201
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Sanchez R, Zhou MM. The PHD finger: a versatile epigenome reader. Trends Biochem Sci 2011; 36:364-72. [PMID: 21514168 DOI: 10.1016/j.tibs.2011.03.005] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/22/2011] [Accepted: 03/23/2011] [Indexed: 12/13/2022]
Abstract
PHD (plant homeodomain) zinc fingers are structurally conserved modules found in proteins that modify chromatin as well as mediate molecular interactions in gene transcription. The original discovery of their role in gene transcription is attributed to the recognition of lysine-methylated histone H3. Recent studies show that PHD fingers have a sophisticated histone sequence reading capacity that is modulated by the interplay between different histone modifications. These studies underscore the functional versatility of PHD fingers as epigenome readers that control gene expression through molecular recruitment of multiprotein complexes of chromatin regulators and transcription factors. Moreover, they reinforce the concept that evolutionary changes in amino acids surrounding ligand binding sites on a conserved structural fold impart great functional diversity upon this family of proteins.
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Affiliation(s)
- Roberto Sanchez
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.
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202
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Meng HX, Hackett JA, Nestor C, Dunican DS, Madej M, Reddington JP, Pennings S, Harrison DJ, Meehan RR. Apoptosis and DNA methylation. Cancers (Basel) 2011; 3:1798-820. [PMID: 24212783 PMCID: PMC3757391 DOI: 10.3390/cancers3021798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 03/11/2011] [Accepted: 03/11/2011] [Indexed: 01/05/2023] Open
Abstract
Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.
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Affiliation(s)
- Huan X. Meng
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - James A. Hackett
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Colm Nestor
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
| | - Donncha S. Dunican
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Monika Madej
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - James P. Reddington
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Sari Pennings
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; E-Mail: (S.P.)
| | - David J. Harrison
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
| | - Richard R. Meehan
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44 (0)-332-2471; Fax: +44 (0) 131 467 8456
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203
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Lempiäinen H, Müller A, Brasa S, Teo SS, Roloff TC, Morawiec L, Zamurovic N, Vicart A, Funhoff E, Couttet P, Schübeler D, Grenet O, Marlowe J, Moggs J, Terranova R. Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice. PLoS One 2011; 6:e18216. [PMID: 21455306 PMCID: PMC3063791 DOI: 10.1371/journal.pone.0018216] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 02/28/2011] [Indexed: 11/19/2022] Open
Abstract
Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis.
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Affiliation(s)
- Harri Lempiäinen
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Arne Müller
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sarah Brasa
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Soon-Siong Teo
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Laurent Morawiec
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natasa Zamurovic
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Axel Vicart
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Enrico Funhoff
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Philippe Couttet
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Olivier Grenet
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jennifer Marlowe
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jonathan Moggs
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Rémi Terranova
- Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail:
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204
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Itoh K, Izumi A, Mori T, Dohmae N, Yui R, Maeda-Sano K, Shirai Y, Kanaoka MM, Kuroiwa T, Higashiyama T, Sugita M, Murakami-Murofushi K, Kawano S, Sasaki N. DNA packaging proteins Glom and Glom2 coordinately organize the mitochondrial nucleoid of Physarum polycephalum. Mitochondrion 2011; 11:575-86. [PMID: 21406253 DOI: 10.1016/j.mito.2011.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 02/03/2011] [Accepted: 03/04/2011] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA (mtDNA) is generally packaged into the mitochondrial nucleoid (mt-nucleoid) by a high-mobility group (HMG) protein. Glom is an mtDNA-packaging HMG protein in Physarum polycephalum. Here we identified a new mtDNA-packaging protein, Glom2, which had a region homologous with yeast Mgm101. Glom2 could bind to an entire mtDNA and worked synergistically with Glom for condensation of mtDNA in vitro. Down-regulation of Glom2 enhanced the alteration of mt-nucleoid morphology and the loss of mtDNA induced by down-regulation of Glom, and impaired mRNA accumulation of some mtDNA-encoded genes. These data suggest that Glom2 may organize the mt-nucleoid coordinately with Glom.
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Affiliation(s)
- Kie Itoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
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205
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Sousa F, Cruz C, Queiroz JA. Amino acids-nucleotides biomolecular recognition: from biological occurrence to affinity chromatography. J Mol Recognit 2011; 23:505-18. [PMID: 21038352 DOI: 10.1002/jmr.1053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this review, the protein-DNA interactions are discussed considering different perspectives, and the biological occurrence of this interaction is explained at atomic level. The evaluation of the amino acid-nucleotide recognition has been investigated analysing datasets for predicting the association preferences and the geometry that favours the interaction. Based on this knowledge, an affinity chromatographic method was developed also exploiting this biological favoured contact. In fact, the implementation of this technique brings the possibility to apply the concept of molecular interactions to the development of new purification methodologies. In addition, the integration of the information recovered by all the different perspectives can bring new insights about some biological mechanisms, though not totally clarified.
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Affiliation(s)
- F Sousa
- CICS-Centro de Investigação em Ciências da Saúde, University of Beira Interior, 6201-001 Covilhã, Portugal.
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206
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Banine F, Matagne V, Sherman LS, Ojeda SR. Brain region-specific expression of Fxyd1, an Mecp2 target gene, is regulated by epigenetic mechanisms. J Neurosci Res 2011; 89:840-51. [PMID: 21394759 DOI: 10.1002/jnr.22608] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 12/23/2010] [Accepted: 01/13/2011] [Indexed: 12/25/2022]
Abstract
Fxyd1 encodes a trans-membrane protein that modulates Na(+) ,K(+) -ATPase activity and is a substrate for multiple protein kinases. Fxyd1 expression is repressed by methyl CpG-binding protein 2 (Mecp2) in the frontal cortex (FC) but not in the cerebellum (CB) of the mouse brain. Consistently with these observations, FXYD1 mRNA abundance is increased in the FC of Rett syndrome (RTT) patients with MECP2 mutations. Because Fxyd1 is implicated in the regulation of neuronal excitability, understanding how Fxyd1 expression is controlled is important. Here we report that basal expression of Fxyd1a and Fxyd1b, the two main alternatively spliced forms of Fxyd1 mRNA, is lower in the FC than in the CB. This difference is accompanied by increased Mecp2 recruitment to the promoter region of these two Fxyd1 mRNA forms. DNA methylation of both promoters is more frequent in the FC than in the CB, and in both cases the most frequently methylated CpG dinucleotides are adjacent to [A/T](4) sequences required for high-affinity Mecp2 binding. Consistently with these features of epigenetic silencing, histone 3 acetylated at lysines 9 and 14 (H3K9/14ac) and histone 3 methylated at lysine 4 (H3K4me3), both activating histone marks, were associated with the Fxyd1 promoter to a lesser degree in the FC than in the CB. These results indicate that differential Fxyd1 expression in these two brain regions is, at least in part, regulated by an epigenetic mechanism involving increased DNA methylation of the two alternative Fxyd1 promoters, enhanced Mecp2 recruitment, and reduced association of activating histones.
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Affiliation(s)
- Fatima Banine
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon, USA
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207
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Xiao G, Wang X, Khodursky AB. Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data. J Am Stat Assoc 2011. [DOI: 10.1198/jasa.2010.ap09504] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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208
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SET/MYND Lysine Methyltransferases Regulate Gene Transcription and Protein Activity. Genes (Basel) 2011; 2:210-8. [PMID: 24710145 PMCID: PMC3924839 DOI: 10.3390/genes2010210] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/25/2011] [Accepted: 02/07/2011] [Indexed: 12/20/2022] Open
Abstract
The SET and MYND (SMYD) family of lysine methyltransferases is defined by a SET domain that is split into two segments by a MYND domain, followed by a cysteine-rich post-SET domain. While members of the SMYD family are important in the SET-mediated regulation of gene transcription, pathological consequences have also been associated with aberrant expression of SMYD proteins. The last decade has witnessed a rapid increase in the studies and corresponding understanding of these highly impactful enzymes. Herein, we review the current body of knowledge related to the SMYD family of lysine methyltransferases and their role in transcriptional regulation, epigenetics, and tumorigenesis.
