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Nagda BM, Nguyen VM, White RT. promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:208-214. [PMID: 38051616 DOI: 10.1109/tcbb.2023.3339597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Accurate identification of DNA promoter sequences is of crucial importance in unraveling the underlying mechanisms that regulate gene transcription. Initiation of transcription is controlled through regulatory transcription factors binding to promoter core regions in the DNA sequence. Detection of promoter regions is necessary if we are to build genetic regulatory networks for biomedical and clinical applications, and for identification of rarely expressed genes. We propose a novel ensemble learning technique using deep recurrent neural networks with convolutional feature extraction and hard negative pattern mining to detect several types of promoter sequences, including promoter sequences with the TATA-box and without the TATA-box, within DNA sequences of four different species. Using extensive independent tests and previously published results, we demonstrate that our method sets a new state-of-the-art of over 98% Matthews correlation coefficient in all eight organism categories for recognizing the stretch of base pairs that code for the promoter region within DNA sequences.
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Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P. Tra1 controls the transcriptional landscape of the aging cell. G3 (BETHESDA, MD.) 2022; 13:6782959. [PMID: 36315064 PMCID: PMC9836359 DOI: 10.1093/g3journal/jkac287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
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Affiliation(s)
- Khaleda Afrin Bari
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Present address for Matthew D Berg: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada,Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Corresponding author: Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada.
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Engineering eukaryote-like regulatory circuits to expand artificial control mechanisms for metabolic engineering in Saccharomyces cerevisiae. Commun Biol 2022; 5:135. [PMID: 35173283 PMCID: PMC8850539 DOI: 10.1038/s42003-022-03070-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/20/2022] [Indexed: 12/22/2022] Open
Abstract
Temporal control of heterologous pathway expression is critical to achieve optimal efficiency in microbial metabolic engineering. The broadly-used GAL promoter system for engineered yeast (Saccharomyces cerevisiae) suffers from several drawbacks; specifically, unintended induction during laboratory development, and unintended repression in industrial production applications, which decreases overall production capacity. Eukaryotic synthetic circuits have not been well examined to address these problems. Here, we explore a modularised engineering method to deploy new genetic circuits applicable for expanding the control of GAL promoter-driven heterologous pathways in S. cerevisiae. Trans- and cis- modules, including eukaryotic trans-activating-and-repressing mechanisms, were characterised to provide new and better tools for circuit design. A eukaryote-like tetracycline-mediated circuit that delivers stringent repression was engineered to minimise metabolic burden during strain development and maintenance. This was combined with a novel 37 °C induction circuit to relief glucose-mediated repression on the GAL promoter during the bioprocess. This delivered a 44% increase in production of the terpenoid nerolidol, to 2.54 g L-1 in flask cultivation. These negative/positive transcriptional regulatory circuits expand global strategies of metabolic control to facilitate laboratory maintenance and for industry applications.
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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Zhou S, Feng S, Qin W, Wang X, Tang Y, Yuan S. Epigenetic Regulation of Spermatogonial Stem Cell Homeostasis: From DNA Methylation to Histone Modification. Stem Cell Rev Rep 2020; 17:562-580. [PMID: 32939648 DOI: 10.1007/s12015-020-10044-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
Spermatogonial stem cells(SSCs)are the ultimate germline stem cells with the potential of self-renewal and differentiation, and a dynamic balance of SSCs play an essential role in spermatogenesis. During the gene expression process, genomic DNA and nuclear protein, working together, contribute to SSC homeostasis. Recently, emerging studies have shown that epigenome-related molecules such as chromatin modifiers play an important role in SSC homeostasis through regulating target gene expression. Here, we focus on two types of epigenetic events, including DNA methylation and histone modification, and summarize their function in SSC homeostasis. Understanding the molecular mechanism during SSC homeostasis will promote the recognition of epigenetic biomarkers in male infertility, and bring light into therapies of infertile patients.Graphical Abstract.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, 510500, Guangzhou, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, 510500, Guangzhou, China.
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China. .,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, 518057, China.
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Han Y, Reyes AA, Malik S, He Y. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature 2020; 579:452-455. [PMID: 32188938 PMCID: PMC7319049 DOI: 10.1038/s41586-020-2087-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair1,2. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers3-8, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation9.
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Affiliation(s)
- Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Alexis A Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA
| | - Sara Malik
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.
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Transcriptional Modulation by Idelalisib Synergizes with Bendamustine in Chronic Lymphocytic Leukemia. Cancers (Basel) 2019; 11:cancers11101519. [PMID: 31601046 PMCID: PMC6826782 DOI: 10.3390/cancers11101519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022] Open
Abstract
The phosphatidyl-inositol 3 kinase (PI3K) δ inhibitor, idelalisib (IDE), is a potent inhibitor of the B-cell receptor pathway and a novel and highly effective agent for the treatment of chronic lymphocytic leukemia (CLL). We evaluated the activities of IDE in comparison to bendamusine (BEN), a commonly used alkylating agent, in primary CLL cells ex vivo. In contrast to BEN, IDE was cytotoxic to cells from extensively-treated patients, including those with a deletion (del)17p. Cross-resistance was not observed between BEN and IDE, confirming their different modes of cytotoxicity. Marked synergy was seen between BEN and IDE, even in cases that were resistant to BEN or IDE individually, and those with deletion (del) 17p. CD40L/interleukin 4 (IL4) co-treatment mimicking the CLL microenvironment increased resistance to IDE, but synergy was retained. PI3Kδ-deficient murine splenic B cells were more resistant to IDE and showed reduced synergy with BEN, thus confirming the importance of functional PI3Kδ protein. Although IDE was observed to induce γH2AX, IDE did not enhance activation of the DNA damage response nor DNA repair activity. Interestingly, IDE decreased global RNA synthesis and was antagonistic with 5,6-Dichlorobenzimidazole 1-b-D-ribofuranoside (DRB), an inhibitor of transcription. These findings add to the increasingly complex cellular effects of IDE, and B cell receptor (BCR) inhibitors in general, in CLL.
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Epigenetics and innate immunity: the ‘unTolld’ story. Immunol Cell Biol 2016; 94:631-9. [DOI: 10.1038/icb.2016.24] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 12/19/2022]
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Kuan CS, See Too WC, Few LL. Sp1 and Sp3 Are the Transcription Activators of Human ek1 Promoter in TSA-Treated Human Colon Carcinoma Cells. PLoS One 2016; 11:e0147886. [PMID: 26807725 PMCID: PMC4725723 DOI: 10.1371/journal.pone.0147886] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 01/08/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ethanolamine kinase (EK) catalyzes the phosphorylation of ethanolamine, the first step in the CDP-ethanolamine pathway for the biosynthesis of phosphatidylethanolamine (PE). Human EK exists as EK1, EK2α and EK2β isoforms, encoded by two separate genes, named ek1 and ek2. EK activity is stimulated by carcinogens and oncogenes, suggesting the involvement of EK in carcinogenesis. Currently, little is known about EK transcriptional regulation by endogenous or exogenous signals, and the ek gene promoter has never been studied. METHODOLOGY/PRINCIPAL FINDINGS In this report, we mapped the important regulatory regions in the human ek1 promoter. 5' deletion analysis and site-directed mutagenesis identified a Sp site at position (-40/-31) that was essential for the basal transcription of this gene. Treatment of HCT116 cells with trichostatin A (TSA), a histone deacetylase inhibitor, significantly upregulated the ek1 promoter activity through the Sp(-40/-31) site and increased the endogenous expression of ek1. Chromatin immunoprecipitation assay revealed that TSA increased the binding of Sp1, Sp3 and RNA polymerase II to the ek1 promoter in HCT116 cells. The effect of TSA on ek1 promoter activity was cell-line specific as TSA treatment did not affect ek1 promoter activity in HepG2 cells. CONCLUSION/SIGNIFICANCE In conclusion, we showed that Sp1 and Sp3 are not only essential for the basal transcription of the ek1 gene, their accessibility to the target site on the ek1 promoter is regulated by histone protein modification in a cell line dependent manner.
