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Targeting Chromatin Complexes in Myeloid Malignancies and Beyond: From Basic Mechanisms to Clinical Innovation. Cells 2020; 9:cells9122721. [PMID: 33371192 PMCID: PMC7767226 DOI: 10.3390/cells9122721] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Accepted: 12/20/2020] [Indexed: 12/12/2022] Open
Abstract
The aberrant function of chromatin regulatory networks (epigenetics) is a hallmark of cancer promoting oncogenic gene expression. A growing body of evidence suggests that the disruption of specific chromatin-associated protein complexes has therapeutic potential in malignant conditions, particularly those that are driven by aberrant chromatin modifiers. Of note, a number of enzymatic inhibitors that block the catalytic function of histone modifying enzymes have been established and entered clinical trials. Unfortunately, many of these molecules do not have potent single-agent activity. One potential explanation for this phenomenon is the fact that those drugs do not profoundly disrupt the integrity of the aberrant network of multiprotein complexes on chromatin. Recent advances in drug development have led to the establishment of novel inhibitors of protein–protein interactions as well as targeted protein degraders that may provide inroads to longstanding effort to physically disrupt oncogenic multiprotein complexes on chromatin. In this review, we summarize some of the current concepts on the role epigenetic modifiers in malignant chromatin states with a specific focus on myeloid malignancies and recent advances in early-phase clinical trials.
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Hu C, Liu M, Zhang W, Xu Q, Ma K, Chen L, Wang Z, He S, Zhu H, Xu N. Upregulation of KLF4 by methylseleninic acid in human esophageal squamous cell carcinoma cells: Modification of histone H3 acetylation through HAT/HDAC interplay. Mol Carcinog 2015; 54:1051-9. [PMID: 24789055 DOI: 10.1002/mc.22174] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 01/01/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) occurs at a very high frequency in certain areas of China. Supplementation with selenium-containing compounds was associated with a significantly lower cancer mortality rate in a study conducted in Linxia, China. Thus, selenium could be a potential anti-esophageal cancer agent. In this study, methylseleninic acid (MSA) could inhibit cell growth of ESCC cells in vitro and in vivo. Upon treated with MSA, the activity of histone deacetylases (HDACs) was decreased and general control nonrepressed protein 5 (GCN5) was upregulated in ESCC cells. Meanwhile, a significant increase of H3K9 acetylation (H3K9ac) was detected. Upregulation of Krüppel-like factor 4 (KLF4) was also observed after MSA treatment. Additionally, the acetylated histone H3 located more at KLF4 promoter region after MSA treatment, shown by chromatin immunoprecipitation (ChIP) assay. Moreover, knockdown of GCN5 decreased the protein level of both H3K9ac and KLF4, along with less cell growth inhibition. Taken all, our results indicated that MSA could inhibit ESCC cell growth, at least in part, by MSA-HDAC/GCN5-H3K9ac-KLF4 axis. To our best knowledge, this is the first report that MSA induced acetylation of histone H3 at Lys9, which might depend on the activities and the balance between HDACs and HATs.
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Affiliation(s)
- Chenfei Hu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Mei Liu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Wei Zhang
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Qing Xu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Kai Ma
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Lechuang Chen
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Zaozao Wang
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Shun He
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR, China
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Zhang B, Dong Q, Su H, Birchler JA, Han F. Histone phosphorylation: its role during cell cycle and centromere identity in plants. Cytogenet Genome Res 2014; 143:144-9. [PMID: 24713809 DOI: 10.1159/000360435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
As the main protein components of chromatin, histones can alter the structural/functional capabilities of chromatin by undergoing extensive post-translational modifications (PTMs) such as phosphorylation, methylation, acetylation, ubiquitination, sumoylation, and so on. These PTMs are thought to transmit signals from the chromatin to the cell machinery to regulate various processes. Histone phosphorylation is associated with chromosome condensation/segregation, activation of transcription, and DNA damage repair. In this review, we focus on how different histone phosphorylations mark for chromatin change during the cell cycle, the relationship between histone phosphorylation and functional centromeres, and the candidate kinases that trigger and the phosphatase or kinase inhibitors that alter histone phosphorylation. Finally, we review the crosstalk between different PTMs.