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209
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Zeng X, Chen S, Huang H. Phosphorylation of EZH2 by CDK1 and CDK2: a possible regulatory mechanism of transmission of the H3K27me3 epigenetic mark through cell divisions. Cell Cycle 2011. [PMID: 21278485 DOI: 10.4161/cc.10.4.14722] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Histone H3 lysine 27 trimethylation (H3K27me3) catalyzed by the enzymatic subunit EZH2 in the Polycomb repressive complex 2 (PRC2) is essential for cells to 'memorize' gene expression patterns through cell divisions and plays an important role in establishing and maintaining cell identity during development. However, how the epigenetic mark is inherited through cell generations remains poorly understood. Recently, we and others demonstrate that CDK1 and CDK2 phosphorylate EZH2 at threonine 350 (T350) and that T350 phosphorylation is important for the binding of EZH2 to PRC2 recruiters, such as noncoding RNAs (ncRNAs) HOTAIR and XIST, and for the effective recruitment of PRC2 to EZH2 target loci in cells. These findings imply that phosphorylation of EZH2 by CDK1 and CDK2 may provide cells a mechanism that enhances EZH2 function during S and G2 phases of the cell cycle, thereby ensuring K27me3 on de novo synthesized H3 incorporated in nascent nucleosomes before sister chromosomes are divided into two daughter cells. Additionally, a potential role of T350 phosphorylation of EZH2 in differing EZH2 from its homolog EZH1 in catalyzing H3K27me3 as well as the interplay between phosphorylation at T350 and other residues (e.g. phosphorylation by p38 at threonine 372 (T372)) in governing EZH2 activity in proliferating versus non-dividing cells are also discussed. Together, CDK phosphorylation of EZH2 at T350 may represent a key regulatory mechanism of EZH2 function that is essential for the maintenance of H3K27me3 marks through cell divisions.
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Affiliation(s)
- Xianzhuo Zeng
- Department of Pathology; Stony Brook University Medical Center; Stony Brook, NY USA
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210
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Zeng X, Chen S, Huang H. Phosphorylation of EZH2 by CDK1 and CDK2: a possible regulatory mechanism of transmission of the H3K27me3 epigenetic mark through cell divisions. Cell Cycle 2011; 10:579-83. [PMID: 21278485 DOI: 10.4161/cc.10.4.14850] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Histone H3 lysine 27 trimethylation (H3K27me3) catalyzed by the enzymatic subunit EZH2 in the Polycomb repressive complex 2 (PRC2) is essential for cells to 'memorize' gene expression patterns through cell divisions and plays an important role in establishing and maintaining cell identity during development. However, how the epigenetic mark is inherited through cell generations remains poorly understood. Recently, we and others demonstrate that CDK1 and CDK2 phosphorylate EZH2 at threonine 350 (T350) and that T350 phosphorylation is important for the binding of EZH2 to PRC2 recruiters, such as noncoding RNAs (ncRNAs) HOTAIR and XIST, and for the effective recruitment of PRC2 to EZH2 target loci in cells. These findings imply that phosphorylation of EZH2 by CDK1 and CDK2 may provide cells a mechanism that enhances EZH2 function during S and G2 phases of the cell cycle, thereby ensuring K27me3 on de novo synthesized H3 incorporated in nascent nucleosomes before sister chromosomes are divided into two daughter cells. Additionally, a potential role of T350 phosphorylation of EZH2 in differing EZH2 from its homolog EZH1 in catalyzing H3K27me3 as well as the interplay between phosphorylation at T350 and other residues (e.g. phosphorylation by p38 at threonine 372 (T372)) in governing EZH2 activity in proliferating versus non-dividing cells are also discussed. Together, CDK phosphorylation of EZH2 at T350 may represent a key regulatory mechanism of EZH2 function that is essential for the maintenance of H3K27me3 marks through cell divisions.
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Affiliation(s)
- Xianzhuo Zeng
- Department of Pathology; Stony Brook University Medical Center; Stony Brook, NY USA
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211
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Sharov AA, Nishiyama A, Piao Y, Correa-Cerro LS, Amano T, Thomas M, Mehta S, Ko MSH. Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics 2011; 12:102. [PMID: 21306619 PMCID: PMC3044670 DOI: 10.1186/1471-2164-12-102] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 02/09/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before. RESULTS We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs) and other genes. Responsive genes (N=4746), which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF) and our new data for 15 organs and tissues. Non-responsive genes (N=9562), which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters. CONCLUSIONS We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.
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Affiliation(s)
- Alexei A Sharov
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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212
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Abstract
Vertebrate development requires the formation of multiple cell types from a single genetic blueprint, an extraordinary feat that is guided by the dynamic and finely tuned reprogramming of gene expression. The sophisticated orchestration of gene expression programs is driven primarily by changes in the patterns of covalent chromatin modifications. These epigenetic changes are directed by cis elements, positioned across the genome, which provide docking sites for transcription factors and associated chromatin modifiers. Epigenetic changes impact all aspects of gene regulation, governing association with the machinery that drives transcription, replication, repair and recombination, a regulatory relationship that is dramatically illustrated in developing lymphocytes. The program of somatic rearrangements that assemble antigen receptor genes in precursor B and T cells has proven to be a fertile system for elucidating relationships between the genetic and epigenetic components of gene regulation. This chapter describes our current understanding of the cross-talk between key genetic elements and epigenetic programs during recombination of the Tcrb locus in developing T cells, how each contributes to the regulation of chromatin accessibility at individual DNA targets for recombination, and potential mechanisms that coordinate their actions.
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213
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Differential microbicidal effects of human histone proteins H2A and H2B on Leishmania promastigotes and amastigotes. Infect Immun 2010; 79:1124-33. [PMID: 21189319 DOI: 10.1128/iai.00658-10] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies have shown that histone proteins can act as antimicrobial peptides in host defense against extracellular bacteria, fungi, and Leishmania promastigotes. In this study, we used human recombinant histone proteins to further study their leishmaniacidal effects and the underlying mechanisms. We found that the histones H2A and H2B (but not H1(0)) could directly and efficiently kill promastigotes of Leishmania amazonensis, L. major, L. braziliensis, and L. mexicana in a treatment dose-dependent manner. Scanning electron microscopy revealed surface disruption of histone-treated promastigotes. More importantly, the preexposure of promastigotes to histone proteins markedly decreased the infectivity of promastigotes to murine macrophages (Mφs) in vitro. However, axenic and lesion-derived amastigotes of L. amazonensis and L. mexicana were relatively resistant to histone treatment, which correlated with the low levels of intracellular H2A in treated amastigotes. To understand the mechanisms underlying these differential responses, we investigated the role of promastigote surface molecules in histone-mediated killing. Compared with the corresponding controls, transgenic L. amazonensis promastigotes expressing lower levels of surface gp63 proteins were more susceptible to histone H2A, while L. major and L. mexicana promastigotes with targeted deletion of the lipophosphoglycan 2 (lpg2) gene (but not the lpg1 gene) were more resistant to histone H2A. We discuss the influence of promastigote major surface molecules in the leishmaniacidal effect of histone proteins. This study provides new information on host innate immunity to different developmental stages of Leishmania parasites.
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214
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Epigenetic regulation of cell life and death decisions and deregulation in cancer. Essays Biochem 2010; 48:121-46. [PMID: 20822491 DOI: 10.1042/bse0480121] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
For every cell, there is a time to live and a time to die. It is apparent that cell life and death decisions are taken by individual cells based on their interpretation of physiological or non-physiological stimuli, or their own self-assessment of internal damage or changes in their environment. Apoptosis or programmed cell death is a key regulator of physiological growth control and regulation of tissue homoeostasis. One of the most important advances in cancer research in recent years is the recognition that cell death, mostly by apoptosis, is crucially involved in the regulation of tumour formation and also critically determines treatment response. The initiation and progression of cancer, traditionally seen as a genetic disease, is now realized to involve epigenetic abnormalities along with genetic alterations. The study of epigenetic mechanisms in cancer, such as DNA methylation, histone modifications and microRNA expression, has revealed a plethora of events that contribute to the neoplastic phenotype through stable changes in the expression of genes critical to cell death pathways. A better understanding of the epigenetic molecular events that regulate apoptosis, together with the reversible nature of epigenetic aberrations, should contribute to the emergence of the promising field of epigenetic therapy.