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Affiliation(s)
- Chee Sian Kuan
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Wei Cun See Too
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ling Ling Few
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
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Comparative molecular genetic analysis of simian and human HIV-1 integrase interactor INI1/SMARCB1/SNF5. Arch Virol 2015; 160:3085-91. [PMID: 26350979 DOI: 10.1007/s00705-015-2585-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
Human integrase interactor 1 (INI1/SMARCB1/SNF5) is a chromatin-remodeling molecule that binds to HIV-1 integrase and enhances proviral DNA integration. INI1 is also known as a tumor suppressor gene and has been found to be mutated in several aggressive tumors such as rhabdoid and lymphoid tumors. To study the function of simian INI1, we screened and cloned simian INI1 cDNA from B lymphoma cells of rhesus monkeys using RT-PCR. Sequence analysis showed 23 single nucleotide differences compared to the human ortholog, which, however, did not result in amino acid changes, and the amino acid sequence is therefore 100% conserved between human and simian INI1. Two alternatively spliced isoforms, INI1a and INI1b, were also found in simian INI1. These two isoforms did not show any functional difference in HIV-1 proviral DNA integration and nuclear localization, suggesting that the specificity of simian INI1 would not be a factor preventing HIV-1 infection of a simian host. Nevertheless, INI1b is expressed only in established cancer cell lines such as Jurkat and COS-7 cells, and not in primary cells, suggesting that INIlb could be an indicator of cell transformation.
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11
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Freeman MD, Mazu T, Miles JS, Darling-Reed S, Flores-Rozas H. Inactivation of chromatin remodeling factors sensitizes cells to selective cytotoxic stress. Biologics 2014; 8:269-80. [PMID: 25484574 PMCID: PMC4238754 DOI: 10.2147/btt.s67046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The SWI/SNF chromatin-remodeling complex plays an essential role in several cellular processes including cell proliferation, differentiation, and DNA repair. Loss of normal function of the SWI/SNF complex because of mutations in its subunits correlates with tumorigenesis in humans. For many of these cancers, cytotoxic chemotherapy is the primary, and sometimes the only, therapeutic alternative. Among the antineoplastic agents, anthracyclines are a common treatment option. Although effective, resistance to these agents usually develops and serious dose-related toxicity, namely, chronic cardiotoxicity, limits its use. Previous work from our laboratory showed that a deletion of the SWI/SNF factor SNF2 resulted in hypersensitivity to doxorubicin. We further investigated the contribution of other chromatin remodeling complex components in the response to cytotoxic chemotherapy. Our results indicate that, of the eight SWI/SNF strains tested, snf2, taf14, and swi3 were the most sensitive and displayed distinct sensitivity to different cytotoxic agents, while snf5 displayed resistance. Our experimental results indicate that the SWI/SNF complex plays a critical role in protecting cells from exposure to cytotoxic chemotherapy and other cytotoxic agents. Our findings may prove useful in the development of a strategy aimed at targeting these genes to provide an alternative by hypersensitizing cancer cells to chemotherapeutic agents.
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Affiliation(s)
- Miles D Freeman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Tryphon Mazu
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Jana S Miles
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Selina Darling-Reed
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Hernan Flores-Rozas
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA
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Im GI, Shin KJ. Epigenetic approaches to regeneration of bone and cartilage from stem cells. Expert Opin Biol Ther 2014; 15:181-93. [DOI: 10.1517/14712598.2015.960838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Wang B, Kettenbach AN, Gerber SA, Loros JJ, Dunlap JC. Neurospora WC-1 recruits SWI/SNF to remodel frequency and initiate a circadian cycle. PLoS Genet 2014; 10:e1004599. [PMID: 25254987 PMCID: PMC4177678 DOI: 10.1371/journal.pgen.1004599] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 07/13/2014] [Indexed: 12/23/2022] Open
Abstract
In the negative feedback loop comprising the Neurospora circadian oscillator, the White Collar Complex (WCC) formed from White Collar-1 (WC-1) and White Collar-2 (WC-2) drives transcription of the circadian pacemaker gene frequency (frq). Although FRQ-dependent repression of WCC has been extensively studied, the mechanism by which the WCC initiates a circadian cycle remains elusive. Structure/function analysis of WC-1 eliminated domains previously thought to transactivate frq expression but instead identified amino acids 100–200 as essential for frq circadian expression. A proteomics-based search for coactivators with WCC uncovered the SWI/SNF (SWItch/Sucrose NonFermentable) complex: SWI/SNF interacts with WCC in vivo and in vitro, binds to the Clock box in the frq promoter, and is required both for circadian remodeling of nucleosomes at frq and for rhythmic frq expression; interestingly, SWI/SNF is not required for light-induced frq expression. These data suggest a model in which WC-1 recruits SWI/SNF to remodel and loop chromatin at frq, thereby activating frq expression to initiate the circadian cycle. Circadian clocks govern behavior in a wide variety of organisms. These clocks are assembled in such a way that proteins encoded by a few dedicated “clock genes” form a complex that acts to reduce their own expression. That is, the genes and proteins participate in a negative feedback loop, and so long as the feedback has delays built in, this system will oscillate. The feedback loops that underlie circadian rhythms in fungi and animals are quite similar in many ways, and while much is known about the proteins themselves, both those that activate the dedicated clock genes and the clock proteins that repress their own expression, relatively little is known about how the initial expression of the clock genes is activated. In Neurospora, a fungal model for these clocks, the proteins that activate expression of the clock gene “frequency” bind to DNA far away from where the coding part of the gene begins, and a mystery has been how this action-at-a-distance works. The answer revealed here is that the activating proteins recruit other proteins to unwrap the DNA and bring the distal site close to the place where the coding part of the gene begins.
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Affiliation(s)
- Bin Wang
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Arminja N. Kettenbach
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Scott A. Gerber
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Jennifer J. Loros
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biochemistry, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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Lee D, Moon S, Yun J, Kim E, Cheong C, Lee W. NMR and Fluorescence Studies of DNA Binding Domain of INI1/hSNF5. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.9.2753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Tzeng M, du Souich C, Cheung HWH, Boerkoel CF. Coffin-Siris syndrome: phenotypic evolution of a novel SMARCA4 mutation. Am J Med Genet A 2014; 164A:1808-14. [PMID: 24700502 DOI: 10.1002/ajmg.a.36533] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/19/2014] [Indexed: 01/10/2023]
Abstract
Coffin-Siris Syndrome (CSS) is an intellectual disability disorder caused by mutation of components of the SWI/SNF chromatin-remodeling complex. We describe the evolution of the phenotypic features for a male patient with CSS from birth to age 7 years and 9 months and by review of reported CSS patients, we expand the phenotype to include neonatal and infantile hypertonia and upper airway obstruction. The propositus had a novel de novo heterozygous missense mutation in exon 17 of SMARCA4 (NM_001128849.1:c.2434C>T (NP_001122321.1:p.Leu812Phe)). This is the first reported mutation within motif Ia of the SMARCA4 SNF2 domain. In summary, SMARCA4-associated CSS is a pleiotropic disorder in which the pathognomic clinical features evolve and for which the few reported individuals do not demonstrate a clear genotype-phenotype correlation.
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Affiliation(s)
- Michael Tzeng
- NIH Undiagnosed Diseases Program, Common Fund, NIH Office of the Director and NHGRI, Bethesda, Maryland
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Das S, Banerjee B, Hossain M, Thangamuniyandi M, Dasgupta S, Chongdar N, Kumar GS, Basu G. Characterization of DNA binding property of the HIV-1 host factor and tumor suppressor protein Integrase Interactor 1 (INI1/hSNF5). PLoS One 2013; 8:e66581. [PMID: 23861745 PMCID: PMC3701577 DOI: 10.1371/journal.pone.0066581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 05/07/2013] [Indexed: 11/19/2022] Open
Abstract
Integrase Interactor 1 (INI1/hSNF5) is a component of the hSWI/SNF chromatin remodeling complex. The INI1 gene is either deleted or mutated in rhabdoid cancers like ATRT (Atypical terratoid and rhabdoid tumor). INI1 is also a host factor for HIV-1 replication. INI1 binds DNA non-specifically. However, the mechanism of DNA binding and its biological role are unknown. From agarose gel retardation assay (AGRA), Ni-NTA pull-down and atomic force microscopy (AFM) studies we show that amino acids 105-183 of INI1 comprise the minimal DNA binding domain (DBD). The INI1 DBD is absent in plants and in yeast SNF5. It is present in Caenorhabditis elegans SNF5, Drosophila melanogaster homologue SNR1 and is a highly conserved domain in vertebrates. The DNA binding property of this domain in SNR1, that is only 58% identical to INI1/hSNF5, is conserved. Analytical ultracentrifugation studies of INI1 DBD and INI1 DBD:DNA complexes at different concentrations show that the DBD exists as a monomer at low protein concentration and two molecules of monomer binds one molecule of DNA. At high protein concentration, it exists as a dimer and binds two DNA molecules. Furthermore, isothermal calorimetry (ITC) experiments demonstrate that the DBD monomer binds DNA with a stoichiometry (N) of ∼0.5 and Kd = 0.94 µM whereas the DBD dimer binds two DNA molecules sequentially with K'd1 = 222 µM and K'd2 = 1.16 µM. Monomeric DBD binding to DNA is enthalpy driven (ΔH = -29.9 KJ/mole). Dimeric DBD binding to DNA is sequential with the first binding event driven by positive entropy (ΔH'1 = 115.7 KJ/mole, TΔS'1 = 136.8 KJ/mole) and the second binding event driven by negative enthalpy (ΔH'2 = -106.3 KJ/mole, TΔS'2 = -75.7 KJ/mole). Our model for INI1 DBD binding to DNA provides new insights into the mechanism of DNA binding by INI1.
