401
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Utley RT, Lacoste N, Jobin-Robitaille O, Allard S, Côté J. Regulation of NuA4 histone acetyltransferase activity in transcription and DNA repair by phosphorylation of histone H4. Mol Cell Biol 2005; 25:8179-90. [PMID: 16135807 PMCID: PMC1234332 DOI: 10.1128/mcb.25.18.8179-8190.2005] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The NuA4 complex is a histone H4/H2A acetyltransferase involved in transcription and DNA repair. While histone acetylation is important in many processes, it has become increasingly clear that additional histone modifications also play a crucial interrelated role. To understand how NuA4 action is regulated, we tested various H4 tail peptides harboring known modifications in HAT assays. While dimethylation at arginine 3 (R3M) had little effect on NuA4 activity, phosphorylation of serine 1 (S1P) strongly decreased the ability of the complex to acetylate H4 peptides. However, R3M in combination with S1P alleviates the repression of NuA4 activity. Chromatin from cells treated with DNA damage-inducing agents shows an increase in phosphorylation of serine 1 and a concomitant decrease in H4 acetylation. We found that casein kinase 2 phosphorylates histone H4 and associates with the Rpd3 deacetylase complex, demonstrating a physical connection between phosphorylation of serine 1 and unacetylated H4 tails. Chromatin immunoprecipitation experiments also link local phosphorylation of H4 with its deacetylation, during both transcription and DNA repair. Time course chromatin immunoprecipitation data support a model in which histone H4 phosphorylation occurs after NuA4 action during double-strand break repair at the step of chromatin restoration and deacetylation. These findings demonstrate that H4 phospho-serine 1 regulates chromatin acetylation by the NuA4 complex and that this process is important for normal gene expression and DNA repair.
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Affiliation(s)
- Rhea T Utley
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), 9 McMahon Street, Quebec City, QC, Canada G1R 2J6
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402
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Kwon Y, Smerdon MJ. DNA repair in a protein-DNA complex: searching for the key to get in. Mutat Res 2005; 577:118-30. [PMID: 15913668 DOI: 10.1016/j.mrfmmm.2005.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 02/12/2005] [Accepted: 02/12/2005] [Indexed: 11/20/2022]
Abstract
An obstacle encountered by nucleotide excision repair (NER) proteins during repair of the genome is the masking of bulky lesions by DNA binding proteins. For example, certain transcription factors are known to be impediments, and suppress damage removal at their recognition sequences. We have used well-defined protein-DNA complexes to study the molecular mechanism(s) used by repair proteins in gaining access to DNA lesions in chromatin. Using transcription factor IIIA (TFIIIA) and the 5S ribosomal RNA gene (5S rDNA), we previously measured position-dependent effects of cyclobutane pyrimidine dimers (CPDs) at five different sites within the internal control region (ICR) on complex formation [Y. Kwon, M.J. Smerdon, Binding of zinc finger protein transcription factor IIIA to its cognate DNA sequence with single UV photoproducts at specific sites and its effect on DNA repair, J. Biol. Chem. 278 (2003) 45451-45459]. We found that CPDs at two of these sites enhance the TFIIIA-rDNA dissociation rate, which correlates with enhanced repair at these two sites. Here, we used a novel approach to directly compare dissociation of randomly damaged rDNA with NER. We refined the relationship between dissociation and repair of the complex by examining all CPD sites in the transcribed strand. A 214 bp 5S rDNA fragment was irradiated with UV light to produce CPDs at dipyrimidine sites and approximately 1 CPD per fragment. Positions of CPDs that alter binding of TFIIIA were determined by T4 endonuclease V mapping of TFIIIA-bound and unbound fractions of UV-irradiated DNA. As expected, the results reveal that dissociation of TFIIIA from the complex is significantly enhanced by CPDs within the ICR. Moreover, the levels of dissociation induced by CPDs were quantitatively compared with their repair efficiency, and indicate that repair rates of most CPDs in the complex closely correlate with the dissociation rates. In addition, changes in dissociation rate are similar to changes in CPD frequency induced by TFIIIA binding. These findings indicate that structural compatibility of a DNA lesion within a protein-DNA complex can determine both lesion frequency and repair efficiency.
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Affiliation(s)
- Youngho Kwon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
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403
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Wang Y, Wysocka J, Perlin JR, Leonelli L, Allis CD, Coonrod SA. Linking covalent histone modifications to epigenetics: the rigidity and plasticity of the marks. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2005; 69:161-9. [PMID: 16117646 DOI: 10.1101/sqb.2004.69.161] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Y Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York 10021, USA
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404
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Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, Hunt DF, Funabiki H, Allis CD. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 2005; 438:1116-22. [PMID: 16222246 DOI: 10.1038/nature04219] [Citation(s) in RCA: 705] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 09/16/2005] [Indexed: 01/01/2023]
Abstract
Tri-methylation of histone H3 lysine 9 is important for recruiting heterochromatin protein 1 (HP1) to discrete regions of the genome, thereby regulating gene expression, chromatin packaging and heterochromatin formation. Here we show that HP1alpha, -beta, and -gamma are released from chromatin during the M phase of the cell cycle, even though tri-methylation levels of histone H3 lysine 9 remain unchanged. However, the additional, transient modification of histone H3 by phosphorylation of serine 10 next to the more stable methyl-lysine 9 mark is sufficient to eject HP1 proteins from their binding sites. Inhibition or depletion of the mitotic kinase Aurora B, which phosphorylates serine 10 on histone H3, causes retention of HP1 proteins on mitotic chromosomes, suggesting that H3 serine 10 phosphorylation is necessary for the dissociation of HP1 from chromatin in M phase. These findings establish a regulatory mechanism of protein-protein interactions, through a combinatorial readout of two adjacent post-translational modifications: a stable methylation and a dynamic phosphorylation mark.
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Affiliation(s)
- Wolfgang Fischle
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA.
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405
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Slany RK. Chromatin control of gene expression: mixed-lineage leukemia methyltransferase SETs the stage for transcription. Proc Natl Acad Sci U S A 2005; 102:14481-2. [PMID: 16203969 PMCID: PMC1253606 DOI: 10.1073/pnas.0507401102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Robert K Slany
- Department of Genetics, University of Erlangen, Staudtstrasse 5, 91058 Erlangen, Germany.
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406
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Mellor J. The dynamics of chromatin remodeling at promoters. Mol Cell 2005; 19:147-57. [PMID: 16039585 DOI: 10.1016/j.molcel.2005.06.023] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2004] [Revised: 04/01/2005] [Accepted: 06/13/2005] [Indexed: 01/08/2023]
Abstract
The nucleosome, the structural unit of chromatin, is known to play a central role in regulating gene transcription from promoters. The last seven years have spawned a vast amount of data on the enzymes that remodel and modify nucleosomes and the rules governing how transcription factors interact with the epigenetic code on histones. Yet despite this effort, there has yet to emerge a unifying mechanism by which nucleosomes are remodeled during gene regulation. Recent advances have allowed nucleosome dynamics on promoters to be studied in real time, dramatically changing how we think about gene regulation on chromatin templates.
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Affiliation(s)
- Jane Mellor
- Division of Molecular Genetics, Department of Biochemistry, University of Oxford, UK.