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215
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Nucleosome structural studies. Curr Opin Struct Biol 2010; 21:128-36. [PMID: 21176878 DOI: 10.1016/j.sbi.2010.11.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 11/17/2010] [Accepted: 11/25/2010] [Indexed: 11/22/2022]
Abstract
Chromatin plays a fundamental role in eukaryotic genomic regulation, and the increasing awareness of the importance of epigenetic processes in human health and disease emphasizes the need for understanding the structure and function of the nucleosome. Recent advances in chromatin structural studies, including the first structures of nucleosomes containing the Widom 601 sequence and the structure of a chromatin protein-nucleosome assembly, have provided new insight into stretching of nucleosomal DNA, nucleosome positioning, binding of metal ions, drugs and therapeutic candidates to nucleosomes, and nucleosome recognition by nuclear proteins. These discoveries ensure promising future prospects for unravelling structural attributes of chromatin.
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216
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Spin JM, Quertermous T, Tsao PS. Chromatin remodeling pathways in smooth muscle cell differentiation, and evidence for an integral role for p300. PLoS One 2010; 5:e14301. [PMID: 21179216 PMCID: PMC3001469 DOI: 10.1371/journal.pone.0014301] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/15/2010] [Indexed: 11/25/2022] Open
Abstract
Background Phenotypic alteration of vascular smooth muscle cells (SMC) in response to injury or inflammation is an essential component of vascular disease. Evidence suggests that this process is dependent on epigenetic regulatory processes. P300, a histone acetyltransferase (HAT), activates crucial muscle-specific promoters in terminal (non-SMC) myocyte differentiation, and may be essential to SMC modulation as well. Results We performed a subanalysis examining transcriptional time-course microarray data obtained using the A404 model of SMC differentiation. Numerous chromatin remodeling genes (up to 62% of such genes on our array platform) showed significant regulation during differentiation. Members of several chromatin-remodeling families demonstrated involvement, including factors instrumental in histone modification, chromatin assembly-disassembly and DNA silencing, suggesting complex, multi-level systemic epigenetic regulation. Further, trichostatin A, a histone deacetylase inhibitor, accelerated expression of SMC differentiation markers in this model. Ontology analysis indicated a high degree of p300 involvement in SMC differentiation, with 60.7% of the known p300 interactome showing significant expression changes. Knockdown of p300 expression accelerated SMC differentiation in A404 cells and human SMCs, while inhibition of p300 HAT activity blunted SMC differentiation. The results suggest a central but complex role for p300 in SMC phenotypic modulation. Conclusions Our results support the hypothesis that chromatin remodeling is important for SMC phenotypic switching, and detail wide-ranging involvement of several epigenetic modification families. Additionally, the transcriptional coactivator p300 may be partially degraded during SMC differentiation, leaving an activated subpopulation with increased HAT activity and SMC differentiation-gene specificity.
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Affiliation(s)
- Joshua M Spin
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America.
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217
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Vogler C, Huber C, Waldmann T, Ettig R, Braun L, Izzo A, Daujat S, Chassignet I, Lopez-Contreras AJ, Fernandez-Capetillo O, Dundr M, Rippe K, Längst G, Schneider R. Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding. PLoS Genet 2010; 6:e1001234. [PMID: 21170357 PMCID: PMC3000355 DOI: 10.1371/journal.pgen.1001234] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 11/03/2010] [Indexed: 01/30/2023] Open
Abstract
The tails of histone proteins are central players for all chromatin-mediated processes. Whereas the N-terminal histone tails have been studied extensively, little is known about the function of the H2A C-terminus. Here, we show that the H2A C-terminal tail plays a pivotal role in regulating chromatin structure and dynamics. We find that cells expressing C-terminally truncated H2A show increased stress sensitivity. Moreover, both the complete and the partial deletion of the tail result in increased histone exchange kinetics and nucleosome mobility in vivo and in vitro. Importantly, our experiments reveal that the H2A C-terminus is required for efficient nucleosome translocation by ISWI-type chromatin remodelers and acts as a novel recognition module for linker histone H1. Thus, we suggest that the H2A C-terminal tail has a bipartite function: stabilisation of the nucleosomal core particle, as well as mediation of the protein interactions that control chromatin dynamics and conformation. Histones are the main protein components of chromatin. The N-terminal tails of histones stick out from the nucleosomes, the building blocks of chromatin, and are involved in the regulation of all DNA–dependent processes. Only Histone H2A has an additional C-terminal tail and currently very little is known about the function of this tail. The H2A C-terminus protrudes from the nucleosome and is located where the DNA enters and leaves the nucleosome. We show here that it can interact with the linker histone H1 that is important for higher order chromatin structure. We also find that this tail is involved in regulating nucleosome dynamics and mobility of H2A itself. The C-terminal H2A tail has also an important function in regulating the activity of chromatin remodelers, enzymes that can reposition nucleosomes. Furthermore we find that cells expressing C-terminally truncated H2A are more sensitive to stress, demonstrating that this tail is important for cellular homeostasis. Together our results reflect a key function of the H2A C-terminus in chromatin biology.
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Affiliation(s)
| | - Claudia Huber
- Biochemie III, University of Regensburg, Regensburg, Germany
| | - Tanja Waldmann
- Max-Planck Institute of Immunobiology, Freiburg, Germany
| | - Ramona Ettig
- German Cancer Research Center (DKFZ) and BioQuant, Research Group Genome Organization and Function, Heidelberg, Germany
| | - Lora Braun
- Max-Planck Institute of Immunobiology, Freiburg, Germany
| | - Annalisa Izzo
- Max-Planck Institute of Immunobiology, Freiburg, Germany
| | - Sylvain Daujat
- Max-Planck Institute of Immunobiology, Freiburg, Germany
| | | | | | | | - Miroslav Dundr
- Rosalind Franklin University, North Chicago, Illinois, United States of America
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) and BioQuant, Research Group Genome Organization and Function, Heidelberg, Germany
| | - Gernot Längst
- Biochemie III, University of Regensburg, Regensburg, Germany
- * E-mail: (GL); (RS)
| | - Robert Schneider
- Max-Planck Institute of Immunobiology, Freiburg, Germany
- * E-mail: (GL); (RS)
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218
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Targeting histone deacetyalses in the treatment of B- and T-cell malignancies. Invest New Drugs 2010; 28 Suppl 1:S58-78. [PMID: 21132350 PMCID: PMC3003796 DOI: 10.1007/s10637-010-9591-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 10/28/2010] [Indexed: 02/06/2023]
Abstract
HDAC inhibitors (HDACI) are now emerging as one of the most promising new classes of drugs for the treatment of select forms of non-Hodgkin’s lymphoma (NHL). They are particularly active in T-cell lymphomas, possibly hodgkin’s lymphoma and indolent B cell lymphomas. Presently, two of these agents, vorinostat and romidepsin, have been approved in the US for the treatment of relapsed and refractory cutaneous T cell lymphomas (CTCL). Initially, these agents were developed with the idea that they affected transcriptional activation and thus gene expression, by modulating chromatin condensation and decondensation. It is now clear that their effects go beyond chromatin and by affecting the acetylation status of histones and other intra-cellular proteins, they modify gene expression and cellular function via multiple pathways. Gene expression profiles and functional genetic analysis has led to further understanding of the various molecular pathways that are affected by these agents including cell cycle regulation, pathways of cellular proliferation, apoptosis and angiogenesis all important in lymphomagenesis. There is also increasing data to support the effects of these agents on T cell receptor and immune function which may explain the high level of activity of these agents in T cell lymphomas and hodgkin’s lymphoma. There is ample evidence of epigenetic dysregulation in lymphomas which may underlie the mechanisms of action of these agents but how these agents work is still not clear. Current HDAC inhibitors can be divided into at least four classes based on their chemical structure. At present several of these HDAC inhibitors are in clinical trials both as single agents and in combination with chemotherapy or other biological agents. They are easy to administer and are generally well tolerated with minimal side effects. Different dosing levels and schedules and the use of isospecific HDAC inhibitors are some of the strategies that are being employed to increase the therapeutic effect of these agents in the treatment of lymphomas. There may also be class differences that translate into specific activity against different lymphoma. HDAC inhibitors will likely be incorporated into combinations of targeted therapies both in the upfront and relapsed setting for lymphomas.