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Affiliation(s)
- Supratik Das
- Department of Biochemistry, University of Calcutta, Kolkata, India.
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Frank R, Sadri N, Bhatti T, Biegel JA, Livolsi VA, Zhang PJ. Proximal-type Epithelioid Sarcoma of the Head and Neck (HN): A Study with Immunohistochemical and Molecular Analysis of SMARCB1. ACTA ACUST UNITED AC 2013; 2. [PMID: 24308011 DOI: 10.4172/2324-9110.1000106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proximal-type epithelioid sarcoma is an aggressive variant of epithelioid sarcoma most often occurring in soft tissues of the proximal limbs, characterized by polygonal cells, marked nuclear atypia, and varied rhabdoid features. Malignant rhabdoid tumor is an aggressive, well characterized entity typically with rhabdoid morphology and involving the kidney of pediatric patients. Rarely, tumors with morphologic and biologic features identical to those in kidney occur in extra-renal sites and are regarded as an extrarenal presentation of the same entity in kidney, named malignant extra-renal rhabdoid tumor. Morphologic and immunophenotypical similarities between proximal-type epithelioid sarcoma and malignant rhabdoid tumor pose a diagnostic challenge and may suggest a relationship between the two. Both tumors are characterized by loss of SMARCB1 (INI1/BAF47/SNF5) expression; however, the molecular events involved differ. Here we describe the immunohistochemical and molecular analysis of three head and neck tumors with morphologic features shared by proximal-type epithelioid sarcoma and malignant rhabdoid tumor. All tumors showed loss of SMARCB1expression. Direct sequencing of the promoter and nine coding exons of SMARCB1, multiplex ligation-dependent probe amplification, and whole genome single nucleotide polymorphism array were performed on the two adult cases and showed only a heterozygous deletion of chromosome 22 in a minority of cells in one of the cases. Though rare, proximal-type epithelioid sarcoma could occur in the head and neck and should be differentiated from other epithelioid tumors by the loss of SMARCB1 expression. The lack of detectable genetic alteration in the SMARCB1 locus in head and neck proximal-type epithelioid sarcoma warrants further investigation into the molecular mechanism underlying loss of SMARCB1 expression.
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Affiliation(s)
- Renee Frank
- Anatomic Pathology, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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18
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Ranneberg-Nilsen T, Rollag H, Slettebakk R, Backe PH, Olsen Ø, Luna L, Bjørås M. The chromatin remodeling factor SMARCB1 forms a complex with human cytomegalovirus proteins UL114 and UL44. PLoS One 2012; 7:e34119. [PMID: 22479537 PMCID: PMC3313996 DOI: 10.1371/journal.pone.0034119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/22/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Human cytomegalovirus (HCMV) uracil DNA glycosylase, UL114, is required for efficient viral DNA replication. Presumably, UL114 functions as a structural partner to other factors of the DNA-replication machinery and not as a DNA repair protein. UL114 binds UL44 (HCMV processivity factor) and UL54 (HCMV-DNA-polymerase). In the present study we have searched for cellular partners of UL114. METHODOLOGY/PRINCIPAL FINDINGS In a yeast two-hybrid screen SMARCB1, a factor of the SWI/SNF chromatin remodeling complex, was found to be an interacting partner of UL114. This interaction was confirmed in vitro by co-immunoprecipitation and pull-down. Immunofluorescence microscopy revealed that SMARCB1 along with BRG-1, BAF170 and BAF155, which are the core SWI/SNF components required for efficient chromatin remodeling, were present in virus replication foci 24-48 hours post infection (hpi). Furthermore a direct interaction was also demonstrated for SMARCB1 and UL44. CONCLUSIONS/SIGNIFICANCE The core SWI/SNF factors required for efficient chromatin remodeling are present in the HCMV replication foci throughout infection. The proteins UL44 and UL114 interact with SMARCB1 and may participate in the recruitment of the SWI/SNF complex to the chromatinized virus DNA. Thus, the presence of the SWI/SNF chromatin remodeling complex in replication foci and its association with UL114 and with UL44 might imply its involvement in different DNA transactions.
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Affiliation(s)
- Toril Ranneberg-Nilsen
- Department of Microbiology, University of Oslo and Oslo University Hospital HF, Oslo, Norway
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19
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Abstract
The reversible acetylation of specific lysine residues on core histones regulates gene transcription in eukaryotes. Since the discovery of GCN5 as the first transcription-regulating histone acetyltransferase (HAT), a variety of HATs have now been identified and shown to acetylate different sites on histones as well as on non-histone proteins, including transcription regulators. In general, purified recombinant HATs expressed in bacteria or in insect cells are able to acetylate free histones and sometimes other substrates in vitro. However, such activity is often restricted to certain substrates and/or is very weak on physiological substrates, such as nucleosomes. Moreover, it does not reflect the actual scenario inside the cell, where HATs generally associate with other proteins to form stable multisubunit complexes. Importantly, these peripheral proteins significantly influence the functions of the catalytic HAT subunit by regulating its intrinsic catalytic activity and/or by modulating its target substrate selectivity. In this chapter, we describe detailed methods for the rapid (two step) and efficient purification of large, multiprotein HAT complexes from nuclear extracts of mammalian epitope-tagged cell lines, including protocols for the generation and large-scale suspension culture of these cell lines. These methods have been used to purify and characterize different human GCN5 HAT complexes that retain activity toward their physiological substrates in vitro.
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20
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Abstract
INTRODUCTION Without any alteration of DNA sequence, heritable changes in gene expression, caused by epigenetic pathways, are gaining a spotlight in research of diseases, and in particular, cancer. Although the dominant paradigm in cancer research, proposed by Vogelstein, suggested that cancer progression was caused by a sequential accumulation of genetic aberrations, basic science studies in epigenetics have now advanced our knowledge enough to apply its concepts and methodology to the study of cancer. In fact, chromatin dynamics and small RNAs are altered far more prevalently in cancer than genetic alterations and most important, can be reversible, lending themselves as attractive therapeutic targets. CONCLUDING REMARKS In the current review, the inactivation of p16 will be utilized as the most prominent example of epigenetic silencing of a tumor suppressor gene in pancreatic cancer. In addition, fundamental insight will be given into why and how epigenetics can be targeted for therapeutic purposes. This knowledge will help the reader in determining the breadth and depth of this field of study with potentially high impact to oncology.