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Affiliation(s)
- B Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Hennig W, Weyrich A. Histone modifications in the male germ line of Drosophila. BMC DEVELOPMENTAL BIOLOGY 2013; 13:7. [PMID: 23433182 PMCID: PMC3602674 DOI: 10.1186/1471-213x-13-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 01/31/2013] [Indexed: 12/18/2022]
Abstract
BACKGROUND In the male germ line of Drosophila chromatin remains decondensed and highly transcribed during meiotic prophase until it is rapidly compacted. A large proportion of the cell cycle-regulated histone H3.1 is replaced by H3.3, a histone variant encoded outside the histone repeat cluster and not subject to cell cycle controlled expression. RESULTS We investigated histone modification patterns in testes of D. melanogaster and D. hydei. In somatic cells of the testis envelope and in germ cells these modification patterns differ from those typically seen in eu- and heterochromatin of other somatic cells. During the meiotic prophase some modifications expected in active chromatin are not found or are found at low level. The absence of H4K16ac suggests that dosage compensation does not take place. Certain histone modifications correspond to either the cell cycle-regulated histone H3.1 or to the testis-specific variant H3.3. In spermatogonia we found H3K9 methylation in cytoplasmic histones, most likely corresponding to the H3.3 histone variant. Most histone modifications persist throughout the meiotic divisions. The majority of modifications persist until the early spermatid nuclei, and only a minority further persist until the final chromatin compaction stages before individualization of the spermatozoa. CONCLUSION Histone modification patterns in the male germ line differ from expected patterns. They are consistent with an absence of dosage compensation of the X chromosome during the male meiotic prophase. The cell cycle-regulated histone variant H3.1 and H3.3, expressed throughout the cell cycle, also vary in their modification patterns. Postmeiotically, we observed a highly complex pattern of the histone modifications until late spermatid nuclear elongation stages. This may be in part due to postmeiotic transcription and in part to differential histone replacement during chromatin condensation.
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Affiliation(s)
- Wolfgang Hennig
- DAAD Laboratory, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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Wang SH, Liao XM, Liu D, Hu J, Yin YY, Wang JZ, Zhu LQ. NGF promotes long-term memory formation by activating poly(ADP-ribose)polymerase-1. Neuropharmacology 2012; 63:1085-92. [DOI: 10.1016/j.neuropharm.2012.06.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 06/16/2012] [Accepted: 06/25/2012] [Indexed: 11/26/2022]
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CBP/p300 and SIRT1 are involved in transcriptional regulation of S-phase specific histone genes. PLoS One 2011; 6:e22088. [PMID: 21789216 PMCID: PMC3137613 DOI: 10.1371/journal.pone.0022088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 06/15/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Histones constitute a type of essential nuclear proteins important for chromatin structure and functions. The expression of major histones is strictly confined to the S phase of a cell cycle and tightly coupled to DNA replication. METHODOLOGY/PRINCIPAL FINDINGS With RT-qPCR and ChIP assays, we investigated transcriptional regulation of the S-phase specific histone genes and found that the acetylation level of histones on core histone gene promoters fluctuated during cell cycle in a pattern similar to RNA polymerase II association. Further, we showed that CBP/p300 and SIRT1 were recruited to histone gene promoters in an NPAT-dependent manner, knockdown of which affected histone acetylation on histone gene promoters and histone gene transcription. SIGNIFICANCE These observations contribute to further understanding of the mechanism by which the expression of canonical histone genes is regulated, and also implicate a link between histone expression and DNA damage repair and cell metabolism.