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219
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Kent NA, Adams S, Moorhouse A, Paszkiewicz K. Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing. Nucleic Acids Res 2010; 39:e26. [PMID: 21131275 PMCID: PMC3061068 DOI: 10.1093/nar/gkq1183] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Microarray and next-generation sequencing techniques which allow whole genome analysis of chromatin structure and sequence-specific protein binding are revolutionizing our view of chromosome architecture and function. However, many current methods in this field rely on biochemical purification of highly specific fractions of DNA prepared from chromatin digested with either micrococcal nuclease or DNaseI and are restricted in the parameters they can measure. Here, we show that a broad size-range of genomic DNA species, produced by partial micrococcal nuclease digestion of chromatin, can be sequenced using paired-end mode next-generation technology. The paired sequence reads, rather than DNA molecules, can then be size-selected and mapped as particle classes to the target genome. Using budding yeast as a model, we show that this approach reveals position and structural information for a spectrum of nuclease resistant complexes ranging from transcription factor-bound DNA elements up to mono- and poly-nucleosomes. We illustrate the utility of this approach in visualizing the MNase digestion landscape of protein-coding gene transcriptional start sites, and demonstrate a comparative analysis which probes the function of the chromatin-remodelling transcription factor Cbf1p.
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Affiliation(s)
- Nicholas A Kent
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.
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220
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Osipovich O, Oltz EM. Regulation of antigen receptor gene assembly by genetic-epigenetic crosstalk. Semin Immunol 2010; 22:313-22. [PMID: 20829065 PMCID: PMC2981692 DOI: 10.1016/j.smim.2010.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/08/2010] [Indexed: 02/05/2023]
Abstract
Many aspects of gene function are coordinated by changes in the epigenome, which include dynamic revisions of chromatin modifications, genome packaging, subnuclear localization, and chromosome conformation. All of these mechanisms are used by developing lymphocytes to regulate the assembly of functional antigen receptor genes by V(D)J recombination. This somatic rearrangement of the genome must be tightly regulated to ensure proper B and T cell development and to avoid chromosomal translocations that cause lymphoid tumors. V(D)J recombination is controlled by a complex interplay between cis-acting regulatory elements that use transcription factors as liaisons to communicate with epigenetic pathways. Genetic-epigenetic crosstalk is a key strategy employed by precursor lymphocytes to modulate chromatin configurations at Ig and Tcr loci and thereby permit or deny access to a single V(D)J recombinase complex. This article describes our current knowledge of how genetic elements orchestrate crosstalk with epigenetic mechanisms to regulate recombinase accessibility via localized, regional, or long-range changes in chromatin.
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Affiliation(s)
- Oleg Osipovich
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eugene M. Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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221
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Watanabe A, Arai M, Koitabashi N, Niwano K, Ohyama Y, Yamada Y, Kato N, Kurabayashi M. Mitochondrial transcription factors TFAM and TFB2M regulate Serca2 gene transcription. Cardiovasc Res 2010; 90:57-67. [PMID: 21113058 DOI: 10.1093/cvr/cvq374] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Sarco(endo)plasmic reticulum Ca²(+)-ATPase 2a (SERCA2a) transports Ca²(+) by consuming ATP produced by mitochondrial respiratory chain enzymes. Messenger RNA (mRNA) for these enzymes is transcribed by mitochondrial transcription factors A (TFAM) and B2 (TFB2M). This study examined whether TFAM and TFB2M coordinately regulate the transcription of the Serca2 gene and mitochondrial genes. METHODS AND RESULTS Nuclear localization of TFAM and TFB2M was demonstrated by immunostaining in rat neonatal cardiac myocytes. Chromatin immunoprecipitation assay and fluorescence correlation spectroscopy revealed that TFAM and TFB2M bind to the -122 to -114 nt and -122 to -117 nt regions of the rat Serca2 gene promoter, respectively. Mutation of these sites resulted in decreased Serca2 gene transcription. In a rat myocardial infarction model, Serca2a mRNA levels significantly correlated with those of Tfam (r = 0.54, P < 0.001) and Tfb2m (r = 0.73, P < 0.001). Overexpression of TFAM and TFB2M blocked hydrogen peroxide- and norepinephrine-induced decreases in Serca2a mRNA levels. In addition, overexpression of TFAM and TFB2M increased the mitochondrial DNA (mtDNA) copy number and mRNA levels of mitochondrial enzymes. CONCLUSION Although TFAM and TFB2M are recognized as mtDNA-specific transcription factors, they also regulate transcription of nuclear DNA, i.e. the Serca2 gene. Our findings suggest a novel paradigm in which the transcription of genes for mitochondrial enzymes that produce ATP and the gene for SERCA2a that consumes ATP is coordinately regulated by the same transcription factors. This mechanism may contribute to maintaining proper cardiac function.
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Affiliation(s)
- Atai Watanabe
- Department of Medicine and Biological Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
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222
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On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 2010; 78:2075-89. [PMID: 20455264 DOI: 10.1002/prot.22723] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Model organisms such as yeast, fly, and worm have played a defining role in the study of many biological systems. A significant challenge remains in translating this information to humans. Of critical importance is the ability to differentiate those components where knowledge of function and interactions may be reliably inferred from those that represent lineage-specific innovations. To address this challenge, we use chromatin modification (CM) as a model system for exploring the evolutionary properties of their components in the context of their known functions and interactions. Collating previously identified components of CM from yeast, worm, fly, and human, we identified a "core" set of 50 CM genes displaying consistent orthologous relationships that likely retain their interactions and functions across taxa. In addition, we catalog many components that demonstrate lineage specific expansions and losses, highlighting much duplication within vertebrates that may reflect an expanded repertoire of regulatory mechanisms. Placed in the context of a high-quality protein-protein interaction network, we find, contrary to existing views of evolutionary modularity, that CM complex components display a mosaic of evolutionary histories: a core set of highly conserved genes, together with sets displaying lineage specific innovations. Although focused on CM, this study provides a template for differentiating those genes which are likely to retain their functions and interactions across species. As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems.
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Affiliation(s)
- Tuan On
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
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223
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Guillemin C, Francastel C. [Heterochromatin compartments and gene silencing: human hematopoietic differentiation as a model study]. Biol Aujourdhui 2010; 204:221-33. [PMID: 20950566 DOI: 10.1051/jbio/2010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Indexed: 11/14/2022]
Abstract
In order to accomplish its differentiation program, the nucleus of a multipotent cell must be sequentially reprogrammed to acquire and maintain new gene expression patterns. When a stem cell is committed to differentiate towards a given lineage, global genome reprogramming involves both repression of non-affiliated genes and selective activation of genes involved in the establishment of the lineage. Accumulating evidence indicates that lineage specific gene expression is determined not only by the availability of specific transcription factors, but also by epigenetic modifications including both local modifications of DNA and chromatin structure, as well as global topological changes in chromosomes and genes positioning in the nucleus. Combined, these different levels of gene regulation allow for fine controls that integrate environmental and intracellular signals to establish appropriate gene expression programs, and hence ultimately determine the identity of the cell. Therefore, epigenetic modifications most likely precede gene activation and play a critical role in the choices of a stem cell to continue to self-renew or to differentiate. However, the cause-effect relationship between chromatin structure, nuclear architecture and cell-fate decisions is still a matter of debate. The pericentromeric heterochromatin compartment will be presented as one of the best studied examples to understand the impact of and positioning of a gene on its transcription. We will set the influence of heterochromatin compartments in the context of hematopoietic differentiation of human multipotent progenitors.