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Affiliation(s)
- Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, 10-24C Guggenheim Building, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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21
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Anamika K, Krebs AR, Thompson J, Poch O, Devys D, Tora L. Lessons from genome-wide studies: an integrated definition of the coactivator function of histone acetyl transferases. Epigenetics Chromatin 2010; 3:18. [PMID: 20961410 PMCID: PMC2972259 DOI: 10.1186/1756-8935-3-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 10/20/2010] [Indexed: 01/24/2023] Open
Abstract
Histone acetylation is one of the key regulatory mechanisms controlling transcriptional activity in eukaryotic cells. In higher eukaryotes, a number of nuclear histone acetyltransferase (HAT) enzymes have been identified, most of which are part of a large multisubunit complex. This diversity, combined with the large number of potentially acetylable lysines on histones, suggested the existence of a specific regulatory mechanism based on the substrate specificity of HATs. Over the past decade, intensive characterisations of the HAT complexes have been carried out. However, the precise mode of action of HATs, and particularly the functional differences amongst these complexes, remains elusive. Here we review current insights into the functional role of HATs, focusing on the specificity of their action. Studies based on biochemical as well as genetic approaches suggested that HATs exert a high degree of specificity in their acetylation spectra and in the cellular processes they regulate. However, a different view emerged recently from genomic approaches that provided genome-wide maps of HAT recruitments. The careful analysis of genomic data suggests that all HAT complexes would be simultaneously recruited to a similar set of loci in the genome, arguing for a low specificity in their function. In this review, we discuss the significance of these apparent contradictions and suggest a new model that integrates biochemical, genetic and genome-wide data to better describe the functional specificity of HAT complexes.
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Affiliation(s)
- Krishanpal Anamika
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France.,Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Arnaud R Krebs
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Julie Thompson
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Olivier Poch
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Didier Devys
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Làszlò Tora
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
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22
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Miki K, Shimizu M, Fujii M, Takayama S, Hossain MN, Ayusawa D. 5-bromodeoxyuridine induces transcription of repressed genes with disruption of nucleosome positioning. FEBS J 2010; 277:4539-48. [PMID: 21040474 DOI: 10.1111/j.1742-4658.2010.07868.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
5-Bromodeoxyuridine (BrdU) modulates the expression of particular genes associated with cellular differentiation and senescence when incorporated into DNA instead of thymidine (dThd). To date, a molecular mechanism for this phenomenon remains a mystery in spite of a large number of studies. Recently, we have demonstrated that BrdU disrupts nucleosome positioning on model plasmids mediated by specific AT-tracts in yeast cells. Here we constructed a cognate plasmid that can form an ordered array of nucleosomes determined by an α2 operator and contains the BAR1 gene as an expression marker gene to examine BAR1 expression in dThd-auxotrophic MATα cells under various conditions. In medium containing dThd, BAR1 expression was completely repressed, associated with the formation of the stable array of nucleosomes. Insertion of AT-tracts into a site of the promoter region slightly increased BAR1 expression and slightly destabilized nucleosome positioning dependent on their sequence specificity. In medium containing BrdU, BAR1 expression was further enhanced, associated with more marked disruption of nucleosome positioning on the promoter region. Disruption of nucleosome positioning seems to be sufficient for full expression of the marker gene if necessary transcription factors are supplied. Incorporation of 5-bromouracil into the plasmid did not weaken the binding of the α2/Mcm1 repressor complex to its legitimate binding site, as revealed by an in vivo UV photofootprinting assay. These results suggest that BrdU increases transcription of repressed genes by disruption of nucleosome positioning around their promoters.
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Affiliation(s)
- Kensuke Miki
- Department of Genome System Science, Yokohama City University, Yokohama, Kanagawa, Japan
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23
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Lu C, Han HD, Mangala LS, Ali-Fehmi R, Newton CS, Ozbun L, Armaiz-Pena GN, Hu W, Stone RL, Munkarah A, Ravoori MK, Shahzad MMK, Lee JW, Mora E, Langley RR, Carroll AR, Matsuo K, Spannuth WA, Schmandt R, Jennings NB, Goodman BW, Jaffe RB, Nick AM, Kim HS, Guven EO, Chen YH, Li LY, Hsu MC, Coleman RL, Calin GA, Denkbas EB, Lim JY, Lee JS, Kundra V, Birrer MJ, Hung MC, Lopez-Berestein G, Sood AK. Regulation of tumor angiogenesis by EZH2. Cancer Cell 2010; 18:185-97. [PMID: 20708159 PMCID: PMC2923653 DOI: 10.1016/j.ccr.2010.06.016] [Citation(s) in RCA: 302] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 02/15/2010] [Accepted: 06/24/2010] [Indexed: 02/03/2023]
Abstract
Although VEGF-targeted therapies are showing promise, new angiogenesis targets are needed to make additional gains. Here, we show that increased Zeste homolog 2 (EZH2) expression in either tumor cells or in tumor vasculature is predictive of poor clinical outcome. The increase in endothelial EZH2 is a direct result of VEGF stimulation by a paracrine circuit that promotes angiogenesis by methylating and silencing vasohibin1 (vash1). Ezh2 silencing in the tumor-associated endothelial cells inhibited angiogenesis mediated by reactivation of VASH1, and reduced ovarian cancer growth, which is further enhanced in combination with ezh2 silencing in tumor cells. Collectively, these data support the potential for targeting ezh2 as an important therapeutic approach.
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Affiliation(s)
- Chunhua Lu
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Hee Dong Han
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Lingegowda S. Mangala
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Rouba Ali-Fehmi
- Department of Pathology, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, MI 48201
| | - Christopher S. Newton
- Department of Cell and Cancer Biology, National Cancer Institute, Bethesda, MD 20892
| | - Laurent Ozbun
- Department of Cell and Cancer Biology, National Cancer Institute, Bethesda, MD 20892
| | - Guillermo N. Armaiz-Pena
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Wei Hu
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Rebecca L. Stone
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Adnan Munkarah
- Women’s Health Services, Henry Ford Health System, Detroit, MI 48202
| | - Murali K. Ravoori
- Department of Experimental Diagnostic Imaging, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 368, Houston, TX 77030
| | - Mian M. K. Shahzad
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
- Baylor College of Medicine, Department of Obstetrics and Gynecology, Houston, TX 77030
| | - Jeong-Won Lee
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 135-710
| | - Edna Mora
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
- Department of Surgery, University of Puerto Rico, San Juan, PR 00935
| | - Robert R. Langley
- Department of Cancer Biology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030
| | - Amy R. Carroll
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Koji Matsuo
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Whitney A. Spannuth
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Rosemarie Schmandt
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Nicholas B. Jennings
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Blake W. Goodman
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Robert B. Jaffe
- Center for Reproductive Sciences, 505 Parnassus, University of California, San Francisco, CA 94143
| | - Alpa M. Nick
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
| | - Hye Sun Kim
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
- Department of Pathology, Cheil General Hospital and Women’s Healthcare Center, Kwandong University College of Medicine, Seoul, Korea 100-380
| | - Eylem Ozturk Guven
- Hacettepe University, Nanotechnology and Nanomedicine Division, Ankara, Turkey 06532
| | - Ya-Huey Chen
- Center for Molecular Medicine, China Medical University and Hospital, Taichung, Taiwan 404
| | - Long-Yuan Li
- Graduate Institute of Cancer Biology, China Medical University and Hospital, Taichung, Taiwan 404
| | - Ming-Chuan Hsu
- Department of Cellular and Molecular Oncology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - Robert L. Coleman
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
- Center for RNAi and Non-Coding RNA, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - George A. Calin
- Center for RNAi and Non-Coding RNA, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
- Department of Experimental Therapeutics, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - Emir B. Denkbas
- Hacettepe University, Nanotechnology and Nanomedicine Division, Ankara, Turkey 06532
| | - Jae Yun Lim
- Department of Systems Biology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - Ju-Seog Lee
- Department of Systems Biology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - Vikas Kundra
- Department of Experimental Diagnostic Imaging, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 368, Houston, TX 77030
| | - Michael J. Birrer
- Department of Medicine, Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA 02114
| | - Mien-Chie Hung
- Center for Molecular Medicine, China Medical University and Hospital, Taichung, Taiwan 404
- Department of Cellular and Molecular Oncology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - Gabriel Lopez-Berestein
- Department of Cancer Biology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030
- Center for RNAi and Non-Coding RNA, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
- Department of Experimental Therapeutics, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
| | - Anil K. Sood
- Department of Gynecologic Oncology, U.T. M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030
- Department of Cancer Biology, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030
- Center for RNAi and Non-Coding RNA, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 950, Houston, TX 77030
- Correspondence and Reprint Requests: Anil K. Sood, Professor, Departments of Gynecologic Oncology and Cancer Biology, The University of Texas, M.D. Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030 Phone: 713-745-5266, Fax: 713-792-7586,
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Herr A, Mckenzie L, Suryadinata R, Sadowski M, Parsons LM, Sarcevic B, Richardson HE. Geminin and Brahma act antagonistically to regulate EGFR-Ras-MAPK signaling in Drosophila. Dev Biol 2010; 344:36-51. [PMID: 20416294 DOI: 10.1016/j.ydbio.2010.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/04/2010] [Accepted: 04/08/2010] [Indexed: 12/21/2022]
Abstract
Geminin was identified in Xenopus as a dual function protein involved in the regulation of DNA replication and neural differentiation. In Xenopus, Geminin acts to antagonize the Brahma (Brm) chromatin-remodeling protein, Brg1, during neural differentiation. Here, we investigate the interaction of Geminin with the Brm complex during Drosophila development. We demonstrate that Drosophila Geminin (Gem) interacts antagonistically with the Brm-BAP complex during wing development. Moreover, we show in vivo during wing development and biochemically that Brm acts to promote EGFR-Ras-MAPK signaling, as indicated by its effects on pERK levels, while Gem opposes this. Furthermore, gem and brm alleles modulate the wing phenotype of a Raf gain-of-function mutant and the eye phenotype of a EGFR gain-of-function mutant. Western analysis revealed that Gem over-expression in a background compromised for Brm function reduces Mek (MAPKK/Sor) protein levels, consistent with the decrease in ERK activation observed. Taken together, our results show that Gem and Brm act antagonistically to modulate the EGFR-Ras-MAPK signaling pathway, by affecting Mek levels during Drosophila development.