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Cruickshank MN, Besant P, Ulgiati D. The impact of histone post-translational modifications on developmental gene regulation. Amino Acids 2010; 39:1087-105. [PMID: 20204433 DOI: 10.1007/s00726-010-0530-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 02/12/2010] [Indexed: 02/06/2023]
Abstract
Eukaryotic genomic DNA is orderly compacted to fit into the nucleus and to inhibit accessibility of specific sequences. DNA is manipulated in many different ways by bound RNA and proteins within the composite material known as chromatin. All of the biological processes that require access to genomic DNA (such as replication, recombination and transcription) therefore are dependent on the precise characteristics of chromatin in eukaryotes. This distinction underlies a fundamental property of eukaryotic versus prokaryotic gene regulation such that chromatin structure must be regulated to precisely repress or relieve repression of particular regions of the genome in an appropriate spatio-temporal manner. As well as playing a key role in structuring genomic DNA, histones are subject to site-specific modifications that can influence the organization of chromatin structure. This review examines the molecular processes regulating site-specific histone acetylation, methylation and phosphorylation with an emphasis on how these processes underpin differentiation-regulated transcription.
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Affiliation(s)
- Mark N Cruickshank
- Biochemistry and Molecular Biology, School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Korolev N, Vorontsova OV, Nordenskiöld L. Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2006; 95:23-49. [PMID: 17291569 DOI: 10.1016/j.pbiomolbio.2006.11.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/15/2006] [Indexed: 11/21/2022]
Abstract
Electrostatic interactions between DNA and DNA-packaging proteins, the histones, contribute substantially to stability of eukaryotic chromatin on all levels of its organization and are particularly important in formation of its elementary structural unit, the nucleosome. The release of DNA from the histones is an unavoidable stage in reading the DNA code. In the present review, we discuss the disassembly/assembly process of the nucleosome from a thermodynamic standpoint by considering it as a competition between an excess of polyanions (DNA and acidic/phosphorylated domains of the nuclear proteins) for binding to a limited pool of polycations (the histones). Results obtained in model systems are used to discuss conditions for the electrostatic component of DNA-protein interactions contributing to chromatin statics and dynamics. We propose a simple set of "electrostatic conditions" for the disassembly/assembly of nucleosome/chromatin and apply these to put forward a number of new interpretations for the observations reported in literature on chromatin. The approach sheds light on the functions of acidic domains in the nuclear proteins (nucleoplasmin and other histone chaperones, HMG proteins, the activation domains in transcriptional activators). It results in a putative explanation for the molecular mechanisms behind epigenetic regulation through histone acetylation, phosphorylation, and other alterations ("the language of covalent histone modification"). We also propose a new explanation for the role of phosphorylation of C-terminal domain of RNA polymerase II for regulation of the DNA transcription. Several other examples from literature on chromatin are discussed to support applicability of electrostatic rules for description of chromatin structure and dynamics.
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Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Abstract
The epigenetic phospho-serine 10 modification of histone H3 has been a puzzle due to its association with two apparently opposed chromatin states. It is found at elevated levels on the highly condensed, transcriptionally inactive mitotic chromosomes yet is also correlated with the more extended chromatin configuration of active genes, euchromatic interband regions, and activated heat shock puffs of Drosophila polytene chromosomes. In addition, phosphorylation of histone H3S10 is up-regulated on the hypertranscribed male X chromosome. Here we review the cellular effects of histone H3S10 phosphorylation and discuss a model for its involvement in regulating chromatin organization and heterochromatization that would be applicable to both interphase and mitotic chromosomes.
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Affiliation(s)
- Kristen M Johansen
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 3154 Molecular Biology Building, Ames, Iowa 50011, USA.