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407
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Sjölinder M, Björk P, Söderberg E, Sabri N, Farrants AKO, Visa N. The growing pre-mRNA recruits actin and chromatin-modifying factors to transcriptionally active genes. Genes Dev 2005; 19:1871-84. [PMID: 16103215 PMCID: PMC1186187 DOI: 10.1101/gad.339405] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In the dipteran Chironomus tentans, actin binds to hrp65, a nuclear protein associated with mRNP complexes. Disruption of the actin-hrp65 interaction in vivo by the competing peptide 65-2CTS reduces transcription drastically, which suggests that the actin-hrp65 interaction is required for transcription. We show that the inhibitory effect of the 65-2CTS peptide on transcription is counteracted by trichostatin A, a drug that inhibits histone deacetylation. We also show that actin and hrp65 are associated in vivo with p2D10, an evolutionarily conserved protein with histone acetyltransferase activity that acts on histone H3. p2D10 is recruited to class II genes in a transcription-dependent manner. We show, using the Balbiani ring genes of C. tentans as a model system, that p2D10 is cotranscriptionally associated with the growing pre-mRNA. We also show that experimental disruption of the actin-hrp65 interaction by the 65-2CTS peptide in vivo results in the release of p2D10 from the transcribed genes, reduced histone H3 acetylation, and a lower level of transcription activity. Furthermore, antibodies against p2D10 inhibit run-on elongation. Our results suggest that actin, hrp65, and p2D10 are parts of a positive feedback mechanism that contributes to maintaining the active transcription state of a gene by recruiting HATs at the RNA level.
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Affiliation(s)
- Mikael Sjölinder
- Department of Molecular Biology and Functional Genomics, The Wenner-Gren Institute, Stockholm University, Sweden
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408
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Gresh L, Bourachot B, Reimann A, Guigas B, Fiette L, Garbay S, Muchardt C, Hue L, Pontoglio M, Yaniv M, Klochendler-Yeivin A. The SWI/SNF chromatin-remodeling complex subunit SNF5 is essential for hepatocyte differentiation. EMBO J 2005; 24:3313-24. [PMID: 16138077 PMCID: PMC1224692 DOI: 10.1038/sj.emboj.7600802] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Accepted: 08/05/2005] [Indexed: 12/26/2022] Open
Abstract
Regulation of gene expression underlies cell differentiation and organogenesis. Both transcription factors and chromatin modifiers are crucial for this process. To study the role of the ATP-dependent SWI/SNF chromatin-remodeling complex in cell differentiation, we inactivated the gene encoding the core complex subunit SNF5/INI1 in the developing liver. Hepatic SNF5 deletion caused neonatal death due to severe hypoglycemia; mutant animals fail to store glycogen and have impaired energetic metabolism. The formation of a hepatic epithelium is also affected in SNF5-deficient livers. Transcriptome analyses showed that SNF5 inactivation is accompanied by defective transcriptional activation of 70% of the genes that are normally upregulated during liver development. These include genes involved in glycogen synthesis, gluconeogenesis and cell-cell adhesion. A fraction of hepatic developmentally activated genes were normally expressed, suggesting that cell differentiation was not completely blocked. Moreover, SNF5-deleted cells showed increased proliferation and we identified several misexpressed genes that may contribute to cell cycle deregulation in these cells. Our results emphasize the role of chromatin remodeling in the activation of cell-type-specific genetic programs and driving cell differentiation.
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Affiliation(s)
- Lionel Gresh
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Brigitte Bourachot
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Andreas Reimann
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Bruno Guigas
- Hormone and Metabolic Research Unit, Christian de Duve Institute of Cellular Pathology, UCL, Brussels, Belgium
| | - Laurence Fiette
- Unité de Recherche et d'Expertise en Histotechnologie et Pathologie, Institut Pasteur, Paris, France
| | - Serge Garbay
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Christian Muchardt
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Louis Hue
- Hormone and Metabolic Research Unit, Christian de Duve Institute of Cellular Pathology, UCL, Brussels, Belgium
| | - Marco Pontoglio
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Moshe Yaniv
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Département de Biologie du Développement, Institut Pasteur, Paris, France
- Unité Expression Génétique et Maladies—CNRS FRE 2850, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France. Tel.: +33 1 4568 8512; Fax: +33 1 4061 3033; E-mail:
| | - Agnès Klochendler-Yeivin
- Department of Cellular Biochemistry and Human Genetics, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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409
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Dirscherl SS, Henry JJ, Krebs JE. Neural and eye-specific defects associated with loss of the imitation switch (ISWI) chromatin remodeler in Xenopus laevis. Mech Dev 2005; 122:1157-70. [PMID: 16169710 DOI: 10.1016/j.mod.2005.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 08/05/2005] [Accepted: 08/05/2005] [Indexed: 12/28/2022]
Abstract
Imitation Switch (ISWI) is a member of the SWI2/SNF2 superfamily of ATP-dependent chromatin remodelers, which regulate transcription and maintain chromatin structure by mobilizing nucleosomes using the energy of ATP. Four distinct ISWI complexes have been identified in Xenopus oocytes. The developmental role of Xenopus ISWI, however, has not previously been investigated in vivo. Here we report the tissue specificity, developmental expression, and requirement of ISWI for development of Xenopus embryos. Whole mount in situ hybridization shows ISWI localized in the lateral sides of the neural plate, brain, eye, and in later stages, the spinal cord. Injection of antisense ISWI RNA, morpholino oligonucleotides or dominant-negative ISWI mutant mRNA into fertilized eggs inhibits gastrulation and neural fold closure. Genes involved in neural patterning and development, such as BMP4 and Sonic hedgehog (Shh), are misregulated in the absence of functional ISWI, and ISWI binds to the BMP4 gene in vivo. Developmental and transcriptional defects caused by dominant-negative ISWI are rescued by co-injection of wild-type ISWI mRNA. Inhibition of ISWI function results in aberrant eye development and the formation of cataracts. These data suggest a critical role for ISWI chromatin remodeling complexes in neural development, including eye differentiation, in the Xenopus laevis embryo.
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Affiliation(s)
- Sara S Dirscherl
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage Alaska 99508, USA
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410
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Hanawa H, Persons DA, Nienhuis AW. Mobilization and mechanism of transcription of integrated self-inactivating lentiviral vectors. J Virol 2005; 79:8410-21. [PMID: 15956585 PMCID: PMC1143763 DOI: 10.1128/jvi.79.13.8410-8421.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Permanent genetic modification of replicating primitive hematopoietic cells by an integrated vector has many potential therapeutic applications. Both oncoretroviral and lentiviral vectors have a predilection for integration into transcriptionally active genes, creating the potential for promoter activation or gene disruption. The use of self-inactivating (SIN) vectors in which a deletion of the enhancer and promoter sequences from the 3' long terminal repeat (LTR) is copied over into the 5' LTR during vector integration is designed to improve safety by reducing the risk of mobilization of the vector genome and the influence of the LTR on nearby cellular promoters. Our results indicate that SIN vectors are mobilized in cells expressing lentiviral proteins, with the frequency of mobilization influenced by features of the vector design. The mechanism of transcription of integrated vector genomes was evaluated using a promoter trap design with a vector encoding tat but lacking an upstream promoter in a cell line in which drug resistance depended on tat expression. In six clones studied, all transcripts originated from cryptic promoters either upstream or within the vector genome. We estimate that approximately 1 in 3,000 integrated vector genomes is transcribed, leading to the inference that activation of cryptic promoters must depend on local features of chromatin structure and the constellation of nearby regulatory elements as well as the nature of the regulatory elements within the vector.
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Affiliation(s)
- Hideki Hanawa
- Division of Experimental Hematology, Department of Hematology/Oncology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Mail Stop #272, Memphis, Tennessee 38105, USA
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411
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Sirover MA. New nuclear functions of the glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase, in mammalian cells. J Cell Biochem 2005; 95:45-52. [PMID: 15770658 DOI: 10.1002/jcb.20399] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent studies establish that the glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), is not simply a classical metabolic protein involved in energy production. Instead, it is a multifunctional protein with defined functions in numerous subcellular processes. New investigations establish a primary role for GAPDH in a variety of critical nuclear pathways apart from its already recognized role in apoptosis. These new roles include its requirement for transcriptional control of histone gene expression, its essential function in nuclear membrane fusion, its necessity for the recognition of fraudulently incorporated nucleotides in DNA, and its mandatory participation in the maintenance of telomere structure. Each of these new functions requires GAPDH association into a series of multienzyme complexes. Although other proteins in those complexes are variable, GAPDH remains the single constant protein in each structure. To undertake these new functions, GAPDH is recruited to the nucleus in S phase or its intracellular distribution is regulated as a function of drug exposure. Other investigations relate a substantial role for nuclear GAPDH in hyperglycemic stress and the development of metabolic syndrome. Considerations of future directions as well as the role of GAPDH post-translational modification as a basis for its multifunctional activities is suggested.