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Affiliation(s)
- Anabel Herr
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
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25
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Pohl U, Dean AF, Ichimura K, Liu L, Nicholson J, Cross J, Collins VP. Genomic analysis of chromosome 22 in synchronous and histologically distinct intracranial tumours in a child. Neuropathol Appl Neurobiol 2010; 36:359-63. [PMID: 20345646 DOI: 10.1111/j.1365-2990.2010.01085.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Ranjan A, Ansari SA, Srivastava R, Mantri S, Asif MH, Sawant SV, Tuli R. A T9G mutation in the prototype TATA-box TCACTATATATAG determines nucleosome formation and synergy with upstream activator sequences in plant promoters. PLANT PHYSIOLOGY 2009; 151:2174-86. [PMID: 19812181 PMCID: PMC2785982 DOI: 10.1104/pp.109.148064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 09/30/2009] [Indexed: 05/19/2023]
Abstract
We had earlier reported that mutations to G and C at the seventh and eighth positions in the prototype TATA-box TCACTATATATAG inhibited light-dependent activation of transcription from the promoter. In this study, we characterized mutations at the ninth position of the prototype TATA-box. Substitution of T at the ninth position with G or C enhanced transcription from the promoter in transgenic tobacco (Nicotiana tabacum) plants. The effect of T9G/C mutations was not light dependent, although the 9G/C TATA-box showed synergy with the light-responsive element (lre). However, the 9G/C mutants in the presence of lre failed to respond to phytochromes, sugar, and calcium signaling, in contrast to the prototype TATA-box with lre. The 9G/C mutation shifted the point of initiation of transcription, and transcription activation was dependent upon the type of activating element present upstream. The synergy in activation was noticed with lre and legumin activators but not with rbcS, Pcec, and PR-1a activators. The 9G mutation resulted in a micrococcal nuclease-sensitive region over the TATA-box, suggesting a nucleosome-free region, in contrast to the prototype promoter, which had a distinct nucleosome on the TATA-box. Thus, the transcriptional augmentation with mutation at the ninth position might be because of the loss of a repressive nucleosomal structure on the TATA-box. In agreement with our findings, the promoters containing TATAGATA as identified by genome-wide analysis of Arabidopsis (Arabidopsis thaliana) are not tightly repressed.
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Affiliation(s)
| | | | | | | | | | - Samir V. Sawant
- National Botanical Research Institute, Council of Scientific and Industrial Research, Lucknow 226001, India
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Garrick D, De Gobbi M, Gibbons R, Higgs DR. Polycomb response elements in vertebrates. Epigenomics 2009; 1:231. [PMID: 22122700 DOI: 10.2217/epi.09.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- David Garrick
- John Radcliffe Hospital, MRC Molecular Haematology Unit, The Weatherall Institute of Molecular Medicine, Headington, Oxford, UK.
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Schneiderman JI, Sakai A, Goldstein S, Ahmad K. The XNP remodeler targets dynamic chromatin in Drosophila. Proc Natl Acad Sci U S A 2009; 106:14472-7. [PMID: 19706533 PMCID: PMC2725014 DOI: 10.1073/pnas.0905816106] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Indexed: 02/08/2023] Open
Abstract
Heterochromatic gene silencing results from the establishment of a repressive chromatin structure over reporter genes. Gene silencing is often variegated, implying that chromatin may stochastically switch from repressive to permissive structures as cells divide. To identify remodeling enzymes involved in reorganizing heterochromatin, we tested 11 SNF2-type chromatin remodelers in Drosophila for effects on gene silencing. Overexpression of five remodelers affects gene silencing, and the most potent de-repressor is the alpha-thalassaemia mental retardation syndrome X-linked (ATRX) homolog X-linked nuclear protein (XNP). Although the mammalian ATRX protein localizes to heterochromatin, Drosophila XNP is not a general component of heterochromatin. Instead, XNP localizes to active genes and to a major focus near the heterochromatin of the X chromosome. The XNP focus corresponds to an unusual decondensed satellite DNA block, and both active genes and the XNP focus are sites of ongoing nucleosome replacement. We suggest that the XNP remodeler modulates nucleosome dynamics at its target sites to limit chromatin accessibility. Although XNP at active genes may contribute to gene silencing, we find that a single focus is present across Drosophila species and that perturbation of this site cripples heterochromatic gene silencing. Thus, the XNP focus appears to be a functional genetic element that can contribute to gene silencing throughout the nucleus.
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Affiliation(s)
- Jonathan I. Schneiderman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | - Akiko Sakai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | - Sara Goldstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | - Kami Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
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The histone gene activator HINFP is a nonredundant cyclin E/CDK2 effector during early embryonic cell cycles. Proc Natl Acad Sci U S A 2009; 106:12359-64. [PMID: 19590016 DOI: 10.1073/pnas.0905651106] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Competency for DNA replication is functionally coupled to the activation of histone gene expression at the onset of S phase to form chromatin. Human histone nuclear factor P (HiNF-P; gene symbol HINFP) bound to its cyclin E/cyclin-dependent kinase 2 (CDK2) responsive coactivator p220(NPAT) is a key regulator of multiple human histone H4 genes that encode a major subunit of the nucleosome. Induction of the histone H4 transcription factor (HINFP)/p220(NPAT) coactivation complex occurs in parallel with the CDK-dependent release of pRB from E2F at the restriction point. Here, we show that the downstream CDK-dependent cell cycle effector HINFP is genetically required and, in contrast to the CDK2/cyclin E complex, cannot be compensated. We constructed a mouse Hinfp-null mutation and found that heterozygous Hinfp mice survive, indicating that 1 allele suffices for embryogenesis. Homozygous loss-of-function causes embryonic lethality: No homozygous Hinfp-null mice are obtained at or beyond embryonic day (E) 6.5. In blastocyst cultures, Hinfp-null embryos exhibit a delay in hatching, abnormal growth, and loss of histone H4 gene expression. Our data indicate that the CDK2/cyclin E/p220(NPAT)/HINFP/histone gene signaling pathway at the G1/S phase transition is an essential, nonredundant cell cycle regulatory mechanism that is established early in embryogenesis.