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10
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Shao Y, Lu J, Zhang G, Liu C, Huang B. Histone acetyltransferase p300 promotes the activation of human WT1 promoter and intronic enhancer. Arch Biochem Biophys 2005; 436:62-8. [PMID: 15752709 DOI: 10.1016/j.abb.2005.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 01/07/2005] [Indexed: 11/22/2022]
Abstract
The Wilms' tumor gene-1 (WT1) encodes a zinc finger protein involved in gene regulation during kidney, gonad, and heart development. In addition to its promoter, a 258 bp intronic enhancer is required for tissue-specific expression of WT1 gene. p300 is a histone acetyltransferase (HAT) and exerts essential functions in gene regulation. Here, we show that p300 increased the expression of endogenous WT1 mRNA and promoted the activation of the WT1 promoter and intronic enhancer. The results also revealed that the adenovirus E1A repressed the p300 function, while the p300-binding defective E1A delta 2-36 did not, and p300 HAT activity was important for its function since p300 mutant with the HAT domain deleted partially abrogated its ability to activate the WT1 promoter and intronic enhancer. Furthermore, p300 and c-Myb synergistically activated the expression of WT1 gene. This study revealed that p300 and its HAT activity were involved in regulation of WT1 transcription.
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Affiliation(s)
- Yangguang Shao
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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Powell DW, Weaver CM, Jennings JL, McAfee KJ, He Y, Weil PA, Link AJ. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol 2004; 24:7249-59. [PMID: 15282323 PMCID: PMC479721 DOI: 10.1128/mcb.24.16.7249-7259.2004] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The SAGA histone acetyltransferase and TFIID complexes play key roles in eukaryotic transcription. Using hierarchical cluster analysis of mass spectrometry data to identify proteins that copurify with components of the budding yeast TFIID transcription complex, we discovered that an uncharacterized protein corresponding to the YPL047W open reading frame significantly associated with shared components of the TFIID and SAGA complexes. Using mass spectrometry and biochemical assays, we show that YPL047W (SGF11, 11-kDa SAGA-associated factor) is an integral subunit of SAGA. However, SGF11 does not appear to play a role in SAGA-mediated histone acetylation. DNA microarray analysis showed that SGF11 mediates transcription of a subset of SAGA-dependent genes, as well as SAGA-independent genes. SAGA purified from a sgf11 Delta deletion strain has reduced amounts of Ubp8p, and a ubp8 Delta deletion strain shows changes in transcription similar to those seen with the sgf11 Delta deletion strain. Together, these data show that Sgf11p is a novel component of the yeast SAGA complex and that SGF11 regulates transcription of a subset of SAGA-regulated genes. Our data suggest that the role of SGF11 in transcription is independent of SAGA's histone acetyltransferase activity but may involve Ubp8p recruitment to or stabilization in SAGA.
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Affiliation(s)
- David W Powell
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA
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Cohen-Armon M, Visochek L, Katzoff A, Levitan D, Susswein AJ, Klein R, Valbrun M, Schwartz JH. Long-Term Memory Requires PolyADP-ribosylation. Science 2004; 304:1820-2. [PMID: 15205535 DOI: 10.1126/science.1096775] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PolyADP-ribose-polymerase 1 is activated in neurons that mediate several forms of long-term memory in Aplysia. Because polyADP-ribosylation of nuclear proteins is a response to DNA damage in virtually all eukaryotic cells, it is surprising that activation of the polymerase occurs during learning and is required for long-term memory. We suggest that fast and transient decondensation of chromatin structure by polyADP-ribosylation enables the transcription needed to form long-term memory without strand breaks in DNA.
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Affiliation(s)
- Malka Cohen-Armon
- Neufeld Cardiac Research Institute, Sheba Medical Center, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.
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Abstract
Immediate early genes (IEG) are rapidly but transiently induced directly by intracellular signaling cascades to alter patterns of gene expression. It has been proposed that histone modifications could be the key to the quick alteration of chromatin structure, as this spread occurs too rapidly to be the consequence of passage of RNA polymerase II. In this review, we will discuss the different modifications on histones and the chromatin remodeling enzymes, allowing the promoter regions of two IEGs, c-fos and c-jun, to be accessed.
