeats can alter the functional organization of chromatin, which may contribute to alterations in the expression of the FMR1 gene and the disease phenotype.
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Affiliation(s)
- J S Godde
- Laboratory of Molecular Embryology, NICHHD, National Institutes of Health, Bethesda, Maryland 20892-5430, USA
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32
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Carotti D, Funiciello S, Lavia P, Caiafa P, Strom R. Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase. Biochemistry 1996; 35:11660-7. [PMID: 8794746 DOI: 10.1021/bi9606051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have characterized the inhibition exerted by histone H1 on the activity of human placenta DNA (cytosine-5-)-methyltransferase. Our experiments demonstrate that the extent of inhibition depends on the DNA base composition, AT-rich substrates being more severely affected than GC-rich substrates and CpG-rich islands. With bacterial SssI methylase, the effect is completely reversed since its activity on AT-rich substrates undergoes a 4-5-fold stimulation upon the addition of H1. Poly(L-lysine) mimicks H1 effects, suggesting an essential role of lysine residues in both the inhibitory and stimulatory effects of H1. By comparison of the different behaviors of the two enzymes, the inhibitory effect over the eukaryotic enzyme might be accounted for by hypothesizing a competition between minor groove-binding motifs (SPKK-like) present in placenta methylase as well as in histone H1.
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Affiliation(s)
- D Carotti
- Department of Biochemical Sciences A. Rossi Fanelli, University of Rome La Sapienza, Italy
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33
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Bruhat A, Jost JP. Phosphorylation/dephosphorylation of the repressor MDBP-2-H1 selectively affects the level of transcription from a methylated promoter in vitro. Nucleic Acids Res 1996; 24:1816-21. [PMID: 8657560 PMCID: PMC145885 DOI: 10.1093/nar/24.10.1816] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have previously shown that in vivo estradiol-dependent dephosphorylation of MDBP-2-H1 (a member of the histone H1 family) correlates with the loss of in vitro preferential binding to methylated DNA. To study the effects of the phosphorylation/dephosphorylation of MDBP-2-H1 on the expression of the avian vitellogenin II gene, we optimised an in vitro transcription system using HeLa nuclear extracts. We show that in the absence of the phosphorylated form of MDBP-2-H1 from rooster, methylation of the vitellogenin II promoter does not affect the transcription. Addition of purified MDBP-2-H1 from rooster to the in vitro transcription system inhibits transcription more efficiently from a methylated than an unmethylated DNA template. Dephosphorylation of rooster MDBP-2-H1 by phosphatase treatment or estradiol treatment of rooster lead to the loss of inhibitory activity of the protein when added to the in vitro transcription assays. These findings indicate that the phosphorylation of MDBP-2-H1 is essential for the repression of the transcription. Taken together these results establish the relationship between the dephosphorylation of MDBP-2-H1 caused by estradiol, the down regulation of its binding activity to methylated DNA and the derepression of vitellogenin II transcription.
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Affiliation(s)
- A Bruhat
- Friedrich Miescher Institute, Basel, Switzerland
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34
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Kato M. Methylation status of Sillago japonica satellite DNA examined by bisulfite modification. Mol Biol Rep 1996; 23:123-7. [PMID: 8983026 DOI: 10.1007/bf00424438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A member of Sillago japonica satellite DNA contained internal subrepeats in its 174 bp unit. S. Japonica genomic DNA isolated from liver tissue was subjected to bisulfite modification, and the DNA sequences of about 40 bp flanked by both subrepeats were amplified by polymerase chain reaction (PCR). This protocol, combination of bisulfite reaction and PCR, converts cytosines in the genomic DNA to thymines in the amplified DNA, whereas 5-methylcytosines in the genomic DNA remain as cytosines. Sequence analysis of the amplified DNA fragments revealed that most of the cytosine residues at CpG were methylated in this region.
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Affiliation(s)
- M Kato
- Laboratory of Molecular Biology, College of Integrated Arts and Sciences, Osaka Prefecture University, Sakai, Japan
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