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Boese A, Sommer P, Holzer D, Maier R, Nehrbass U. Integrase interactor 1 (Ini1/hSNF5) is a repressor of basal human immunodeficiency virus type 1 promoter activity. J Gen Virol 2009; 90:2503-2512. [PMID: 19515827 DOI: 10.1099/vir.0.013656-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Integrase interactor 1 (Ini1/hSNF5/BAF47/SMARCB1), the core subunit of the ATP-dependent chromatin-remodelling complex SWI/SNF, is a cellular interaction partner of the human immunodeficiency virus type 1 (HIV-1) integrase. Ini1/hSNF5 is recruited to HIV-1 pre-integration complexes before nuclear migration, suggesting a function in the integration process itself or a contribution to the preferential selection of transcriptionally active genes as integration sites of HIV-1. More recent evidence indicates, however, that, whilst Ini1/hSNF5 is dispensable for HIV-1 transduction per se, it may have an inhibitory effect on the early steps of HIV-1 replication but facilitates proviral transcription by enhancing Tat function. These partially contradictory observations prompted an investigation of the immediate and long-term effects of Ini1/hSNF5 depletion on the basal transcriptional potential of the virus promoter. Using small interfering RNAs, it was shown that Ini1/hSNF5-containing SWI/SNF complexes mediate transcriptional repression of the basal activity of the integrated HIV-1 long terminal repeat. Transient depletion of Ini1/hSNF5 during integration was accompanied by an early boost of HIV-1 replication. After the reappearance of Ini1/hSNF5, expression levels decreased and this was associated with increased levels of histone methylation at the virus promoter in the long term, indicative of epigenetic gene silencing. These results demonstrate the opposing effects of Ini1/hSNF5-containing SWI/SNF complexes on basal and Tat-dependent transcriptional activity of the HIV-1 promoter. It is proposed that Ini1/hSNF5 may be recruited to the HIV-1 pre-integration complex to initiate, immediately after integration, one of two mutually exclusive transcription programmes, namely post-integration latency or high-level, Tat-dependent gene expression.
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Affiliation(s)
- Annette Boese
- Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea
| | - Peter Sommer
- Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea
| | - Daniela Holzer
- EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Reinhard Maier
- Kantonal Hospital St Gallen, CH-9007 St Gallen, Switzerland
| | - Ulf Nehrbass
- Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea
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31
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Koga M, Ishiguro H, Yazaki S, Horiuchi Y, Arai M, Niizato K, Iritani S, Itokawa M, Inada T, Iwata N, Ozaki N, Ujike H, Kunugi H, Sasaki T, Takahashi M, Watanabe Y, Someya T, Kakita A, Takahashi H, Nawa H, Muchardt C, Yaniv M, Arinami T. Involvement of SMARCA2/BRM in the SWI/SNF chromatin-remodeling complex in schizophrenia. Hum Mol Genet 2009; 18:2483-94. [DOI: 10.1093/hmg/ddp166] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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32
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Kohashi K, Izumi T, Oda Y, Yamamoto H, Tamiya S, Taguchi T, Iwamoto Y, Hasegawa T, Tsuneyoshi M. Infrequent SMARCB1/INI1 gene alteration in epithelioid sarcoma: a useful tool in distinguishing epithelioid sarcoma from malignant rhabdoid tumor. Hum Pathol 2009; 40:349-55. [DOI: 10.1016/j.humpath.2008.08.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2008] [Revised: 08/05/2008] [Accepted: 08/14/2008] [Indexed: 10/21/2022]
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Cortez CC, Jones PA. Chromatin, cancer and drug therapies. Mutat Res 2008; 647:44-51. [PMID: 18691602 PMCID: PMC2631123 DOI: 10.1016/j.mrfmmm.2008.07.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/08/2008] [Accepted: 07/09/2008] [Indexed: 05/26/2023]
Abstract
The structure and organization of chromatin have attracted a great deal of attention recently because of their implications for the field of epigenetics. DNA methylation and the post-translational modifications that occur on histones can specify transcriptional competency. During cancer development, tumor suppressor genes become silenced by DNA hypermethylation and chromatin modifiers no longer perform in their usual manner. Current epigenetic therapy has been able to take advantage of the reversibility of these epimutations. Progress has been made in the treatment of hematological malignancies and some solid tumors. As the knowledge of how chromatin regulates gene expression is enhanced, improvements in the treatment of cancer can be made.
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Affiliation(s)
| | - Peter A. Jones
- Corresponding author at: USC/Norris Comprehensive Cancer Center, Department of Urology and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles CA, 90033, USA. Tel.: 323 865 0740; fax: 323 865 0102. E-mail address: (P.A. Jones)
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SMARCB1/INI1 Protein Expression in Round Cell Soft Tissue Sarcomas Associated With Chromosomal Translocations Involving EWS: A Special Reference to SMARCB1/INI1 Negative Variant Extraskeletal Myxoid Chondrosarcoma. Am J Surg Pathol 2008; 32:1168-74. [DOI: 10.1097/pas.0b013e318161781a] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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Affiliation(s)
- J Adam Hall
- Department of Biological Sciences, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA
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36
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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Nagy Z, Tora L. Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation. Oncogene 2007; 26:5341-57. [PMID: 17694077 DOI: 10.1038/sj.onc.1210604] [Citation(s) in RCA: 313] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transcription in eukaryotes is a tightly regulated, multistep process. Gene-specific transcriptional activators, several different co-activators and general transcription factors are necessary to access specific loci to allow precise initiation of RNA polymerase II transcription. As the dense chromatin folding of the genome does not allow the access of these sites by the huge multiprotein transcription machinery, remodelling is required to loosen up the chromatin structure for successful transcription initiation. In the present review, we summarize the recent evolution of our understanding of the function of two histone acetyl transferases (ATs) from metazoan organisms: GCN5 and PCAF. Their overall structure and the multiprotein complexes in which they are carrying out their activities are discussed. Metazoan GCN5 and PCAF are subunits of at least two types of multiprotein complexes, one having a molecular weight of 2 MDa (SPT3-TAF9-GCN5 acetyl transferase/TATA binding protein (TBP)-free-TAF complex/PCAF complexes) and a second type with about a size of 700 kDa (ATAC complex). These complexes possess global histone acetylation activity and locus-specific co-activator functions together with AT activity on non-histone substrates. Thus, their biological functions cover a wide range of tasks and render them indispensable for the normal function of cells. That deregulation of the global and/or specific AT activities of these complexes leads to the cancerous transformation of the cells highlights their importance in cellular processes. The possible effects of GCN5 and PCAF in tumorigenesis are also discussed.
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Affiliation(s)
- Z Nagy
- Transcription Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, France
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38
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Kohashi K, Oda Y, Yamamoto H, Tamiya S, Izumi T, Ohta S, Taguchi T, Suita S, Tsuneyoshi M. Highly aggressive behavior of malignant rhabdoid tumor: a special reference to SMARCB1/INI1 gene alterations using molecular genetic analysis including quantitative real-time PCR. J Cancer Res Clin Oncol 2007; 133:817-24. [PMID: 17486366 DOI: 10.1007/s00432-007-0223-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Accepted: 03/23/2007] [Indexed: 01/04/2023]
Abstract
PURPOSE SMARCB1/INI1, which negatively regulates cell cycle progression from G0/G1 into the S-phase via the p16INK4a-RB-E2F pathway, has been reported to be inactivated homozygously by deletion and/or mutations in malignant rhabdoid tumor (MRT). In the current study, we investigated the alteration of the SMARCB1/INI1 gene using simple methods, and its gene product at the protein level. Moreover, we investigated the status of hyperphosphorylation in RB protein, known as a key cell cycle molecule. METHODS Three cell lines and 11 formalin-fixed, paraffin-embedded specimens of MRT were investigated. SMARCB1/INI1 gene alteration was analyzed with simple methods as a quantitative real-time PCR and direct sequencing method. Furthermore, SMARCB1/INI1 and RB protein were immunohistochemically evaluated. RESULTS In 12 of 14 cases, we detected genetic alterations comprised of nine (including three cell lines) homozygous deletions and three mutations, which can induce abnormal expression of gene products. At the protein level, SMARCB1/INI1 immunohistochemical expressions were not detected in any cases. Twelve out of 14 cases showed high-level (+5) expression of tRB (both hyperphosphorylated and underphosphorylated RB), combined with low-level (+1) expression of uRB (underphosphorylated RB), indicating a high rate of hyperphosphorylation. CONCLUSIONS We could analyze the SMARCB1/INI1 gene alteration with simple methods, and SMARCB1/INI1 gene alteration was found in 12 of 14 cases. Especially, quantitative real-time PCR was a convenient and accurate method. In addition, a high rate of hyperphosphorylation of RB gene was recognized. These results suggest that the clinically aggressive character of MRT is caused by the inactivation of the SMARCB1/INI1 gene.