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Affiliation(s)
- Judy Chia Ghee Sng
- Laboratory of Molecular Pharmacology, Kanazawa University Graduate School of Natural Science and Technology, Ishikawa, Japan
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Lu P, Nakorchevskiy A, Marcotte EM. Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A 2003; 100:10370-5. [PMID: 12934019 PMCID: PMC193568 DOI: 10.1073/pnas.1832361100] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells grow in dynamically evolving populations, yet this aspect of experiments often goes unmeasured. A method is proposed for measuring the population dynamics of cells on the basis of their mRNA expression patterns. The population's expression pattern is modeled as the linear combination of mRNA expression from pure samples of cells, allowing reconstruction of the relative proportions of pure cell types in the population. Application of the method, termed expression deconvolution, to yeast grown under varying conditions reveals the population dynamics of the cells during the cell cycle, during the arrest of cells induced by DNA damage and the release of arrest in a cell cycle checkpoint mutant, during sporulation, and following environmental stress. Using expression deconvolution, cell cycle defects are detected and temporally ordered in 146 yeast deletion mutants; six of these defects are independently experimentally validated. Expression deconvolution allows a reinterpretation of the cell cycle dynamics underlying all previous microarray experiments and can be more generally applied to study most forms of cell population dynamics.
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Affiliation(s)
- Peng Lu
- Department of Chemistry and Biochemistry, Center for Computational Biology and Bioinformatics, 1 University Station, A4800, University of Texas, Austin, TX 78712-0159, USA
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Ogden SK, Lee KC, Wernke-Dollries K, Stratton SA, Aronow B, Barton MC. p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression. J Biol Chem 2001; 276:42057-62. [PMID: 11572852 DOI: 10.1074/jbc.c100381200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many of the functions ascribed to p53 tumor suppressor protein are mediated through transcription regulation. We have shown that p53 represses hepatic-specific alpha-fetoprotein (AFP) gene expression by direct interaction with a composite HNF-3/p53 DNA binding element. Using solid-phase, chromatin-assembled AFP DNA templates and analysis of chromatin structure and transcription in vitro, we find that p53 binds DNA and alters chromatin structure at the AFP core promoter to regulate transcription. Chromatin assembled in the presence of hepatoma extracts is activated for AFP transcription with an open, accessible core promoter structure. Distal (-850) binding of p53 during chromatin assembly, but not post-assembly, reverses transcription activation concomitant with promoter inaccessibility to restriction enzyme digestion. Inhibition of histone deacetylase activity by trichostatin-A (TSA) addition, prior to and during chromatin assembly, activated chromatin transcription in parallel with increased core promoter accessibility. Chromatin immunoprecipitation analyses showed increased H3 and H4 acetylated histones at the core promoter in the presence of TSA, while histone acetylation remained unchanged at the site of distal p53 binding. Our data reveal that p53 targets chromatin structure alteration at the core promoter, independently of effects on histone acetylation, to establish repressed AFP gene expression.
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Affiliation(s)
- S K Ogden
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati and Children's Hospital Research Foundation, Cincinnati, Ohio 45267, USA
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16
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Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis C, Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J 2001; 20:5232-41. [PMID: 11566886 PMCID: PMC125272 DOI: 10.1093/emboj/20.18.5232] [Citation(s) in RCA: 319] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent studies show that heterochromatin-associated protein-1 (HP1) recognizes a 'histone code' involving methylated Lys9 (methyl-K9) in histone H3. Using in situ immunofluorescence, we demonstrate that methyl-K9 H3 and HP1 co-localize to the heterochromatic regions of Drosophila polytene chromosomes. NMR spectra show that methyl-K9 binding of HP1 occurs via its chromo (chromosome organization modifier) domain. This interaction requires methyl-K9 to reside within the proper context of H3 sequence. NMR studies indicate that the methylated H3 tail binds in a groove of HP1 consisting of conserved residues. Using fluorescence anisotropy and isothermal titration calorimetry, we determined that this interaction occurs with a K(D) of approximately 100 microM, with the binding enthalpically driven. A V26M mutation in HP1, which disrupts its gene silencing function, severely destabilizes the H3-binding interface, and abolishes methyl-K9 H3 tail binding. Finally, we note that sequence diversity in chromo domains may lead to diverse functions in eukaryotic gene regulation. For example, the chromo domain of the yeast histone acetyltransferase Esa1 does not interact with methyl- K9 H3, but instead shows preference for unmodified H3 tail.