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Affiliation(s)
- Michael A Sirover
- Department of Pharmacology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA.
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412
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Abstract
Mammalian cells harbor numerous small non-protein-coding RNAs, including small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs) and small double-stranded RNAs, which regulate gene expression at many levels including chromatin architecture, RNA editing, RNA stability, translation, and quite possibly transcription and splicing. These RNAs are processed by multistep pathways from the introns and exons of longer primary transcripts, including protein-coding transcripts. Most show distinctive temporal- and tissue-specific expression patterns in different tissues, including embryonal stem cells and the brain, and some are imprinted. Small RNAs control a wide range of developmental and physiological pathways in animals, including hematopoietic differentiation, adipocyte differentiation and insulin secretion in mammals, and have been shown to be perturbed in cancer and other diseases. The extent of transcription of non-coding sequences and the abundance of small RNAs suggests the existence of an extensive regulatory network on the basis of RNA signaling which may underpin the development and much of the phenotypic variation in mammals and other complex organisms and which may have different genetic signatures from sequences encoding proteins.
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Affiliation(s)
- John S Mattick
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.
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413
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Cheng X, Collins RE, Zhang X. Structural and sequence motifs of protein (histone) methylation enzymes. ACTA ACUST UNITED AC 2005; 34:267-94. [PMID: 15869391 PMCID: PMC2733851 DOI: 10.1146/annurev.biophys.34.040204.144452] [Citation(s) in RCA: 257] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
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Affiliation(s)
- Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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414
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Wilson CB, Makar KW, Shnyreva M, Fitzpatrick DR. DNA methylation and the expanding epigenetics of T cell lineage commitment. Semin Immunol 2005; 17:105-19. [PMID: 15737572 DOI: 10.1016/j.smim.2005.01.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During their development from progenitors, lymphocytes make a series of cell fate decisions. These decisions reflect and require changes in overall programs of gene expression. To maintain cellular identity, programs of gene expression must be iterated through mitosis in a heritable manner by epigenetic processes, which include DNA methylation, methyl-CpG-binding proteins, histone modifications, transcription factors and higher order chromatin structure. Current evidence is consistent with the notion that DNA methylation acts in concert with other epigenetic processes to limit the probability of aberrant gene expression and to stabilize, rather than to initiate, cell fate decisions. In particular, DNA methylation appears to be a non-redundant repressor of CD8 expression in TCR-gammadelta T cells and Th2 cytokine expression in Th1 and CD8 T cells, and is required to enforce clonally restricted Ly49 and KIR gene expression in NK cells. However, most of our knowledge is derived from in vitro studies, and the importance of DNA methylation in memory cell lineage fidelity in vivo remains to be shown convincingly.
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415
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Wang L, Kametani Y, Katano I, Habu S. T-cell specific enhancement of histone H3 acetylation in 5' flanking region of the IL-2 gene. Biochem Biophys Res Commun 2005; 331:589-94. [PMID: 15850801 DOI: 10.1016/j.bbrc.2005.03.216] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2005] [Indexed: 12/21/2022]
Abstract
The IL-2 gene expression is highly T-cell specific in an activation-dependent manner. However, little is known about how T-cell specific expression is regulated, although related transcription factors have been identified. To address this issue, we examined the chromatin structure change of the IL-2 gene by analyzing histone acetylation status in the upstream of IL-2 gene transcription initiation site. Interestingly, the histone acetylation level was found to be higher in various sites on the widespread upstream region in resting T-cells than resting B-cells. After T-cell stimulation with PMA and ionomycin, the same regions were further acetylated on histone H3. Particularly, the distal enhancer region showed prompt enhancement of histone acetylation, followed by the IL-2 mRNA expression. These results suggest that the 5' flanking region including the distal enhancer region of the IL-2 gene is already accessible in T cells with constitutive acetylation of histone H3,which may serve for T-cell specific IL-2 expression.
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Affiliation(s)
- Lili Wang
- Department of Immunology, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan
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416
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Gordon F, Luger K, Hansen JC. The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays. J Biol Chem 2005; 280:33701-6. [PMID: 16033758 DOI: 10.1074/jbc.m507048200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Salt-dependent oligomerization of nucleosomal arrays is related to fiber-fiber interactions and global chromosome structure. Previous studies have shown that the H2A/H2B and H3/H4 N-terminal domain (NTD) pairs are able to mediate array oligomerization. However, because of technical barriers, the function(s) of the individual core histone NTDs have not been investigated. To address this question, all possible combinations of "tailless" nucleosomal arrays were assembled from native and NTD-deleted recombinant Xenopus core histones and tandemly repeated 5 S rDNA. The recombinant arrays were characterized by differential centrifugation over the range of 0-50 mm MgCl2 to determine how each NTD affects salt-dependent oligomerization. Results indicate that all core histone NTDs participate in the oligomerization process and that the NTDs function additively and independently. These observations provide direct biochemical evidence linking all four core histone NTDs to the assembly and maintenance of global chromatin structures.
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Affiliation(s)
- Faye Gordon
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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417
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Kwaks THJ, Sewalt RGAB, van Blokland R, Siersma TJ, Kasiem M, Kelder A, Otte AP. Targeting of a histone acetyltransferase domain to a promoter enhances protein expression levels in mammalian cells. J Biotechnol 2005; 115:35-46. [PMID: 15607223 DOI: 10.1016/j.jbiotec.2004.07.012] [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] [Received: 05/03/2004] [Revised: 07/19/2004] [Accepted: 07/30/2004] [Indexed: 01/07/2023]
Abstract
Silencing of transfected genes in mammalian cells is a fundamental problem that probably involves the (in)accessibility status of chromatin. A potential solution to this problem is to provide a cell with protein factors that make the chromatin of a promoter more open or accessible for transcription. We tested this by targeting such proteins to different promoters. We found that targeting the p300 histone acetyltransferase (HAT) domain to strong viral or cellular promoters is sufficient to result in higher expression levels of a reporter protein. In contrast, targeting the chromatin-remodeling factor Brahma does not result in stable, higher protein expression levels. The long-term effects of the targeted p300HAT domain on protein expression levels are positively reinforced, when also anti-repressor elements are applied to flank the reporter construct. These elements were previously shown to be potent blockers of chromatin-associated repressors. The simultaneous application of the targeted p300HAT domain and anti-repressor elements conveys long-term stability to protein expression. Whereas no copy number dependency is achieved by targeting of the p300HAT domain alone, copy number dependency is improved when anti-repressor elements are included. We conclude that targeting of protein domains such as HAT domains helps to facilitate expression of transfected genes in mammalian cells. However, the simultaneous application of other genomic elements such as the anti-repressor elements prevents silencing more efficiently.
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Affiliation(s)
- T H J Kwaks
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 406, 1098 SM Amsterdam, The Netherlands
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418
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Koyanagi M, Baguet A, Martens J, Margueron R, Jenuwein T, Bix M. EZH2 and histone 3 trimethyl lysine 27 associated with Il4 and Il13 gene silencing in Th1 cells. J Biol Chem 2005; 280:31470-7. [PMID: 16009709 DOI: 10.1074/jbc.m504766200] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Differentiation of naïve CD4 T cells toward the T helper 1 (T(H)1) and T helper 2 (T(H)2) fates involves the transcriptional repression and enhancement, respectively, of Il4 and Il13, adjacent chromosome 11 genes encoding the canonical T(H)2 cytokines interleukin-4 and interleukin-13. Proper execution of this developmental fate choice during immune responses is critical to host defense and, when misregulated, leads to susceptibility to infectious microbes and to allergic and autoimmune diseases. Here, using chromatin immunoprecipitation and real time reverse transcription PCR we identify the Polycomb family histone methyltransferase EZH2 as the enzyme responsible for methylating lysine 27 of histone H3 at the Il4-Il13 locus of T(H)1 but not T(H)2 cells, implicating EZH2 in the mechanism of Il4 and Il13 transcriptional silencing.