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Affiliation(s)
- Kenichi Kohashi
- Department of Anatomic Pathology, Pathological Sciences, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
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39
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Abstract
The SWI/SNF chromatin remodeling complex is an essential regulator of transcription of cellular genes. HIV-1 infection induces exit of a core component of SWI/SNF, Ini1, into the cytoplasm and its association with the viral pre-integration complex. Several recent papers published in EMBO Journal, Journal of Biological Chemistry, and Retrovirology provide new information regarding possible functions of Ini1 and SWI/SNF in HIV life cycle. It appears that Ini1 has an inhibitory effect on pre-integration steps of HIV replication, but also contributes to stimulation of Tat-mediated transcription. This stimulation involves displacement of the nucleosome positioned at the HIV promoter.
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Affiliation(s)
- Michael Bukrinsky
- The George Washington University, Department of Microbiology, Immunology and Tropical Medicine, Washington, DC 20037, USA.
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40
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de la Serna IL, Ohkawa Y, Imbalzano AN. Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers. Nat Rev Genet 2006; 7:461-73. [PMID: 16708073 DOI: 10.1038/nrg1882] [Citation(s) in RCA: 281] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The initiation of cellular differentiation involves alterations in gene expression that depend on chromatin changes, at the level of both higher-order structures and individual genes. Consistent with this, chromatin-remodelling enzymes have key roles in differentiation and development. The functions of ATP-dependent chromatin-remodelling enzymes have been studied in several mammalian differentiation pathways, revealing cell-type-specific and gene-specific roles for these proteins that add another layer of precision to the regulation of differentiation. Recent studies have also revealed a role for ATP-dependent remodelling in regulating the balance between proliferation and differentiation, and have uncovered intriguing links between chromatin remodelling and other cellular processes during differentiation, including recombination, genome organization and the cell cycle.
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Affiliation(s)
- Ivana L de la Serna
- Department of Biochemistry and Cancer Biology, Medical University of Ohio, 3035 Arlington Avenue, Toledo, Ohio 43606, USA
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41
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Maroun M, Delelis O, Coadou G, Bader T, Ségéral E, Mbemba G, Petit C, Sonigo P, Rain JC, Mouscadet JF, Benarous R, Emiliani S. Inhibition of early steps of HIV-1 replication by SNF5/Ini1. J Biol Chem 2006; 281:22736-43. [PMID: 16772295 DOI: 10.1074/jbc.m604849200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To replicate, human immunodeficiency virus, type 1 (HIV-1) needs to integrate a cDNA copy of its RNA genome into a chromosome of the host cell, a step controlled by the viral integrase (IN) protein. Viral integration involves the participation of several cellular proteins. SNF5/Ini1, a subunit of the SWI/SNF chromatin remodeling complex, was the first cofactor identified to interact with IN. We report here that SNF5/Ini1 interferes with early steps of HIV-1 replication. Inhibition of SNF5/Ini1 expression by RNA interference increases HIV-1 replication. Using quantitative PCR, we show that both the 2-long terminal repeat circle and integrated DNA forms accumulate upon SNF5/Ini1 knock down. By yeast two-hybrid assay, we screened a library of HIV-1 IN random mutants obtained by PCR random mutagenesis using SNF5/Ini1 as prey. Two different mutants of interaction, IN E69G and IN K71R, were impaired for SNF5/Ini1 interaction. The E69G substitution completely abolished integrase catalytic activity, leading to a replication-defective virus. On the contrary, IN K71R retained in vitro integrase activity. K71R substitution stimulates viral replication and results in higher infectious titers. Taken together, these results suggest that, by interacting with IN, SNF5/Ini1 interferes with early steps of HIV-1 infection.
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Affiliation(s)
- Marlène Maroun
- Institut Cochin, Département Maladies Infectieuses, F-75014 Paris, Inserm, U567, F-75014 Paris, France
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Zibara K, Garin G, McGregor JL. Identification, structural, and functional characterization of a new early gene (6A3-5, 7 kb): implication in the proliferation and differentiation of smooth muscle cells. J Biomed Biotechnol 2005; 2005:254-70. [PMID: 16192684 PMCID: PMC1224700 DOI: 10.1155/jbb.2005.254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arterial smooth muscle cells (SMCs) play a major role in atherosclerosis and restenosis. Differential display was used to compare transcription profiles of synthetic SMCs to proliferating rat cultured SMC line. An isolated cDNA band (6A3-5) was shown by northern (7 kb) to be upregulated in the proliferating cell line. A rat tissue northern showed differential expression of this gene in different tissues. Using 5' RACE and screening of a rat brain library, part of the cDNA was cloned and sequenced (5.4 kb). Sequence searches showed important similarities with a new family of transcription factors, bearing ARID motifs. A polyclonal antibody was raised and showed a protein band of 175 kd, which is localized intracellularly. We also showed that 6A3-5 is upregulated in dedifferentiated SMC (P9) in comparison to contractile SMC ex vivo (P0). This work describes cloning, structural, and functional characterization of a new early gene involved in SMC phenotype modulation.
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Affiliation(s)
- Kazem Zibara
- INSERM XR331, Faculty of Medicine RTH Laënnec, 69372 Lyon, France
- *Kazem Zibara:
| | - Gwenaële Garin
- Genomics and Atherothrombosis Laboratory, Thrombosis Research Institute, London
SW3 6LR, UK
| | - John L. McGregor
- Center for Cardiovascular Biology and Medicine, King's College, University of London,
London WC2R 2LS, UK
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Zraly CB, Marenda DR, Dingwall AK. SNR1 (INI1/SNF5) mediates important cell growth functions of the Drosophila Brahma (SWI/SNF) chromatin remodeling complex. Genetics 2005; 168:199-214. [PMID: 15454538 PMCID: PMC1448117 DOI: 10.1534/genetics.104.029439] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
SNR1 is an essential subunit of the Drosophila Brahma (Brm) ATP-dependent chromatin remodeling complex, with counterparts in yeast (SNF5) and mammals (INI1). Increased cell growth and wing patterning defects are associated with a conditional snr1 mutant, while loss of INI1 function is directly linked with aggressive cancers, suggesting important roles in development and growth control. The Brm complex is known to function during G1 phase, where it appears to assist in restricting entry into S phase. In Drosophila, the activity of DmcycE/CDK2 is rate limiting for entry into S phase and we previously found that the Brm complex can suppress a reduced growth phenotype associated with a hypomorphic DmcycE mutant. Our results reveal that SNR1 helps mediate associations between the Brm complex and DmcycE/CDK2 both in vitro and in vivo. Further, disrupting snr1 function suppressed DmcycEJP phenotypes, and increased cell growth defects associated with the conditional snr1E1 mutant were suppressed by reducing DmcycE levels. While the snr1E1-dependent increased cell growth did not appear to be directly associated with altered expression of G1 or G2 cyclins, transcription of the G2-M regulator string/cdc25 was reduced. Thus, in addition to important functions of the Brm complex in G1-S control, the complex also appears to be important for transcription of genes required for cell cycle progression.
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Affiliation(s)
- Claudia B Zraly
- Oncology Institute, Cardinal Bernardin Cancer Center, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153, USA
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Enukashvily N, Donev R, Sheer D, Podgornaya O. Satellite DNA binding and cellular localisation of RNA helicase P68. J Cell Sci 2005; 118:611-22. [PMID: 15657085 DOI: 10.1242/jcs.01605] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We purified a 68-kDa protein from the mouse nuclear matrix using ion exchange and affinity chromatography. Column fractions were tested for specific binding to mouse minor satellite DNA using a gel mobility shift assay. The protein was identified by mass spectrometry as RNA helicase P68. In fixed cells, P68 was found to shuttle in and out of SC35 domains, forming fibres and granules in a cell-cycle dependent manner. Analysis of the P68 sequence revealed a short potential coiled-coil domain that might be involved in the formation of P68 fibres. Contacts between centromeres and P68 granules were observed during all phases of the cycle but they were most prominent in mitosis. At this stage, P68 was found in both the centromeric regions and the connections between chromosomes. Direct interaction of P68/DEAD box RNA helicase with satellite DNAs in vitro has not been demonstrated for any other members of the RNA helicase family.
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Affiliation(s)
- Natella Enukashvily
- Cell Cultures Department, Institute of Cytology, Tikhoretsky, 4, St Petersburg, 194064, Russia.