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Affiliation(s)
- Claire Guillemin
- CNRS, Université Paris Diderot, UMR7216, Épigénétique et Destin Cellulaire, Paris, France
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224
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Narayan PJ, Dragunow M. High content analysis of histone acetylation in human cells and tissues. J Neurosci Methods 2010; 193:54-61. [DOI: 10.1016/j.jneumeth.2010.08.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/26/2010] [Accepted: 08/26/2010] [Indexed: 11/26/2022]
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225
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Abstract
HDAC, by modifiing relations between DNA and histones, are major proteins of the epigenetic regulation. They play part in the signal transduction and in many cellular processes: cell cycle control, apoptosis, protein degradation, angiogenesis, invasion and cell motility. In several models of cancer HDAC inhibitors (HDACIs) are able to up regulate tumor suppressing gene (p53, p21, pRB...) and to down regulate oncogenes (SRC, HIF-Ialpha,HER2...). Many inhibitors are currently in clinical development and promising results have been reported in cutaneous T cell lymphoma, Hodgkin's disease and non-hodgkin lymphoma. Combination with chemotherapy and molecular targeted agents seem to be effective in myeloma, lung cancer and myeloïd neoplasms. In this review, we focus on recent biologic and clinical data that highlitght the anti-neoplastic role of HDACIs.
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226
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Yamamoto D, Shima K, Matsuo K, Nishioka T, Chen CY, Hu GF, Sasaki A, Tsuji T. Ornithine decarboxylase antizyme induces hypomethylation of genome DNA and histone H3 lysine 9 dimethylation (H3K9me2) in human oral cancer cell line. PLoS One 2010; 5:e12554. [PMID: 20838441 PMCID: PMC2933235 DOI: 10.1371/journal.pone.0012554] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 07/31/2010] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Methylation of CpG islands of genome DNA and lysine residues of histone H3 and H4 tails regulates gene transcription. Inhibition of polyamine synthesis by ornithine decarboxylase antizyme-1 (OAZ) in human oral cancer cell line resulted in accumulation of decarboxylated S-adenosylmethionine (dcSAM), which acts as a competitive inhibitor of methylation reactions. We anticipated that accumulation of dcSAM impaired methylation reactions and resulted in hypomethylation of genome DNA and histone tails. METHODOLOGY/PRINCIPAL FINDINGS Global methylation state of genome DNA and lysine residues of histone H3 and H4 tails were assayed by Methylation by Isoschizomers (MIAMI) method and western blotting, respectively, in the presence or absence of OAZ expression. Ectopic expression of OAZ mediated hypomethylation of CpG islands of genome DNA and histone H3 lysine 9 dimethylation (H3K9me2). Protein level of DNA methyltransferase 3B (DNMT3B) and histone H3K9me specific methyltransferase G9a were down-regulated in OAZ transfectant. CONCLUSIONS/SIGNIFICANCE OAZ induced hypomethylation of CpG islands of global genome DNA and H3K9me2 by down-regulating DNMT3B and G9a protein level. Hypomethylation of CpG islands of genome DNA and histone H3K9me2 is a potent mechanism of induction of the genes related to tumor suppression and DNA double strand break repair.
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Affiliation(s)
- Daisuke Yamamoto
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Oral and Maxillofacial Surgery, Okayama University Graduate School, Okayama, Japan
| | - Kaori Shima
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kou Matsuo
- Division of Oral Pathology, Department of Biosciences, Kyushu Dental College, Kitakyushu, Japan
| | - Takashi Nishioka
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chang Yan Chen
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Guo-fu Hu
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Akira Sasaki
- Department of Oral and Maxillofacial Surgery, Okayama University Graduate School, Okayama, Japan
| | - Takanori Tsuji
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
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227
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Requirement for the phospho-H2AX binding module of Crb2 in double-strand break targeting and checkpoint activation. Mol Cell Biol 2010; 30:4722-31. [PMID: 20679488 DOI: 10.1128/mcb.00404-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Activation of DNA damage checkpoints requires the rapid accumulation of numerous factors to sites of genomic lesions, and deciphering the mechanisms of this targeting is central to our understanding of DNA damage response. Histone modification has recently emerged as a critical element for the correct localization of damage response proteins, and one key player in this context is the fission yeast checkpoint mediator Crb2. Accumulation of Crb2 at ionizing irradiation-induced double-strand breaks (DSBs) requires two distinct histone marks, dimethylated H4 lysine 20 (H4K20me2) and phosphorylated H2AX (pH2AX). A tandem tudor motif in Crb2 directly binds H4K20me2, and this interaction is required for DSB targeting and checkpoint activation. Similarly, pH2AX is required for Crb2 localization to DSBs and checkpoint control. Crb2 can directly bind pH2AX through a pair of C-terminal BRCT repeats, but the functional significance of this binding has been unclear. Here we demonstrate that loss of its pH2AX-binding activity severely impairs the ability of Crb2 to accumulate at ionizing irradiation-induced DSBs, compromises checkpoint signaling, and disrupts checkpoint-mediated cell cycle arrest. These impairments are similar to that reported for abolition of pH2AX or mutation of the H4K20me2-binding tudor motif of Crb2. Intriguingly, a combined ablation of its two histone modification binding modules yields a strikingly additive reduction in Crb2 activity. These observations argue that binding of the Crb2 BRCT repeats to pH2AX is critical for checkpoint activity and provide new insight into the mechanisms of chromatin-mediated genome stability.
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228
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Sugimura K, Fukushima Y, Ishida M, Ito S, Nakamura M, Mori Y, Okumura K. Cell cycle-dependent accumulation of histone H3.3 and euchromatic histone modifications in pericentromeric heterochromatin in response to a decrease in DNA methylation levels. Exp Cell Res 2010; 316:2731-46. [PMID: 20599948 DOI: 10.1016/j.yexcr.2010.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 06/21/2010] [Accepted: 06/21/2010] [Indexed: 01/08/2023]
Abstract
In mammals, DNA methylation is an important epigenetic mark that is associated with gene silencing, particularly in constitutive heterochromatin. However, the effect of DNA methylation on other epigenetic properties of chromatin is controversial. In this study, we show that inhibition of DNA methylation in mouse fibroblast cells affects histone modification and the subnuclear localization of histone H3.3 in a cell cycle-dependent manner. Using a DNA methyltransferase (Dnmt) inhibitor 5-aza-2'-deoxycytidine (5-aza-dC), we found that reduced levels of DNA methylation were associated with the activation of transcription from centromeric and pericentromeric satellite repeats. The de-repressed pericentromeric chromatin was enriched in euchromatic histone modifications such as acetylation of histone H4, and di- and tri-methylation of lysine 4 on histone H3. Spatio-temporal analysis showed that the accumulation of these euchromatic histone modifications occurred during the second S phase following 5-aza-dC treatment, corresponding precisely with a shift in replication timing of the pericentromeric satellite repeats from middle/late S phase to early S phase. Moreover, we found that histone H3.3 was deposited on the pericentromeric heterochromatin prior to the accumulation of the euchromatic histone modifications. These results suggest that DNA CpG methylation is essential for the proper organization of pericentromeric heterochromatin in differentiated mouse cells.
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Affiliation(s)
- Kazuto Sugimura
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie, Japan.
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229
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Abstract
Epigenetic mechanisms, such as DNA methylation and histone modifications, drive stable, clonally propagated changes in gene expression and can therefore serve as molecular mediators of pathway dysfunction in neoplasia. Myelodysplastic syndrome (MDS) is characterized by frequent epigenetic abnormalities, including the hypermethylation of genes that control proliferation, adhesion, and other characteristic features of this leukemia. Aberrant DNA hypermethylation is associated with a poor prognosis in MDS that can be accounted for by more rapid progression to acute myeloid leukemia. In turn, treatment with drugs that modify epigenetic pathways (DNA methylation and histone deacetylation inhibitors) induces durable remissions and prolongs life in MDS, offering some hope and direction in the future management of this deadly disease.