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Affiliation(s)
- Madoka Koyanagi
- Department of Immunology, University of Washington, Seattle, Washington 98195-7650, USA
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419
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Tongaonkar P, French SL, Oakes ML, Vu L, Schneider DA, Beyer AL, Nomura M. Histones are required for transcription of yeast rRNA genes by RNA polymerase I. Proc Natl Acad Sci U S A 2005; 102:10129-34. [PMID: 16002464 PMCID: PMC1177414 DOI: 10.1073/pnas.0504563102] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleosomes and their histone components have generally been recognized to act negatively on transcription. However, purified upstream activating factor (UAF), a transcription initiation factor required for RNA polymerase (Pol) I transcription in Saccharomyces cerevisiae, contains histones H3 and H4 and four nonhistone protein subunits. Other studies have shown that histones H3 and H4 are associated with actively transcribed rRNA genes. To examine their functional role in Pol I transcription, we constructed yeast strains in which synthesis of H3 is achieved from the glucose-repressible GAL10 promoter. We found that partial depletion of H3 (approximately 50% depletion) resulted in a strong inhibition (>80%) of Pol I transcription. A combination of biochemical analysis and electron microscopic (EM) analysis of Miller chromatin spreads indicated that initiation and elongation steps and rRNA processing were compromised upon histone depletion. A clear decrease in relative amounts of UAF, presumably caused by reduced stability, was also observed under the conditions of H3 depletion. Therefore, the observed inhibition of initiation can be explained, in part, by the decrease in UAF concentration. In addition, the EM results suggested that the defects in rRNA transcript elongation and processing may be a result of loss of histones from rRNA genes rather than (or in addition to) an indirect consequence of effects of histone depletion on expression of other genes. Thus, these results show functional importance of histones associated with actively transcribed rRNA genes.
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Affiliation(s)
- Prasad Tongaonkar
- Department of Biological Chemistry, University of California, Irvine, CA 92697-1700, USA
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420
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Bali P, Pranpat M, Bradner J, Balasis M, Fiskus W, Guo F, Rocha K, Kumaraswamy S, Boyapalle S, Atadja P, Seto E, Bhalla K. Inhibition of histone deacetylase 6 acetylates and disrupts the chaperone function of heat shock protein 90: a novel basis for antileukemia activity of histone deacetylase inhibitors. J Biol Chem 2005; 280:26729-34. [PMID: 15937340 DOI: 10.1074/jbc.c500186200] [Citation(s) in RCA: 613] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydroxamic acid (HAA) analogue pan-histone deacetylase (HDAC) inhibitors (HDIs) LAQ824 and LBH589 have been shown to induce acetylation and inhibit the ATP binding and chaperone function of heat shock protein (HSP) 90. This promotes the polyubiquitylation and degradation of the pro-growth and pro-survival client proteins Bcr-Abl, mutant FLT-3, c-Raf, and AKT in human leukemia cells. HDAC6 is a member of the class IIB HDACs. It is predominantly cytosolic, microtubule-associated alpha-tubulin deacetylase that is also known to promote aggresome inclusion of the misfolded polyubiquitylated proteins. Here we demonstrate that in the Bcr-abl oncogene expressing human leukemia K562 cells, HDAC6 can be co-immunoprecipitated with HSP90, and the knock-down of HDAC6 by its siRNA induced the acetylation of HSP90 and alpha-tubulin. Depletion of HDAC6 levels also inhibited the binding of HSP90 to ATP, reduced the chaperone association of HSP90 with its client proteins, e.g. Bcr-Abl, and induced polyubiquitylation and partial depletion of Bcr-Abl. Conversely, the ectopic overexpression of HDAC6 inhibited LAQ824-induced acetylation of HSP90 and alpha-tubulin and reduced LAQ824-mediated depletion of Bcr-Abl, AKT, and c-Raf. Collectively, these findings indicate that HDAC6 is also an HSP90 deacetylase. Targeted inhibition of HDAC6 leads to acetylation of HSP90 and disruption of its chaperone function, resulting in polyubiquitylation and depletion of pro-growth and pro-survival HSP90 client proteins including Bcr-Abl. Depletion of HDAC6 sensitized human leukemia cells to HAA-HDIs and proteasome inhibitors.
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Affiliation(s)
- Purva Bali
- Department of Interdisciplinary Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida 33612, USA
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421
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Sun J, Zhang Q, Schlick T. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc Natl Acad Sci U S A 2005; 102:8180-5. [PMID: 15919827 PMCID: PMC1140479 DOI: 10.1073/pnas.0408867102] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.
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Affiliation(s)
- Jian Sun
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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422
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Ganapathi M, Srivastava P, Sutar SKD, Kumar K, Dasgupta D, Pal Singh G, Brahmachari V, Brahmachari SK. Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. BMC Bioinformatics 2005; 6:126. [PMID: 15918906 PMCID: PMC1173084 DOI: 10.1186/1471-2105-6-126] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Accepted: 05/26/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group. RESULTS In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes. CONCLUSION The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome.
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Affiliation(s)
- Mythily Ganapathi
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi -110007, India
| | - Pragya Srivastava
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi -110007, India
| | | | - Kaushal Kumar
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi -110007, India
| | - Dipayan Dasgupta
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi -110007, India
| | - Gajinder Pal Singh
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi -110007, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Samir K Brahmachari
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi -110007, India
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423
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Biel M, Wascholowski V, Giannis A. Epigenetik - ein Epizentrum der Genregulation: Histone und histonmodifizierende Enzyme. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461346] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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424
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Bhalla KN. Epigenetic and chromatin modifiers as targeted therapy of hematologic malignancies. J Clin Oncol 2005; 23:3971-93. [PMID: 15897549 DOI: 10.1200/jco.2005.16.600] [Citation(s) in RCA: 259] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetic regulation of gene expression is mediated through alterations in the DNA methylation status, covalent modifications of core nucleosomal histones, rearrangement of histones, and by RNA interference. It is now abundantly clear that deregulation of epigenetic mechanisms cooperates with genetic alterations in the development and progression of cancer and leukemia. Epigenetic deregulation affects several aspects of tumor cell biology, including cell growth, cell cycle control, differentiation, DNA repair, and cell death. This raises the strong possibility that reversing deregulated epigenetic mechanisms may be an effective treatment strategy for leukemia and cancer. This treatment strategy may either be designed to separately or collectively target the specific perturbations in the epigenetic mechanisms found in human hematologic malignancies. The following review describes our current understanding of the important deregulated epigenetic mechanisms and the preclinical and clinical development of epigenetic and chromatin modifiers in the therapy of these disorders.
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Affiliation(s)
- Kapil N Bhalla
- Department of Interdisciplinary Oncology, H. Lee Moffitt Cancer Center and Research Institute University of South Florida, Tampa, FL 33612, USA.