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Kumar RC, Thakur MK. Sex steroids reduce DNaseI accessibility of androgen receptor promoter in adult male mice brain. ACTA ACUST UNITED AC 2005; 131:1-7. [PMID: 15530646 DOI: 10.1016/j.molbrainres.2004.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2004] [Indexed: 11/30/2022]
Abstract
We have previously reported that androgen receptor (AR) expression is inversely correlated to its promoter methylation and is regulated by sex steroids. As chromatin structure plays an important role in transcriptional regulation, the effect of sex steroids on DNaseI accessibility of chromatin of AR promoter was examined in the brain cortex of adult and old mice of both sexes. Nuclei were digested with different concentrations of DNaseI and the extracted DNA was further cleaved by PstI and analyzed by Southern hybridization with DIG-labeled 695-bp AR promoter. With 50 U DNaseI, the intensity of PstI-specific 1.45-kb band was lower in intact female as compared to male groups, suggesting increased nuclease accessibility in female than male. Although gonadectomy increased DNaseI accessibility remarkably in male and female of both ages, testosterone decreased the accessibility in adult but increased in old male. Estradiol, on the other hand, decreased DNaseI accessibility in both adult male and old female but increased in old male and adult female. Thus, these findings suggest that the chromatin conformation of AR promoter varies with age and sex and its accessibility to DNaseI is reduced by testosterone and estradiol in the brain cortex of adult male mice.
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Affiliation(s)
- R C Kumar
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Banaras Hindu University Varanasi, Uttar Pradesh 221 005, India
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46
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Nakao M, Minami T, Ueda Y, Sakamoto Y, Ichimura T. Epigenetic System: A Pathway to Malignancies and a Therapeutic Target. Int J Hematol 2004; 80:103-7. [PMID: 15481437 DOI: 10.1532/ijh97.04052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cancer cells possess both genetic and epigenetic alterations that dysregulate essential cellular processes, leading to disordered cell proliferation and differentiation. Oncogenes and tumor suppressor genes have been found to be activated and inactivated, respectively, in malignant cells. Epigenetic regulation of the genome is mediated by interactions between DNA methylation, chromatin, and modifications of histones and various transcriptional regulators. Recent studies have shown that some components of the epigenetic system as well as epigenetically mutated genes are diagnostic and therapeutic targets in cancer. We discuss the molecular basis of the epigenetic mechanism in association with the development of cancer.
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Affiliation(s)
- Mitsuyoshi Nakao
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan.
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Zelent A, Greaves M, Enver T. Role of the TEL-AML1 fusion gene in the molecular pathogenesis of childhood acute lymphoblastic leukaemia. Oncogene 2004; 23:4275-83. [PMID: 15156184 DOI: 10.1038/sj.onc.1207672] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Balanced chromosomal translocations are frequently associated with haematopoietic neoplasms and often involve genes that encode transcription factors, which play critical roles in normal haematopoiesis. Fusion oncoproteins that arise from chimeric genes generated by such translocations are usually stable and consistent molecular markers for a given disease subtype and contribute to the leukaemogenic processes. The t(12;21)(p13;q22) chromosomal translocation is the most frequent illegitimate gene recombination in paediatric cancer, occurring in approximately 25% of common (c) B-cell precursor acute lymphoblastic leukaemia (cALL) cases. The rearrangement results in the in-frame fusion of the 5' region of the ETS-related gene, TEL (ETV6), to almost the entire AML1 (RUNX1) locus and is associated with favourable prognosis following conventional therapeutic strategies. We discuss here the prenatal origins of the TEL/AML1 translocation as an initiating mutation, the role of TEL-AML1 in cellular transformation and the molecular mechanisms by which the chimeric protein imposes altered patterns of gene expression.
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Affiliation(s)
- Arthur Zelent
- Section of Haematological Oncology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.
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48
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Abstract
We developed a model system to study glucocorticoid receptor (GR)-mediated chromatin remodeling by the BRG1 complex. Introduction of the BRG1 ATPase into the SW-13 cell line initiates the formation of a functional remodeling complex. This complex is able to induce transcriptional activation from a transiently transfected promoter with wild-type and chromatin-remodeling-deficient BRG1 mutants, suggesting that the complex possesses a coactivator function independent from remodeling. Transactivation from a chromatin template requires the BRG1 remodeling function, which induces regions of hypersensitivity and transcription factor loading onto the integrated MMTV promoter. We report that BRG1 remodeling activity is required for GR-mediated transactivation and that this activity cannot be replaced by other ATP-dependent remodeling proteins. Further characterization of the BRG1-associated factors (BAFs) present in these cells (for example, the expression of BAF250 but not BAF180) reveals that the BAF complex rather than the polybromo-associated BAF complex is the necessary and sufficient chromatin-remodeling component with which the receptor functions in vivo. These results in conjunction with previous findings demonstrate that the GR functions with multiple forms of the SWI/SNF complex in vivo.
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Affiliation(s)
- Kevin W Trotter
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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Bucheli M, Sweder K. In UV-irradiated Saccharomyces cerevisiae, overexpression of Swi2/Snf2 family member Rad26 increases transcription-coupled repair and repair of the non-transcribed strand. Mol Microbiol 2004; 52:1653-63. [PMID: 15186415 DOI: 10.1111/j.1365-2958.2004.04081.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleotide excision repair (NER) in eukaryotes is a pathway conserved from yeast to humans that removes many bulky chemical adducts and UV-induced photoproducts from DNA in a relatively error-free manner. In addition to the recognition and excision of DNA damage throughout the genome (GGR), there exists a mechanism, transcription-coupled nucleotide excision repair (TCR), for recognizing some types of DNA damage in the transcribed strand of genes in Escherichia coli, yeast and mammalian cells. An obstacle in the repair of the transcribed strand of active genes is the RNA polymerase complex stalled at sites of DNA damage. The stalled RNA polymerase complex may then mediate recruitment of repair proteins to damage in the transcribed strand. Proteins enabling TCR are the Cockayne syndrome B (CSB) protein in humans and its yeast homologue Rad26. Both CSB and Rad26 belong to the Swi2/Snf2 family of DNA-dependent ATPases, which change DNA accessibility to proteins by altering chromatin structure. To address how Rad26 functions in yeast repair, we used the genetic approach of overexpressing Rad26 and examined phenotypic changes, i.e. changes in NER. We found that repair of both the transcribed and the non-transcribed strands is increased. In addition, overexpression of Rad26 partially bypasses the requirement for Rad7 in GGR, specifically in the repair of non-transcribed sequences. As TCR takes place in very localized regions of DNA (i.e. within genes) in wild-type cells, we propose that overexpression of recombinant Rad26 increases accessibility of the damaged DNA in chromatin for interaction with repair proteins.
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Affiliation(s)
- Miriam Bucheli
- Program in Microbiology and Molecular Genetics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, NJ, USA
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Marenda DR, Zraly CB, Dingwall AK. The Drosophila Brahma (SWI/SNF) chromatin remodeling complex exhibits cell-type specific activation and repression functions. Dev Biol 2004; 267:279-93. [PMID: 15013794 DOI: 10.1016/j.ydbio.2003.10.040] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 10/25/2003] [Indexed: 11/21/2022]
Abstract
The Brahma (Brm) complex of Drosophila melanogaster is a SWI/SNF-related chromatin remodeling complex required to correctly maintain proper states of gene expression through ATP-dependent effects on chromatin structure. The SWI/SNF complexes are comprised of 8-11 stable components, even though the SWI2/SNF2 (BRM, BRG1, hBRM) ATPase subunit alone is partially sufficient to carry out chromatin remodeling in vitro. The remaining subunits are required for stable complex assembly and/or proper promoter targeting in vivo. Our data reveals that SNR1 (SNF5-Related-1), a highly conserved subunit of the Brm complex, is required to restrict complex activity during the development of wing vein and intervein cells, illustrating a functional requirement for SNR1 in modifying whole complex activation functions. Specifically, we found that snr1 and brm exhibited opposite mutant phenotypes in the wing and differential misregulation of genes required for vein and intervein cell development, including rhomboid, decapentaplegic, thick veins, and blistered, suggesting possible regulatory targets for the Brm complex in vivo. Our genetic results suggest a novel mechanism for SWI/SNF-mediated gene repression that relies on the function of a 'core' subunit to block or shield BRM (SWI2/SNF2) activity in specific cells. The SNR1-mediated repression is dependent on cooperation with histone deacetylases (HDAC) and physical associations with NET, a localized vein repressor.
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Affiliation(s)
- Daniel R Marenda
- Department of Biology, Syracuse University, Syracuse, NY 13244-1270, USA
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