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Affiliation(s)
- Jean-Pierre Issa
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
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230
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Rekowski MVW, Giannis A. Histone acetylation modulation by small molecules: a chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:760-7. [PMID: 20493978 DOI: 10.1016/j.bbagrm.2010.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Accepted: 05/08/2010] [Indexed: 12/18/2022]
Abstract
Histone acetyltransferases (HATs) are enzymes able to acetylate lysine side chains of histones. They play essential roles in normal cell function as well as in pathogenesis of a broad set of diseases, including multiple cancers, HIV, diabetes mellitus, and neurodegenerative disorders. Moreover, several HATs are able to acetylate various non-histone protein substrates e.g. transcription factors, enzymes involved in glycolysis, fatty acid and glycogen metabolism, the tricarboxylic acid and urea cycles, suggesting that lysine acetylation represents an important regulatory mechanism similar to protein phosphorylation. Small molecule inhibitors of histone acetyltransferases have been developed in the last years and proved to be powerful tools to provide new insights into the mechanisms and the role of protein acetylation in gene regulation. This article highlights recent advances in the development of small molecule modulators of histone acetyltransferases.
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Affiliation(s)
- Margarete von Wantoch Rekowski
- Department of Chemistry and Mineralogy, Institute for Organic Chemistry, University of Leipzig, Johannisallee 29, D-04103 Leipzig, Germany
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231
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Nair TM. Sequence periodicity in nucleosomal DNA and intrinsic curvature. BMC STRUCTURAL BIOLOGY 2010; 10 Suppl 1:S8. [PMID: 20487515 PMCID: PMC2873831 DOI: 10.1186/1472-6807-10-s1-s8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. RESULTS Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. CONCLUSIONS The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.
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Affiliation(s)
- T Murlidharan Nair
- Department of Biological sciences, Indiana University South Bend, 1700 Mishawaka Ave, South Bend, IN-46634, USA.
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232
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Füllgrabe J, Hajji N, Joseph B. Cracking the death code: apoptosis-related histone modifications. Cell Death Differ 2010; 17:1238-43. [PMID: 20467440 DOI: 10.1038/cdd.2010.58] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The degradation and compaction of chromatin are long-standing hallmark features of apoptosis. The histones, chief protein components of chromatin, are subjected to a wide range of post-translational modifications. An increasing body of evidence suggests that combinations of epigenetic histone modifications influence the overall chromatin structure and have clear functional consequences in cellular processes including apoptosis. This review describes the work to date on the post-translational modification of histones during apoptosis, their regulation by enzymatic complexes and discusses the existence of the apoptotic histone code.
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Affiliation(s)
- J Füllgrabe
- Department of Oncology Pathology, Cancer Centrum Karolinska, Karolinska Institutet, Stockholm, Sweden
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233
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Abstract
Aging is a multifaceted process characterized by genetic and epigenetic changes in the genome. The genetic component of aging received initially all of the attention. Telomere attrition and accumulation of mutations due to a progressive deficiency in the repair of DNA damage with age remain leading causes of genomic instability. However, epigenetic mechanisms have now emerged as key contributors to the alterations of genome structure and function that accompany aging. The three pillars of epigenetic regulation are DNA methylation, histone modifications, and noncoding RNA species. Alterations of these epigenetic mechanisms affect the vast majority of nuclear processes, including gene transcription and silencing, DNA replication and repair, cell cycle progression, and telomere and centromere structure and function. Here, we summarize the lines of evidence indicating that these epigenetic defects might represent a major factor in the pathophysiology of aging and aging-related diseases, especially cancer.
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Affiliation(s)
- Susana Gonzalo
- Radiation and Cancer Biology Division, Dept. of Radiation Oncology, Washington Univ. School of Medicine, 4511 Forest Park, St. Louis, MO 63108, USA.
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Odd-skipped related 2 is epigenetically regulated in cellular quiescence. Biochem Biophys Res Commun 2010; 396:831-6. [PMID: 20450884 DOI: 10.1016/j.bbrc.2010.04.159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 11/20/2022]
Abstract
Cellular behavior and development are extensively altered during the transition from cell cycle into quiescence, though the mechanism involved in establishing and maintaining quiescence is largely unknown. We found that Odd-skipped related 2 (Osr2) was up-regulated during cellular quiescence by serum starvation as well as culturing to confluence. To investigate the regulatory mechanism of Osr2 under these conditions, we characterized the mouse Osr2 promoter. CpG islands in the flanking region of the transcription start site were predominantly methylated in exponentially growing cells, resulting in silencing of Osr2 expression. In addition, CpG demethylation in quiescence caused activation of Osr2 expression, while acetylation of the H3 and H4 histones during quiescence also led to an increase in Osr2 expression. These results suggest that epigenetically regulated Osr2 plays an important role in cellular quiescence and proliferation.
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Repression of IP-10 by interactions between histone deacetylation and hypermethylation in idiopathic pulmonary fibrosis. Mol Cell Biol 2010; 30:2874-86. [PMID: 20404089 DOI: 10.1128/mcb.01527-09] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Targeted repression of a subset of key genes involved in tissue remodeling is a cardinal feature of idiopathic pulmonary fibrosis (IPF). The mechanism is unclear but is potentially important in disease pathogenesis and therapeutic targeting. We have previously reported that defective histone acetylation is responsible for the repression of the antifibrotic cyclooxygenase-2 gene. Here we extended our study to the repression of another antifibrotic gene, the potent angiostatic chemokine gamma interferon (IFN-gamma)-inducible protein of 10 kDa (IP-10), in lung fibroblasts from patients with IPF. We revealed that this involved not only histone deacetylation, as with cyclooxygenase-2 repression, but also histone H3 hypermethylation, as a result of decreased recruitment of histone acetyltransferases and increased presence of histone deacetylase (HDAC)-containing repressor complexes, histone methyltransferases G9a and SUV39H1, and heterochromatin protein 1 at the IP-10 promoter, leading to reduced transcription factor binding. More importantly, treatment of diseased cells with HDAC or G9a inhibitors similarly reversed the repressive histone deacetylation and hypermethylation and restored IP-10 expression. These findings strongly suggest that epigenetic dysregulation involving interactions between histone deacetylation and hypermethylation is responsible for targeted repression of IP-10 and potentially other antifibrotic genes in fibrotic lung disease and that this is amenable to therapeutic targeting.
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Maltepe E, Bakardjiev AI, Fisher SJ. The placenta: transcriptional, epigenetic, and physiological integration during development. J Clin Invest 2010; 120:1016-25. [PMID: 20364099 DOI: 10.1172/jci41211] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The placenta provides critical transport functions between the maternal and fetal circulations during intrauterine development. Formation of this interface relies on coordinated interactions among transcriptional, epigenetic, and environmental factors. Here we describe these mechanisms in the context of the differentiation of placental cells (trophoblasts) and synthesize current knowledge about how they interact to generate a functional placenta. Developing an understanding of these pathways contributes to an improvement of our models for studying trophoblast biology and sheds light on the etiology of pregnancy complications and the in utero programming of adult diseases.
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Affiliation(s)
- Emin Maltepe
- Department of Pediatrics, Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, 513 Parnassus Ave. HSE-1401, Box 1346, San Francisco, CA 94143-1346, USA.