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Affiliation(s)
| | | | | | | | | | - Joel C. Eissenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908 and
Edward A.Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA Corresponding author e-mail:
S.A.Jacobs and S.D.Taverna contributed equally to this work
| | | | - Sepideh Khorasanizadeh
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908 and
Edward A.Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA Corresponding author e-mail:
S.A.Jacobs and S.D.Taverna contributed equally to this work
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Abstract
p300/CBP transcriptional co-activator proteins play a central role in co-ordinating and integrating multiple signal-dependent events with the transcription apparatus, allowing the appropriate level of gene activity to occur in response to diverse physiological cues that influence, for example, proliferation, differentiation and apoptosis. p300/CBP activity can be under aberrant control in human disease, particularly in cancer, which may inactivate a p300/CBP tumour-suppressor-like activity. The transcription regulating-properties of p300 and CBP appear to be exerted through multiple mechanisms. They act as protein bridges, thereby connecting different sequence-specific transcription factors to the transcription apparatus. Providing a protein scaffold upon which to build a multicomponent transcriptional regulatory complex is likely to be an important feature of p300/CBP control. Another key property is the presence of histone acetyltransferase (HAT) activity, which endows p300/CBP with the capacity to influence chromatin activity by modulating nucleosomal histones. Other proteins, including the p53 tumour suppressor, are targets for acetylation by p300/CBP. With the current intense level of research activity, p300/CBP will continue to be in the limelight and, we can be confident, yield new and important information on fundamental processes involved in transcriptional control.
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Affiliation(s)
- H M Chan
- Division of Biochemistry and Molecular Biology, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
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Rice JC, Allis CD. Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr Opin Cell Biol 2001; 13:263-73. [PMID: 11343896 DOI: 10.1016/s0955-0674(00)00208-8] [Citation(s) in RCA: 482] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Post-translational addition of methyl groups to the amino-terminal tails of histone proteins was discovered more than three decades ago. Only now, however, is the biological significance of lysine and arginine methylation of histone tails being elucidated. Recent findings indicate that methylation of certain core histones is catalyzed by a family of conserved proteins known as the histone methyltransferases (HMTs). New evidence suggests that site-specific methylation, catalyzed by HMTs, is associated with various biological processes ranging from transcriptional regulation to epigenetic silencing via heterochromatin assembly. Taken together, these new findings suggest that histone methylation may provide a stable genomic imprint that may serve to regulate gene expression as well as other epigenetic phenomena.
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Affiliation(s)
- J C Rice
- Department of Biochemistry and Molecular Genetics, University of Virginia, Health Sciences Center, Box 800733 Jordan Hall, Room 6222, Charlottesville, VA 22908-0733, USA
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Santisteban MS, Kalashnikova T, Smith MM. Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes. Cell 2000; 103:411-22. [PMID: 11081628 DOI: 10.1016/s0092-8674(00)00133-1] [Citation(s) in RCA: 252] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nucleosomes impose a block to transcription that can be overcome in vivo by remodeling complexes such as SNF/SWI and histone modification complexes such as SAGA. Mutations in the major core histones relieve transcriptional repression and bypass the requirement for SNF/SWI and SAGA. We have found that the variant histone H2A.Z regulates gene transcription, and deletion of the gene encoding H2A.Z strongly increases the requirement for SNF/SWI and SAGA. This synthetic genetic interaction is seen at the level of single genes and acts downstream of promoter nucleosome reorganization. H2A.Z is preferentially crosslinked in vivo to intergenic DNA at the PH05 and GAL1 loci, and this association changes with transcriptional activation. These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure.