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425
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Beard BC, Stevenson JJ, Wilson SH, Smerdon MJ. Base excision repair in nucleosomes lacking histone tails. DNA Repair (Amst) 2005; 4:203-9. [PMID: 15590328 DOI: 10.1016/j.dnarep.2004.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2004] [Accepted: 09/18/2004] [Indexed: 10/26/2022]
Abstract
Recently, we developed an in vitro system using human uracil DNA glycosylase (UDG), AP endonuclease (APE), DNA polymerase beta (pol beta) and rotationally positioned DNA containing a single uracil associated with a 'designed' nucleosome, to test short-patch base excision repair (BER) in chromatin. We found that UDG and APE carry out their catalytic activities with reduced efficiency on nucleosome substrates, showing a distinction between uracil facing 'out' or 'in' from the histone surface, while DNA polymerase beta (pol beta) is completely inhibited by nucleosome formation. In this report, we tested the inhibition of BER enzymes by the N-terminal 'tails' of core histones that take part in both inter- and intra-nucleosome interactions, and contain sites of post-translational modifications. Histone tails were removed by limited trypsin digestion of 'donor' nucleosome core particles and histone octamers were exchanged onto a nucleosome-positioning DNA sequence containing a single G:U mismatch. The data indicate that UDG and APE activities are not significantly enhanced with tailless nucleosomes, and the distinction between rotational settings of uracil on the histone surface is unaffected. More importantly, the inhibition of pol beta activity is not relieved by removal of the histone tails, even though these tails interact with DNA in the G:U mismatch region. Finally, inclusion of X-ray cross complement group protein 1 (XRCC1) or Werner syndrome protein (WRN) had no effect on the BER reactions. Thus, additional activities may be required in cells for efficient BER of at least some structural domains in chromatin.
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Affiliation(s)
- Brian C Beard
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
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426
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Davies E, Teng KS, Conlan RS, Wilks SP. Ultra-high resolution imaging of DNA and nucleosomes using non-contact atomic force microscopy. FEBS Lett 2005; 579:1702-6. [PMID: 15757664 DOI: 10.1016/j.febslet.2005.02.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 02/02/2005] [Accepted: 02/02/2005] [Indexed: 10/25/2022]
Abstract
Visualisation of nano-scale biomolecules aids understanding and development in molecular biology and nanotechnology. Detailed structure of nucleosomes adsorbed to mica has been captured in the absence of chemical-anchoring techniques, demonstrating the usefulness of non-contact atomic force microscopy (NC-AFM) for ultra-high resolution biomolecular imaging. NC-AFM offers significant advantages in terms of resolution, speed and ease of sample preparation when compared to techniques such as cryo-electron microscopy and X-ray crystallography. In the absence of chemical modification, detailed structure of DNA deposited on a gold substrate was observed for the first time using NC-AFM, opening up possibilities for investigating the electrical properties of unmodified DNA.
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Affiliation(s)
- Emma Davies
- Multidisciplinary Nanotechnology Centre, School of Engineering, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK.
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427
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Jaeger S, Barends S, Giegé R, Eriani G, Martin F. Expression of metazoan replication-dependent histone genes. Biochimie 2005; 87:827-34. [PMID: 16164992 DOI: 10.1016/j.biochi.2005.03.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Revised: 02/24/2005] [Accepted: 03/18/2005] [Indexed: 11/18/2022]
Abstract
Histone proteins are essential components of eukaryotic chromosomes. In metazoans, they are produced from the so-called replication-dependent histone genes. The biogenesis of histones is tightly coupled to DNA replication in a stoichiometric manner because an excess of histones is highly toxic for the cell. Therefore, a strict cell cycle-regulation of critical factors required for histone expression ensures exclusive S-phase expression. This review focuses on the molecular mechanisms responsible for such a fine expression regulation. Among these, a large part will be dedicated to post-transcriptional events occurring on histone mRNA, like histone mRNA 3' end processing, nucleo-cytoplasmic mRNA export, translation and mRNA degradation. Many factors are involved, including an RNA-binding protein called HBP, also called SLBP (for hairpin- or stem-loop-binding protein) that binds to a conserved hairpin located in the 3' UTR part of histone mRNA. HBP plays a pivotal role in the expression of histone genes since it is necessary for most of the steps of histone mRNA metabolism in the cell. Moreover, the strict S-phase expression pattern of histones is achieved through a fine cell cycle-regulation of HBP. A large part of the discussion will be centered on the critical role of HBP in histone biogenesis.
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Affiliation(s)
- Sophie Jaeger
- Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15, rue René Descartes, 67084 Strasbourg cedex, France
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428
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Zabaronick SR, Tyler JK. The histone chaperone anti-silencing function 1 is a global regulator of transcription independent of passage through S phase. Mol Cell Biol 2005; 25:652-60. [PMID: 15632066 PMCID: PMC543432 DOI: 10.1128/mcb.25.2.652-660.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the function of the histone H3/H4 chaperones anti-silencing function 1 (Asf1p) and chromatin assembly factor 1 (CAF-1) in global transcriptional regulation in budding yeast. Deletion of ASF1 or CAF-1 components led to global transcriptional misregulation, both activation and repression, of genes scattered throughout the 16 yeast chromosomes. To investigate direct effects on gene regulation, we developed an approach to destabilize Asf1p that results in its rapid degradation within minutes of transcriptional repression. Upon degradation of Asf1p, rapid global changes in gene expression occur without the requirement for passage through S phase or de novo protein synthesis. In particular, we demonstrate that the previously reported influence of Asf1p on histone gene expression is not a direct effect of loss of Asf1p. These data indicate that the histone chaperones CAF-1 and Asf1p regulate the gene expression of a broad array of genes in yeast and, in the case of Asf1p, this is likely to be due to a direct role in chromatin modulation during transcriptional regulation.
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Affiliation(s)
- Susan R Zabaronick
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 East 17th Ave., Aurora, CO 80010, USA
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429
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Abstract
Post-translational modification is a major mechanism by which protein function is regulated in eukaryotes. Instead of single-site action, many proteins such as histones, p53, RNA polymerase II, tubulin, Cdc25C and tyrosine kinases are modified at multiple sites by modifications like phosphorylation, acetylation, methylation, ubiquitination, sumoylation and citrullination. Multisite modification on a protein constitutes a complex regulatory program that resembles a dynamic 'molecular barcode' and transduces molecular information to and from signaling pathways. This program imparts effects through 'loss-of-function' and 'gain-of-function' mechanisms. Among the latter, covalent modifications specifically recruit a diverse array of modules, including the SH2 domain, 14-3-3, WW domain, Polo box, BRCT repeat, bromodomain, chromodomain, Tudor domain and motifs binding to ubiquitin and other protein modifiers. Such recruitments are often modulated by modifications occurred at neighboring and distant sites. Multisite modification thus coordinates intermolecular and intramolecular signaling for the qualitative and quantitative control of protein function in vivo.
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Affiliation(s)
- Xiang-Jiao Yang
- Molecular Oncology Group, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada H3A 1A1.
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430
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Phinney BS, Thelen JJ. Proteomic Characterization of A Triton-Insoluble Fraction from Chloroplasts Defines A Novel Group of Proteins Associated with Macromolecular Structures. J Proteome Res 2005; 4:497-506. [PMID: 15822927 DOI: 10.1021/pr049791k] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomic analysis of a Triton X-100 insoluble, 30,000 x g pellet from purified pea chloroplasts resulted in the identification of 179 nonredundant proteins. This chloroplast fraction was mostly depleted of chloroplast membranes since only 23% and 9% of the identified proteins were also observed in envelope and thylakoid membranes, respectively. One of the most abundant proteins in this fraction was sulfite reductase, a dual function protein previously shown to act as a plastid DNA condensing protein. Approximately 35 other proteins known (or predicted) to be associated with high-density protein-nucleic acid particles (nucleoids) were also identified including a family of DNA gyrases, as well as proteins involved in plastid transcription and translation. Although nucleoids appeared to be the predominant component of 30k x g Triton-insoluble chloroplast preparations, multi-enzyme protein complexes were also present including each subunit to the pyruvate dehydrogenase and acetyl-CoA carboxylase multi-enzyme complexes, as well as a proposed assembly of the first three enzymes of the Calvin cycle. Approximately 18% of the proteins identified were annonated as unknown or hypothetical proteins and another 20% contained "putative" or "like" in the identifier tag. This is the first proteomic characterization of a membrane-depleted, high-density fraction from plastids and demonstrates the utility of this simple procedure to isolate intact macromolecular structures from purified organelles for analysis of protein-protein and protein-nucleic acid interactions.