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RCC1 uses a conformationally diverse loop region to interact with the nucleosome: a model for the RCC1-nucleosome complex. J Mol Biol 2010; 398:518-29. [PMID: 20347844 DOI: 10.1016/j.jmb.2010.03.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 02/24/2010] [Accepted: 03/19/2010] [Indexed: 01/15/2023]
Abstract
The binding of RCC1 (regulator of chromosome condensation 1) to chromatin is critical for cellular processes such as mitosis, nucleocytoplasmic transport, and nuclear envelope formation because RCC1 recruits the small GTPase Ran (Ras-related nuclear protein) to chromatin and sets up a Ran-GTP gradient around the chromosomes. However, the molecular mechanism by which RCC1 binds to nucleosomes, the repeating unit of chromatin, is not known. We have used biochemical approaches to test structural models for how the RCC1 beta-propeller protein could bind to the nucleosome. In contrast to the prevailing model, RCC1 does not appear to use the beta-propeller face opposite to its Ran-binding face to interact with nucleosomes. Instead, we find that RCC1 uses a conformationally flexible loop region we have termed the switchback loop in addition to its N-terminal tail to bind to the nucleosome. The juxtaposition of the RCC1 switchback loop to its Ran binding surface suggests a novel mechanism for how nucleosome-bound RCC1 recruits Ran to chromatin. Furthermore, this model accounts for previously unexplained observations for how Ran can interact with the nucleosome both dependent and independent of RCC1 and how binding of the nucleosome can enhance RCC1's Ran nucleotide exchange activity.
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238
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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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239
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Kapoor P, Kumar A, Naik R, Ganguli M, Siddiqi MI, Sahasrabuddhe AA, Gupta CM. Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase. Nucleic Acids Res 2010; 38:3308-17. [PMID: 20147461 PMCID: PMC2879525 DOI: 10.1093/nar/gkq051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leishmania actin (LdACT) is an unconventional form of eukaryotic actin in that it markedly differs from other actins in terms of its filament forming as well as toxin and DNase-1-binding properties. Besides being present in the cytoplasm, cortical regions, flagellum and nucleus, it is also present in the kinetoplast where it appears to associate with the kinetoplast DNA (kDNA). However, nothing is known about its role in this organelle. Here, we show that LdACT is indeed associated with the kDNA disc in Leishmania kinetoplast, and under in vitro conditions, it specifically binds DNA primarily through electrostatic interactions involving its unique DNase-1-binding region and the DNA major groove. We further reveal that this protein exhibits DNA-nicking activity which requires its polymeric state as well as ATP hydrolysis and through this activity it converts catenated kDNA minicircles into open form. In addition, we show that LdACT specifically binds bacterial type II topoisomerase and inhibits its decatenation activity. Together, these results strongly indicate that LdACT could play a critical role in kDNA remodeling.
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Affiliation(s)
- Prabodh Kapoor
- Division of Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil Palace, CSIR, Lucknow 226001, India
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Sinha B, Bhattacharya D, Sinha DK, Talwar S, Maharana S, Gupta S, Shivashankar G. Dynamic Organization of Chromatin Assembly and Transcription Factories in Living Cells. Methods Cell Biol 2010; 98:57-78. [DOI: 10.1016/s0091-679x(10)98003-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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242
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Lu Z, Scott I, Webster BR, Sack MN. The emerging characterization of lysine residue deacetylation on the modulation of mitochondrial function and cardiovascular biology. Circ Res 2009; 105:830-41. [PMID: 19850949 DOI: 10.1161/circresaha.109.204974] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is emerging recognition of a novel fuel and redox sensing regulatory program that controls cellular adaptation via nonhistone protein lysine residue acetyl posttranslation modifications. This program functions in tissues with high energy demand and oxidative capacity and is highly enriched in the heart. Deacetylation is regulated by NAD(+)-dependent activation of the sirtuin family of proteins, whereas acetyltransferase modifications are controlled by less clearly delineated acetyltransferases. Subcellular localization specific protein targets of lysine-acetyl modification have been identified in the nucleus, cytoplasm, and mitochondria. Despite distinct subcellular localizations, these modifications appear, in large part, to modify mitochondrial properties including respiration, energy production, apoptosis, and antioxidant defenses. These mitochondrial regulatory programs are important in cardiovascular biology, although how protein acetyl modifications effects cardiovascular pathophysiology has not been extensively explored. This review will introduce the role of nonhistone protein lysine residue acetyl modifications, discuss their regulation and biochemistry and present the direct and indirect data implicating their involvement in the heart and vasculature.
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Affiliation(s)
- Zhongping Lu
- Translational Medicine Branch, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
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243
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Buranapramest M, Chakravarti D. Chromatin remodeling and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:193-234. [PMID: 20374705 DOI: 10.1016/s1877-1173(09)87006-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nuclear receptors (NRs) constitute a large family of ligand-dependent transcription factors that play key roles in development, differentiation, metabolism, and homeostasis. They participate in these processes by coordinating and regulating the expression of their target genes. The eukaryotic genome is packaged as chromatin and is generally inhibitory to the process of transcription. NRs overcome this barrier by recruiting two classes of chromatin remodelers, histone modifying enzymes and ATP-dependent chromatin remodelers. These remodelers alter chromatin structure at target gene promoters by posttranslational modification of histone tails and by disrupting DNA-histone interactions, respectively. In the presence of ligand, NRs promote transcription by recruiting remodeling enzymes that increase promoter accessibility to the basal transcription machinery. In the absence of ligand a subset of NRs recruit remodelers that establish and maintain a closed chromatin environment, to ensure efficient gene silencing. This chapter reviews the chromatin remodeling enzymes associated with NR gene control, with an emphasis on the mechanisms of NR-mediated repression.
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Affiliation(s)
- Manop Buranapramest
- Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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244
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Elias MC, Nardelli SC, Schenkman S. Chromatin and nuclear organization in Trypanosoma cruzi. Future Microbiol 2009; 4:1065-74. [DOI: 10.2217/fmb.09.74] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A total of 100 years have passed since the discovery of the protozoan Trypanosoma cruzi, the etiologic agent of Chagas’ disease. Since its discovery, the molecular and cellular biology of this early divergent eukaryote, as well as its interactions with the mammalian and insect hosts, has progressed substantially. It is now clear that this parasite presents unique mechanisms controlling gene expression, DNA replication, cell cycle and differentiation, generating several morphological forms that are adapted to survive in different hosts. In recent years, the relationship between the chromatin structure and nuclear organization with the unusual transcription, splicing, DNA replication and DNA repair mechanisms have been investigated in T. cruzi. This article reviews the relevant aspects of these mechanisms in relation to chromatin and nuclear organization.
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Affiliation(s)
| | - Sheila Cristina Nardelli
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, R. Botucatu 862 8a, 04023-062 São Paulo, Brazil
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, R. Botucatu 862 8a, 04023-062 São Paulo, Brazil
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Trelle MB, Salcedo-Amaya AM, Cohen AM, Stunnenberg HG, Jensen ON. Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum. J Proteome Res 2009; 8:3439-50. [PMID: 19351122 DOI: 10.1021/pr9000898] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational modifications (PTMs) of histone tails play a key role in epigenetic regulation of gene expression in a range of organisms from yeast to human; however, little is known about histone proteins from the parasite that causes malaria in humans, Plasmodium falciparum. We characterized P. falciparum histone PTMs using advanced mass spectrometry driven proteomics. Acid-extracted proteins were resolved in SDS-PAGE, in-gel trypsin digested, and analyzed by reversed-phase LC-MS/MS. Through the combination of Q-TOF and LTQ-FT mass spectrometry we obtained high mass accuracy of both precursor and fragment ions, which is a prerequisite for high-confidence identifications of multisite peptide modifications. We utilize MS/MS fragment marker ions to validate the identification of histone modifications and report the m/z 143 ion as a novel MS/MS marker ion for monomethylated lysine. We identified all known P. falciparum histones and mapped 44 different modifications, providing a comprehensive view of epigenetic marks in the parasite. Interestingly, the parasite exhibits a histone modification pattern that is distinct from its human host. A general preponderance for modifications associated with a transcriptionally permissive state was observed. Additionally, a novel differentiation in the modification pattern of the two histone H2B variants (H2B and H2Bv) was observed, suggesting divergent functions of the two H2B variants in the parasite. Taken together, our results provide a first comprehensive map of histone modifications in P. falciparum and highlight the utility of tandem MS for detailed analysis of peptides containing multiple PTMs.