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MESH Headings
- Adenosine Triphosphatases
- Alleles
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/physiology
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/physiology
- Fungal Proteins/genetics
- Fungal Proteins/physiology
- Gene Deletion
- Gene Expression Regulation, Fungal
- Genes, Essential/genetics
- Genes, Fungal/genetics
- Genes, Fungal/physiology
- Histones/chemistry
- Histones/genetics
- Histones/metabolism
- Hot Temperature
- Macromolecular Substances
- Membrane Transport Proteins/genetics
- Molecular Conformation
- Nuclear Proteins
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Phenotype
- Phosphate Transport Proteins
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Kinases/genetics
- Protein Kinases/physiology
- Protein Subunits
- Recombinant Fusion Proteins
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Suppression, Genetic/genetics
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- M S Santisteban
- Department of Microbiology and Cancer Center, University of Virginia, Charlottesville 22908, USA
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20
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Leach TJ, Mazzeo M, Chotkowski HL, Madigan JP, Wotring MG, Glaser RL. Histone H2A.Z is widely but nonrandomly distributed in chromosomes of Drosophila melanogaster. J Biol Chem 2000; 275:23267-72. [PMID: 10801889 DOI: 10.1074/jbc.m910206199] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Variant histones that differ in amino acid sequence from S-phase histones are widespread in eukaryotes, yet the structural changes they cause to nucleosomes and how those changes affect relevant cellular processes have not been determined. H2A.F/Z is a highly conserved family of H2A variants. H2Av, the H2A.F/Z variant of Drosophila melanogaster, was localized in polytene chromosomes by indirect immunofluorescence and in diploid chromosomes by chromatin immunoprecipitation. H2Av was widely distributed in the genome and not limited to sites of active transcription. H2Av was present in thousands of euchromatic bands and the heterochromatic chromocenter of polytene chromosomes, and the H2Av antibody precipitated both transcribed and nontranscribed genes as well as noncoding euchromatic and heterochromatic sequences. The distribution of H2Av was not uniform. The complex banding pattern of H2Av in polytene chromosomes did not parallel the concentration of DNA, as did the pattern of immunofluorescence using H2A antibodies, and the density of H2Av measured by immunoprecipitation varied between different sequences. Of the sequences assayed, H2Av was least abundant on 1. 688 satellite sequences and most abundant on the hsp70 genes. Finally, transcription caused, to an equivalent extent, both H2Av and H2A to be less tightly associated with DNA.
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Affiliation(s)
- T J Leach
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, State University of New York, Albany, New York 12201-2002, USA
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21
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Clayton AL, Rose S, Barratt MJ, Mahadevan LC. Phosphoacetylation of histone H3 on c-fos- and c-jun-associated nucleosomes upon gene activation. EMBO J 2000; 19:3714-26. [PMID: 10899125 PMCID: PMC313972 DOI: 10.1093/emboj/19.14.3714] [Citation(s) in RCA: 321] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The induction of immediate-early (IE) genes, including proto-oncogenes c-fos and c-jun, correlates well with a nucleosomal response, the phosphorylation of histone H3 and HMG-14 mediated via extracellular signal regulated kinase or p38 MAP kinase cascades. Phosphorylation is targeted to a minute fraction of histone H3, which is also especially susceptible to hyperacetylation. Here, we provide direct evidence that phosphorylation and acetylation of histone H3 occur on the same histone H3 tail on nucleosomes associated with active IE gene chromatin. Chromatin immunoprecipitation (ChIP) assays were performed using antibodies that specifically recognize the doubly-modified phosphoacetylated form of histone H3. Analysis of the associated DNA shows that histone H3 on c-fos- and c-jun-associated nucleosomes becomes doubly-modified, the same H3 tails becoming both phosphorylated and acetylated, only upon gene activation. This study reveals potential complications of occlusion when using site-specific antibodies against modified histones, and shows also that phosphorylated H3 is more sensitive to trichostatin A (TSA)-induced hyperacetylation than non-phosphorylated H3. Because MAP kinase-mediated gene induction is implicated in controlling diverse biological processes, histone H3 phosphoacetylation is likely to be of widespread significance.