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Affiliation(s)
- Brett S Phinney
- Michigan State University, Proteomics and Mass Spectrometry Facility, East Lansing, Michigan 48824, USA
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431
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Hammiche A, German MJ, Hewitt R, Pollock HM, Martin FL. Monitoring cell cycle distributions in MCF-7 cells using near-field photothermal microspectroscopy. Biophys J 2005; 88:3699-706. [PMID: 15722424 PMCID: PMC1305516 DOI: 10.1529/biophysj.104.053926] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microspectroscopic techniques such as Fourier transform infrared (FTIR) have played an important role in "fingerprinting" the biochemical composition of cellular components. Based on structure and function, complex biomolecules absorb energy in the mid-infrared (lambda = 2-20 microm) yielding characteristic vibrational infrared (IR) spectra. However, optical detection FTIR microspectroscopy may not be suitable for IR-absorbing sample materials. Photothermal microspectroscopy (PTMS) permits the direct measurement of heat generated as a result of sample material absorbing radiation. This approach generates true absorption spectra and is implemented by interfacing a scanning probe microscope and an FTIR spectrometer. Detection is performed using a near-field ultra-miniaturized temperature sensor. Employing PTMS, IR spectra of MCF-7 cells were examined in spectral regions (900-2000 cm(-1)) corresponding to proteins, DNA, RNA, glycoproteins, carbohydrates, lipids, and levels of protein phosphorylation. As a cell passes through the cell cycle, its nuclear material decondenses and condenses and this has led to ambiguity as to whether the intensity of such spectral regions may be associated with the G(1)-, S- or G(2)-phases of the cell cycle. Cultured cells were tracked over a time course known to correspond to marked alterations in cell-cycle distributions, as determined using flow cytometry. Experiments were carried out in the absence or presence of lindane, a pesticide known to induce G(1)-arrest in MCF-7 cells. Significant (P < 0.05) elevations in spectral intensities were associated with exponentially growing cell populations, predominantly in S-phase or G(2)-phase, compared to more quiescent populations predominantly in G(1)-phase. Increases in the absorption band at 970 cm(-1), associated with elevated protein phosphorylation, were observed in vibrational spectra of exponentially growing cell populations compared to those exhibiting a slowing in their growth kinetics. These results seem to suggest that intracellular bulk changes, associated with transit through the cell cycle, can be tracked using PTMS.
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Affiliation(s)
- Azzedine Hammiche
- Department of Physics, Institute of Environmental and Natural Sciences, Lancaster University, Lancaster, United Kingdom
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432
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Ranganath RM. Harnessing the developmental potential of nucellar cells: barriers and opportunities. Trends Biotechnol 2005; 22:504-10. [PMID: 15450743 DOI: 10.1016/j.tibtech.2004.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Angiosperm nucellar cells can either use or avoid meiosis in vivo, depending on the developmental context. This unique ability contrasts with the conditions required in vitro, either for a reconstituted oocyte to avoid meiosis and produce clones by somatic cell nuclear transfer (SCNT), or for mammalian stem cells to undergo meiosis and produce synthetic sex cells (gametes). Current biotechnological initiatives to harness the potential of nucellar cells are based on the transfer of apomixis genes to sexual crop plants with the aim of producing clones through seeds. The elusive genetic basis of apomixis compels us to examine whether this process involves epigenetic factors. The elegant and versatile developmental platform available in nucellar cells should be explored as a genome-scale science and compared with mammalian stem cell biology for a holistic understanding of developmental programming and reprogramming in eukaryotes.
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Affiliation(s)
- R M Ranganath
- Cytogenetics and Developmental Biology Laboratory, Department of Botany, Bangalore University, Jnanabharathi Campus, Bangalore 560056, India.
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433
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Role of coactivators in transcriptional activation by the aryl hydrocarbon receptor. Arch Biochem Biophys 2005; 433:379-86. [PMID: 15581594 DOI: 10.1016/j.abb.2004.09.031] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/24/2004] [Indexed: 11/29/2022]
Abstract
The aryl hydrocarbon receptor (AHR) mediates the carcinogenic and other toxic effects of a variety of environmental pollutants, including 2,37,8-tetrachlorodibenzo-p-dioxin (TCDD), and some polycyclic aromatic hydrocarbons (PAHs). In most if not all cases, these deleterious effects depend upon modulation of gene transcription effected by the ligand-bound AHR. The responsive genes required for toxicity of TCDD have yet to be defined. However, induction of Cyp1a1 is known to represent a significant event in the toxicity of PAHs. Furthermore, the Cyp1a1 gene provides a model system for studying the mechanism of gene transcription by AHR. This review discusses the roles of transcriptional coactivator proteins in induction of Cyp1a1 by AHR ligands. Coactivators physically associate with the gene upon induction, and provide a bridge between AHR molecules, located at 5'enhancer elements, and general transcription factors, located at the promoter of the gene. Studies on the endogenous Cyp1a1 gene in its natural chromosomal setting are emphasized. The recent development of several new experimental techniques including the chromatin immunoprecipitation (ChIP) assay, RNA interference, and real-time PCR has provided a major boost to such studies. Future directions for research are also discussed. Since variations in coactivator expression or activity may result in inter-individual differences in response to AHR ligands, and may also underlie tissue-specific differences in sensitivity to such ligands during development, and in adulthood, the role of coactivators in transcriptional activation by AHR constitutes a very important area of research.
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434
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Abstract
Breaking apart chromosomes is not a matter to be taken lightly. The possible negative outcomes are obvious: loss of information, unstable chromosomes, chromosomal translocations, tumorigenesis, or cell death. Utilizing DNA rearrangement to generate the desired diversity in the antigen receptor loci is a risky business, and it must be carefully controlled. In general, the regulation is so precise that the negative consequences are minimal or not apparent. They are visible only when the process of V(D)J recombination goes awry, as for example in some chromosomal translocations associated with lymphoid tumors. Regulation is imposed not only to prevent the generation of random breaks in the DNA, but also to direct rearrangement to the appropriate locus or subregion of a locus in the appropriate cell at the appropriate time. Antigen receptor rearrangement is regulated essentially at four different levels: expression of the RAG1/2 recombinase, intrinsic biochemical properties of the recombinase and the cleavage reaction, the post-cleavage /DNA repair stage of the process, and accessibility of the substrate to the recombinase. Within each of these broad categories, multiple mechanisms are used to achieve the desired aims. The major focus of this review is on accessibility control and the role of chromatin and nuclear architecture in achieving this regulation, although other issues are touched upon.
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MESH Headings
- Alleles
- Chromatin/chemistry
- DNA Repair
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Regulation, Enzymologic
- Gene Rearrangement, B-Lymphocyte
- Gene Rearrangement, T-Lymphocyte
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Histones/chemistry
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Immunoglobulin Heavy Chains/immunology
- Nuclear Proteins
- Nucleosomes/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
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Affiliation(s)
- Marjorie A Oettinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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435
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Abstract
Histones are a major component of chromatin, the protein-DNA complex fundamental to genome packaging, function, and regulation. A fraction of histones are nonallelic variants that have specific expression, localization, and species-distribution patterns. Here we discuss recent progress in understanding how histone variants lead to changes in chromatin structure and dynamics to carry out specific functions. In addition, we review histone variant assembly into chromatin, the structure of the variant chromatin, and post-translational modifications that occur on the variants.
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436
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Aoyagi S, Trotter KW, Archer TK. ATP-dependent chromatin remodeling complexes and their role in nuclear receptor-dependent transcription in vivo. VITAMINS AND HORMONES 2005; 70:281-307. [PMID: 15727808 DOI: 10.1016/s0083-6729(05)70009-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nuclear receptors (NRs) are ligand-dependent transcription factors that mediate transcription of target genes in chromatin. Modulation of chromatin structure plays an important part in the NR-mediated transcription process. ATP-dependent chromatin remodeling complexes have been shown to be intimately involved in NR-mediated transcription. In this review, we examine the role of chromatin remodeling complexes in facilitating the recruitment of coregulators and basal transcription factors. In addition, the role of subunit specificity within the chromatin remodeling complexes, the complexes' influence on remodeling activity, and complexes' recruitment to the NR-responsive promoters are discussed.