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Affiliation(s)
- Morten B Trelle
- Department of Biochemistry and Molecular Biology, Protein Research Group, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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246
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Blanquet PR, Mariani J, Fournier B. Temporal assessment of histone H3 phospho-acetylation and casein kinase 2 activation in dentate gyrus from ischemic rats. Brain Res 2009; 1302:10-20. [PMID: 19765564 DOI: 10.1016/j.brainres.2009.09.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 08/31/2009] [Accepted: 09/08/2009] [Indexed: 11/30/2022]
Abstract
Hippocampal dentate gyrus possesses an exceptional capacity of adaptation to ischemic insults. Recently, using a transient global ischemic model in the adult rat, we identified a neuroprotective signalling cascade in the dentate gyrus involving calcium/calmodulin-dependent protein kinase IV (CaMKIV), cyclic AMP response element (CRE)-binding protein (CREB) and brain-derived neurotrophic factor (BDNF), a major regulator of survival. We have shown that intracerebroventricular injections of anti-BDNF and anti-CREB are sufficient to cause substantial tissular damages and apoptotic deaths in late periods (48-72 h) after ischemia. Herein, we provide immunohistochemical and biochemical evidence that antibody-induced impairment of the protective CaMKIV/CREB/BDNF pathway induces an apparent duality of response in the dentate gyrus. The experimental protocol is performed as follows: (a) rats are anesthetized and vertebral arteries are occluded by electrocauterization; (b) on the following day, transient global ischemia is produced by occlusion of carotid arteries for 25 min; (c) finally, rats are infused with the pharmacologic agents into the left cerebral ventricle and then perfusion-fixed at different time points after ischemia for immunohistochemical and immunoblotting analyses. After infusion with anti-CaMKIV, phosphorylation of mitogen-activated protein kinases (MAPK) MKK3, MKK6 and p38 and phospho-acetylation of histone H3 occur at 6 h after ischemia without presence of any caspase-9 activation and cellular injuries. In contrast, infusion of anti-BDNF or anti-CREB surprisingly results in a remarkable stimulation of casein kinase 2 (CK2) and caspase-9 activities at 48-72 h post-insult. This is accompanied by the disappearance of phosphorylation of MKK(3/6) and p38 and phospho-acetylation of histone H3. These results suggest that: (1) activation of a MKK(3/6)/p38/H3 cascade at early periods post-ischemia may be capable of causing a short transient protective effect in the dentate gyrus; (2) CK2 might be implicated in inhibition of activity of molecules such as MKK(3/6), p38 and deacetylases at late periods post-insult, thereby promoting injuries and cell deaths in the dentate cell layer.
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Affiliation(s)
- P R Blanquet
- Laboratoire Développement et Vieillissement du Système Nerveux, UMR 7102 CNRS-UPMC (Neurobiologie des Processus Adaptatifs), Université P & M Curie, 9 Quai Saint-Bernard, Bâtiment B, 4(e)Etage, Boîte 14, 75005, Paris, France.
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247
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FoxA1 binding directs chromatin structure and the functional response of a glucocorticoid receptor-regulated promoter. Mol Cell Biol 2009; 29:5413-25. [PMID: 19687299 DOI: 10.1128/mcb.00368-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Reconstitution of the glucocorticoid receptor (GR)-regulated mouse mammary tumor virus (MMTV) promoter in Xenopus oocytes was used to monitor the effects of different transcription factor contexts. Three constitutively binding factors, nuclear factor 1 (NF1), octamer transcription factor 1 (Oct1), and the Forkhead box A1 (FoxA1), were shown to act in concert, to direct the chromatin structure, and to enhance the GR response. FoxA1 has a dominant effect in the absence of hormone and induces a cluster of DNase I-hypersensitive sites in the segment comprising bp -400 to +25. This FoxA1-mediated chromatin remodeling does not induce MMTV transcription, as opposed to that of the GR. However, the robust FoxA1-dependent chromatin opening has the following drastic functional consequences on the hormone regulation: (i) GR-DNA binding is facilitated, as revealed by dimethyl sulfate in vivo footprinting, leading to increased hormone-induced transcription, and (ii) the GR antagonist RU486 is converted into a partial agonist in the presence of FoxA1 via ligand-independent GR activation. We conclude that FoxA1 mediates a preset chromatin structure and directs a context-specific response of a nuclear receptor. Furthermore, the alternative nucleosome arrangement induced by GR and FoxA1 implies this to be determined by constitutive binding of transcription factors rather than by the DNA sequence itself.
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248
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Probing structural stability of chromatin assembly sorted from living cells. Biochem Biophys Res Commun 2009; 385:518-22. [DOI: 10.1016/j.bbrc.2009.05.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 05/18/2009] [Indexed: 11/20/2022]
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249
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Wu T, Yuan T, Tsai SN, Wang C, Sun SM, Lam HM, Ngai SM. Mass spectrometry analysis of the variants of histone H3 and H4 of soybean and their post-translational modifications. BMC PLANT BIOLOGY 2009; 9:98. [PMID: 19643030 PMCID: PMC2732622 DOI: 10.1186/1471-2229-9-98] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 07/31/2009] [Indexed: 05/21/2023]
Abstract
BACKGROUND Histone modifications and histone variants are of importance in many biological processes. To understand the biological functions of the global dynamics of histone modifications and histone variants in higher plants, we elucidated the variants and post-translational modifications of histones in soybean, a legume plant with a much bigger genome than that of Arabidopsis thaliana. RESULTS In soybean leaves, mono-, di- and tri-methylation at Lysine 4, Lysine 27 and Lysine 36, and acetylation at Lysine 14, 18 and 23 were detected in HISTONE H3. Lysine 27 was prone to being mono-methylated, while tri-methylation was predominant at Lysine 36. We also observed that Lysine 27 methylation and Lysine 36 methylation usually excluded each other in HISTONE H3. Although methylation at HISTONE H3 Lysine 79 was not reported in A. thaliana, mono- and di-methylated HISTONE H3 Lysine 79 were detected in soybean. Besides, acetylation at Lysine 8 and 12 of HISTONE H4 in soybean were identified. Using a combination of mass spectrometry and nano-liquid chromatography, two variants of HISTONE H3 were detected and their modifications were determined. They were different at positions of A31F41S87S90 (HISTONE variant H3.1) and T31Y41H87L90 (HISTONE variant H3.2), respectively. The methylation patterns in these two HISTONE H3 variants also exhibited differences. Lysine 4 and Lysine 36 methylation were only detected in HISTONE H3.2, suggesting that HISTONE variant H3.2 might be associated with actively transcribing genes. In addition, two variants of histone H4 (H4.1 and H4.2) were also detected, which were missing in other organisms. In the histone variant H4.1 and H4.2, the amino acid 60 was isoleucine and valine, respectively. CONCLUSION This work revealed several distinct variants of soybean histone and their modifications that were different from A. thaliana, thus providing important biological information toward further understanding of the histone modifications and their functional significance in higher plants.
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Affiliation(s)
- Tao Wu
- Department of Biology and State (China) Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Tiezheng Yuan
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Sau-Na Tsai
- Department of Biology and State (China) Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Chunmei Wang
- Department of Biology and State (China) Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Sai-Ming Sun
- Department of Biology and State (China) Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Hon-Ming Lam
- Department of Biology and State (China) Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Sai-Ming Ngai
- Department of Biology and State (China) Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, PR China
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Abstract
The packaging of chromosomal DNA by nucleosomes condenses and organizes the genome, but occludes many regulatory DNA elements. However, this constraint also allows nucleosomes and other chromatin components to actively participate in the regulation of transcription, chromosome segregation, DNA replication, and DNA repair. To enable dynamic access to packaged DNA and to tailor nucleosome composition in chromosomal regions, cells have evolved a set of specialized chromatin remodeling complexes (remodelers). Remodelers use the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes. Here, we address many aspects of remodeler biology: their targeting, mechanism, regulation, shared and unique properties, and specialization for particular biological processes. We also address roles for remodelers in development, cancer, and human syndromes.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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