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Affiliation(s)
- A L Clayton
- Nuclear Signalling Laboratory, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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22
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Mizzen CA, McLachlan DR. Capillary electrophoresis of histone H1 variants at neutral pH in dynamically modified fused- silica tubing. Electrophoresis 2000; 21:2359-67. [PMID: 10939446 DOI: 10.1002/1522-2683(20000701)21:12<2359::aid-elps2359>3.0.co;2-b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Existing methods for the analysis of histone H1 by capillary electrophoresis (CE) employ acidic buffers (pH <3.0) to suppress silanol ionization and minimize the loss of these extremely basic proteins by adsorption to capillary walls. Here we describe the use of Polybrene (PB) as a dynamic modification reagent in a simple procedure that facilitates the analysis of chicken H1 at neutral pH. PB is adsorbed to the inner surfaces of capillaries to render them cationic prior to use and a low concentration of PB is included in the electrolyte to replenish the coating during use. Inclusion of ethylenediaminetetraacetic acid (EDTA) in the electrolyte results in the assembly of a dynamic cation-exchange layer upon the immobilized PB that influences the relative mobilities of H1 variants. The six nonallelic variants of H1 known in this species as well as certain allelic variants are resolved. Because the procedure is effective in preventing the adsorption of proteins as basic as H1 at neutral pH, this strategy should facilitate CE analyses of many basic proteins under conditions that maintain their native conformation.
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Affiliation(s)
- C A Mizzen
- Centre for Research in Neurodegenerative Diseases, University of Toronto, ON, Canada.
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Lo WS, Trievel RC, Rojas JR, Duggan L, Hsu JY, Allis CD, Marmorstein R, Berger SL. Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol Cell 2000; 5:917-26. [PMID: 10911986 DOI: 10.1016/s1097-2765(00)80257-9] [Citation(s) in RCA: 439] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multiple covalent modifications exist in the amino-terminal tails of core histones, but whether a relationship exists between them is unknown. We examined the relationship between serine 10 phosphorylation and lysine 14 acetylation in histone H3 and have found that, in vitro, several HAT enzymes displayed increased activity on H3 peptides bearing phospho-Ser-10. This augmenting effect of Ser-10 phosphorylation on acetylation by yGcn5 was lost by substitution of alanine for arginine 164 [Gcn5(R164A)], a residue close to Ser-10 in the structure of the ternary tGcn5/CoA/histone H3 complex. Gcn5(R164A) had reduced activity in vivo at a subset of Gcn5-dependent promoters, and, strikingly, transcription of this same subset of genes was also impaired by substitution of serine 10 to alanine in the histone H3 tail. These observations suggest that transcriptional regulation occurs by multiple mechanistically linked covalent modifications of histones.
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Affiliation(s)
- W S Lo
- Molecular Genetics Program, Wistar Institute, Philadelphia, Pennsylvania 19024, USA
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Abstract
Histone proteins and the nucleosomes they form with DNA are the fundamental building blocks of eukaryotic chromatin. A diverse array of post-translational modifications that often occur on tail domains of these proteins has been well documented. Although the function of these highly conserved modifications has remained elusive, converging biochemical and genetic evidence suggests functions in several chromatin-based processes. We propose that distinct histone modifications, on one or more tails, act sequentially or in combination to form a 'histone code' that is, read by other proteins to bring about distinct downstream events.
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Affiliation(s)
- B D Strahl
- Department of Biochemistry and Molecular Genetics, University of Virginia Health Science Center, Charlottesville 22908, USA
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