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Affiliation(s)
- Sayura Aoyagi
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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437
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Zhong XY, Gebhardt S, Hillermann R, Tofa KC, Holzgreve W, Hahn S. Circulatory nucleosome levels are significantly increased in early and late-onset preeclampsia. Prenat Diagn 2005; 25:700-3. [PMID: 16050002 DOI: 10.1002/pd.1204] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Elevations in circulatory DNA, as measured by real-time PCR, have been observed in pregnancies with manifest preeclampsia. Recent reports have indicated that circulatory nucleosome levels are elevated in the periphery of cancer patients. We have now examined whether circulatory nucleosome levels are similarly elevated in cases with preeclampsia. METHODS Maternal plasma samples were prepared from 17 cases with early onset preeclampsia (<34 weeks gestation) with 14 matched normotensive controls, as well as 15 cases late-onset preeclampsia (>34 weeks gestation) with 10 matched normotensive controls. Levels of circulatory nucleosomes were quantified by commercial ELISA (enzyme-linked immunosorbant assay). RESULTS The level of circulatory nucleosomes was significantly elevated in both study preeclampsia groups, compared to the matched normotensive control group (p = 0.000 and p = 0.001, respectively). CONCLUSIONS Our data suggests that preeclampsia is associated with the elevated presence of circulatory nucleosomes, and that this phenomenon occurs in both early- and late-onset forms of the disorder.
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Affiliation(s)
- Xiao Yan Zhong
- University Women's Hospital/Department of Research, University of Basel, Switzerland
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438
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Happel N, Sommer A, Hänecke K, Albig W, Doenecke D. Topoisomerase inhibitor induced dephosphorylation of H1 and H3 histones as a consequence of cell cycle arrest. J Cell Biochem 2005; 95:1235-47. [PMID: 15962304 DOI: 10.1002/jcb.20494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Posttranslational modifications of histones have an integral function in the structural and functional organization of chromatin. Several changes in the modification state of histones could be observed after induction of apoptosis with topoisomerase inhibitors and other inducers. Most of these studies include the analysis of the state of phosphorylation of histones, and the results are to some extent controversial, depending on cell lines and agents used. In the present study we compared the kinetics of the dephosphorylation of H1 and H3 histones with apoptosis markers after treatment of leukemic cell lines with topoisomerase inhibitors. In parallel, we determined cell cycle parameters in detail. Dephosphorylation of both histone classes started within 1 h of induction, and no direct correlation with timing and intensity of the investigated apoptotic features could be observed. In contrast, we show that the effect of topoisomerase inhibitors on the state of H1 and H3 phosphorylation is not directly related to apoptosis, but reflects the changes in the cell cycle distribution of cells treated with these inducers.
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Affiliation(s)
- Nicole Happel
- Institute for Biochemistry and Molecular Cell Biology, University of Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
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439
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Abstract
In development, cells pass on established gene expression patterns to daughter cells over multiple rounds of cell division. The cellular memory of the gene expression state is termed maintenance, and the proteins required for this process are termed maintenance proteins. The best characterized are proteins of the Polycomb and trithorax Groups that are required for silencing and maintenance of activation of target loci, respectively. These proteins act through DNA elements termed maintenance elements. Here, we re-examine the genetics and molecular biology of maintenance proteins. We discuss molecular models for the maintenance of activation and silencing, and the establishment of epigenetic marks, and suggest that maintenance proteins may play a role in propagating the mark through DNA synthesis.
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Affiliation(s)
- Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
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440
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Abstract
A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases. Integration of datasets and improved technologies will provide the way forward.
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Affiliation(s)
- Fred van Leeuwen
- Netherlands Cancer Institute, Plesmanlaan 121,1066 CX Amsterdam, The Netherlands
| | - Bas van Steensel
- Netherlands Cancer Institute, Plesmanlaan 121,1066 CX Amsterdam, The Netherlands
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441
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Bottardi S, Bourgoin V, Pierre-Charles N, Milot E. Onset and inheritance of abnormal epigenetic regulation in hematopoietic cells. Hum Mol Genet 2004; 14:493-502. [PMID: 15615768 DOI: 10.1093/hmg/ddi046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abnormal epigenetic regulation of gene expression contributes significantly to a variety of human pathologies including cancer. Deletion of hypersensitive site 2 (HS2) at the human beta-globin locus control region can lead to abnormal epigenetic regulation of globin genes in transgenic mice. Here, two HS2-deleted transgenic mouse lines were used as model to demonstrate that heritable alteration of chromatin organization at the human beta-globin locus in multipotent hematopoietic progenitors contributes to the abnormal expression of the beta-globin gene in mature erythroid cells. This alteration is characterized by specific patterns of histone covalent modifications that are inherited during erythropoiesis and, moreover, is plastic because it can be reverted by transient treatment with the histone deacetylase inhibitor Trichostatin A. Altogether, our results indicate that aberrant epigenetic regulation can be detected and modified before tissue-specific gene transcription, a finding which may lead to novel strategies for the prevention of chromatin-related pathologies.
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Affiliation(s)
- Stefania Bottardi
- Guy-Bernier Research Centre, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, 5415 Boulevard l'Assomption, Montreal, Quebec, Canada H1T 2M4
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442
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Cosgrove MS, Boeke JD, Wolberger C. Regulated nucleosome mobility and the histone code. Nat Struct Mol Biol 2004; 11:1037-43. [PMID: 15523479 DOI: 10.1038/nsmb851] [Citation(s) in RCA: 252] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 09/30/2004] [Indexed: 12/22/2022]
Abstract
Post-translational modifications of the histone tails are correlated with distinct chromatin states that regulate access to DNA. Recent proteomic analyses have revealed several new modifications in the globular nucleosome core, many of which lie at the histone-DNA interface. We interpret these modifications in light of previously published data and propose a new and testable model for how cells implement the histone code by modulating nucleosome dynamics.
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Affiliation(s)
- Michael S Cosgrove
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 733 North Broadway Street, Baltimore, Maryland 21205, USA
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443
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Jónsson ZO, Jha S, Wohlschlegel JA, Dutta A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol Cell 2004; 16:465-77. [PMID: 15525518 DOI: 10.1016/j.molcel.2004.09.033] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 06/03/2004] [Accepted: 08/18/2004] [Indexed: 01/25/2023]
Abstract
The Rvb1p and Rvb2p (or TIP48 and TIP49) nuclear ATP binding proteins are universally conserved in eukaryotes and essential for viability of yeasts. Rvbp associate with each other as a double hexamer, with YHR034c and with two complexes involved in chromatin remodeling, Ino80.com and Swr1.com. Loss of Rvb1p or Ino80p affects many yeast promoters similarly. Rvbp are not essential for the recruitment of Ino80p to promoters but are essential for the catalytic activity of Ino80.com. Loss of Rvbp leads to loss of the functionally critical Arp5p in Ino80.com. Rvb2p associates with Arp5p in vitro in a reaction dependent on the presence of ATP and Ino80p. Therefore, Rvbp are required for the structural and functional integrity of the Ino80 chromatin remodeling complex.
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Affiliation(s)
- Zophonías O Jónsson
- University of Virginia School of Medicine, Jordan 1240, 1300 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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444
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Huynh VAT, Robinson PJJ, Rhodes D. A method for the in vitro reconstitution of a defined "30 nm" chromatin fibre containing stoichiometric amounts of the linker histone. J Mol Biol 2004; 345:957-68. [PMID: 15644197 DOI: 10.1016/j.jmb.2004.10.075] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Revised: 10/20/2004] [Accepted: 10/26/2004] [Indexed: 10/26/2022]
Abstract
An understanding of the role of higher-order chromatin structure in the regulation of cellular processes such as transcription will require knowledge of the structure of the "30 nm" chromatin fibre and its folding and unfolding pathways. We report an in vitro chromatin reconstitution system, which uses arrays of 12 and 19 copies of a 200 bp repeat of the Widom 601 DNA sequence. Since this DNA sequence binds the histone octamer with much higher affinity than mixed sequence DNA, we have used competitor DNA in the reconstitutions to control the loading of both the histone octamer and linker histone onto the 601 DNA arrays. Using this method we have obtained nucleosome arrays that have one histone octamer and one H5 bound per 200 bp repeat, and hence have the stoichiometric composition of native chromatin. To obtain highly compact 30 nm chromatin fibres, we have investigated a number of folding buffer conditions including varying NaCl or MgCl(2) concentrations. Sedimentation velocity analysis shows that the reconstituted nucleosome arrays have the same folding properties as native chromatin and form highly compact structures in high NaCl concentrations or 1mM MgCl(2). Negative stain and electron cryo-microscopy of the folded arrays show a homogeneous population of folded particles with a uniform diameter of 34 nm. The data presented provide good evidence that the reconstitution method we have developed produces, for the first time, a defined population of folded 30 nm fibres suitable for detailed structural investigation.
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Affiliation(s)
- Van A T Huynh
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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445
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Li G, Levitus M, Bustamante C, Widom J. Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 2004; 12:46-53. [PMID: 15580276 DOI: 10.1038/nsmb869] [Citation(s) in RCA: 477] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Accepted: 11/04/2004] [Indexed: 11/09/2022]
Abstract
DNA wrapped in nucleosomes is sterically occluded, creating obstacles for proteins that must bind it. How proteins gain access to DNA buried inside nucleosomes is not known. Here we report measurements of the rates of spontaneous nucleosome conformational changes in which a stretch of DNA transiently unwraps off the histone surface, starting from one end of the nucleosome, and then rewraps. The rates are rapid. Nucleosomal DNA remains fully wrapped for only approximately 250 ms before spontaneously unwrapping; unwrapped DNA rewraps within approximately 10-50 ms. Spontaneous unwrapping of nucleosomal DNA allows any protein rapid access even to buried stretches of the DNA. Our results explain how remodeling factors can be recruited to particular nucleosomes on a biologically relevant timescale, and they imply that the major impediment to entry of RNA polymerase into a nucleosome is rewrapping of nucleosomal DNA, not unwrapping.
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Affiliation(s)
- Gu Li
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500, USA
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446
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Martins RP, Ostermeier GC, Krawetz SA. Nuclear Matrix Interactions at the Human Protamine Domain. J Biol Chem 2004; 279:51862-8. [PMID: 15452126 DOI: 10.1074/jbc.m409415200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The compact eukaryotic genome must be selectively opened to grant trans-factor access to cis-regulatory elements to overcome the primary barrier to gene transcription. The mechanism that governs the selective opening of chromatin domains (i.e. potentiation) remains poorly understood. In the absence of a well defined locus control region, the nuclear matrix is considered the primary candidate regulating the opening of the multigenic PRM1 --> PRM2 --> TNP2 human protamine domain. To directly examine its role, four lines of transgenic mice with different configurations of flanking nuclear matrix attachment regions (MARs) encompassing the protamine domain were created. We show that upon removal of the MARs, the locus becomes subject to position effects. The 3' MAR alone may be sufficient to protect against silencing. In concert, the MARs bounding this domain likely synergize to regulate the expression of the various members of this gene cluster. Interestingly, the MARs may convey a selective reproductive advantage, such that constructs bearing both 5' and 3' MARs are passed to their offspring with greater frequency. Thus, the MARs bounding the PRM1 --> PRM2 --> TNP2 protamine domain have many and varied functions.
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Affiliation(s)
- Rui Pires Martins
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan 4820, USA
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447
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Bergman Y, Cedar H. A stepwise epigenetic process controls immunoglobulin allelic exclusion. Nat Rev Immunol 2004; 4:753-61. [PMID: 15459667 DOI: 10.1038/nri1458] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
During the differentiation of T and B cells, immune-receptor loci in the genome must be made sterically accessible so that they can undergo rearrangement. Here, we discuss how this is carried out by the stepwise removal of epigenetic repression mechanisms - such as later-replication timing, heterochromatization, histone hypo-acetylation and DNA methylation - in a manner that initially favours one allele in each cell. We propose that this mechanism of allelic exclusion might also be the basis for the generation of gene diversity in other systems.
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Affiliation(s)
- Yehudit Bergman
- Department of Experimental Medicine, Hebrew University Medical School, Ein Kerem, Jerusalem 91120, Israel
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448
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Abstract
Epigenetic mechanisms act to change the accessibility of chromatin to transcriptional regulation locally and globally via modifications of the DNA and by modification or rearrangement of nucleosomes. Epigenetic gene regulation collaborates with genetic alterations in cancer development. This is evident from every aspect of tumor biology including cell growth and differentiation, cell cycle control, DNA repair, angiogenesis, migration, and evasion of host immunosurveillance. In contrast to genetic cancer causes, the possibility of reversing epigenetic codes may provide new targets for therapeutic intervention.
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Affiliation(s)
- Anders H Lund
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.
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449
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Li X, Sakashita G, Matsuzaki H, Sugimoto K, Kimura K, Hanaoka F, Taniguchi H, Furukawa K, Urano T. Direct Association with Inner Centromere Protein (INCENP) Activates the Novel Chromosomal Passenger Protein, Aurora-C. J Biol Chem 2004; 279:47201-11. [PMID: 15316025 DOI: 10.1074/jbc.m403029200] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A family of serine/threonine kinase Aurora constitutes a key regulator in the orchestration of mitotic events. The human Aurora paralogues Aurora-A, Aurora-B, and Aurora-C have a highly conserved catalytic domain. Extensive studies on the role of Aurora-A and Aurora-B have revealed distinct localizations and functions in regulating mitotic processes, whereas little is known about Aurora-C. The present study shows that human Aurora-C is a chromosomal passenger protein that forms complexes with Aurora-B and inner centromere protein (INCENP), which are known passenger proteins. We show that INCENP binds and activates Aurora-C in vivo and in vitro. Furthermore, Aurora-C co-expressed with INCENP elicits the phosphorylation of endogenous histone H3 in mammalian cells, even though this phosphorylation is not sufficient to establish chromosome condensation in interphase cells. We therefore suggest that Aurora-C is a novel chromosomal passenger protein that cooperates with Aurora-B to regulate mitotic chromosome dynamics in mammalian cells.
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Affiliation(s)
- Xiangyu Li
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550.
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450
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Park YJ, Chodaparambil JV, Bao Y, McBryant SJ, Luger K. Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding. J Biol Chem 2004; 280:1817-25. [PMID: 15516689 DOI: 10.1074/jbc.m411347200] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic chromatin is highly dynamic and turns over rapidly even in the absence of DNA replication. Here we show that the acidic histone chaperone nucleosome assembly protein 1 (NAP-1) from yeast reversibly removes and replaces histone protein dimer H2A-H2B or histone variant dimers from assembled nucleosomes, resulting in active histone exchange. Transient removal of H2A-H2B dimers facilitates nucleosome sliding along the DNA to a thermodynamically favorable position. Histone exchange as well as nucleosome sliding is independent of ATP and relies on the presence of the C-terminal acidic domain of yeast NAP-1, even though this region is not required for histone binding and chromatin assembly. Our results suggest a novel role for NAP-1 (and perhaps other acidic histone chaperones) in mediating chromatin fluidity by incorporating histone variants and assisting nucleosome sliding. NAP-1 may function either untargeted (if acting alone) or may be targeted to specific regions within the genome through interactions with additional factors.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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