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Kong L, Liu Y, Wang X, Chang C. Insight into the Role of Epigenetic Processes in Abiotic and Biotic Stress Response in Wheat and Barley. Int J Mol Sci 2020; 21:ijms21041480. [PMID: 32098241 PMCID: PMC7073019 DOI: 10.3390/ijms21041480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Environmental stresses such as salinity, drought, heat, freezing, heavy metal and even pathogen infections seriously threaten the growth and yield of important cereal crops including wheat and barley. There is growing evidence indicating that plants employ sophisticated epigenetic mechanisms to fine-tune their responses to environmental stresses. Here, we provide an overview of recent developments in understanding the epigenetic processes and elements—such as DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs—involved in plant responses to abiotic and biotic stresses in wheat and barley. Potentials of exploiting epigenetic variation for the improvement of wheat and barley are discussed.
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Affiliation(s)
- Lingyao Kong
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Yanna Liu
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- Correspondence: ; Tel.: +86-532-85953227
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2
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Loss of ISWI Function in Drosophila Nuclear Bodies Drives Cytoplasmic Redistribution of Drosophila TDP-43. Int J Mol Sci 2018; 19:ijms19041082. [PMID: 29617352 PMCID: PMC5979594 DOI: 10.3390/ijms19041082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Abstract
Over the past decade, evidence has identified a link between protein aggregation, RNA biology, and a subset of degenerative diseases. An important feature of these disorders is the cytoplasmic or nuclear aggregation of RNA-binding proteins (RBPs). Redistribution of RBPs, such as the human TAR DNA-binding 43 protein (TDP-43) from the nucleus to cytoplasmic inclusions is a pathological feature of several diseases. Indeed, sporadic and familial forms of amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration share as hallmarks ubiquitin-positive inclusions. Recently, the wide spectrum of neurodegenerative diseases characterized by RBPs functions’ alteration and loss was collectively named proteinopathies. Here, we show that TBPH (TAR DNA-binding protein-43 homolog), the Drosophila ortholog of human TDP-43 TAR DNA-binding protein-43, interacts with the arcRNA hsrω and with hsrω-associated hnRNPs. Additionally, we found that the loss of the omega speckles remodeler ISWI (Imitation SWI) changes the TBPH sub-cellular localization to drive a TBPH cytoplasmic accumulation. Our results, hence, identify TBPH as a new component of omega speckles and highlight a role of chromatin remodelers in hnRNPs nuclear compartmentalization.
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3
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Lo Piccolo L, Attardi A, Bonaccorso R, Li Greci L, Giurato G, Ingrassia AMR, Onorati MC. ISWI ATP-dependent remodeling of nucleoplasmic ω-speckles in the brain of Drosophila melanogaster. J Genet Genomics 2016; 44:85-94. [PMID: 28209301 DOI: 10.1016/j.jgg.2016.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/21/2016] [Accepted: 12/18/2016] [Indexed: 12/27/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to the RNA-binding proteins family. They are involved in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs. These proteins participate in every step of mRNA cycle, such as mRNA export, localization, translation, stability and alternative splicing. At least 14 major hnRNPs, which have structural and functional homologues in mammals, are expressed in Drosophila melanogaster. Until now, six of these hnRNPs are known to be nucleus-localized and associated with the long non-coding RNA (lncRNA) heat shock responsive ω (hsrω) in the omega speckle compartments (ω-speckles). The chromatin remodeler ISWI is the catalytic subunit of several ATP-dependent chromatin-remodeling complexes, and it is an essential factor for organization of ω-speckles. Indeed, in ISWI null mutant, severe defects in ω-speckles structure are detectable. Here, we clarify the role of ISWI in the hnRNPs‒hsrω interaction. Moreover, we describe how ISWI by its remodeling activity, controls hsrω and hnRNPs engagement in ω-speckles. Finally, we demonstrate that the sequestration of hnRNPs in ω-speckles nuclear compartment is a fundamental event in gene expression control and represents a key step in the regulation of several pathways.
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Affiliation(s)
- Luca Lo Piccolo
- STEBICEF Department, University of Palermo, Palermo 90128, Italy
| | - Andrea Attardi
- STEBICEF Department, University of Palermo, Palermo 90128, Italy
| | - Rosa Bonaccorso
- STEBICEF Department, University of Palermo, Palermo 90128, Italy
| | - Lorenzo Li Greci
- STEBICEF Department, University of Palermo, Palermo 90128, Italy
| | - Giorgio Giurato
- Genomix4Life Srl, University of Salerno, Baronissi Campus, Salerno 84081, Italy
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4
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De la Fuente IM. Elements of the cellular metabolic structure. Front Mol Biosci 2015; 2:16. [PMID: 25988183 PMCID: PMC4428431 DOI: 10.3389/fmolb.2015.00016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/19/2022] Open
Abstract
A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra,” Consejo Superior de Investigaciones CientíficasGranada, Spain
- Department of Mathematics, University of the Basque Country, UPV/Euskal Herriko UnibertsitateaLeioa, Spain
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5
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A genetic screen and transcript profiling reveal a shared regulatory program for Drosophila linker histone H1 and chromatin remodeler CHD1. G3-GENES GENOMES GENETICS 2015; 5:677-87. [PMID: 25628309 PMCID: PMC4390582 DOI: 10.1534/g3.115.016709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chromatin structure and activity can be modified through ATP-dependent repositioning of nucleosomes and posttranslational modifications of core histone tails within nucleosome core particles and by deposition of linker histones into the oligonucleosome fiber. The linker histone H1 is essential in metazoans. It has a profound effect on organization of chromatin into higher-order structures and on recruitment of histone-modifying enzymes to chromatin. Here, we describe a genetic screen for modifiers of the lethal phenotype caused by depletion of H1 in Drosophila melanogaster. We identify 41 mis-expression alleles that enhance and 20 that suppress the effect of His1 depletion in vivo. Most of them are important for chromosome organization, transcriptional regulation, and cell signaling. Specifically, the reduced viability of H1-depleted animals is strongly suppressed by ubiquitous mis-expression of the ATP-dependent chromatin remodeling enzyme CHD1. Comparison of transcript profiles in H1-depleted and Chd1 null mutant larvae revealed that H1 and CHD1 have common transcriptional regulatory programs in vivo. H1 and CHD1 share roles in repression of numerous developmentally regulated and extracellular stimulus-responsive transcripts, including immunity-related and stress response-related genes. Thus, linker histone H1 participates in various regulatory programs in chromatin to alter gene expression.
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Vilasi S, Carrotta R, Mangione MR, Campanella C, Librizzi F, Randazzo L, Martorana V, Marino Gammazza A, Ortore MG, Vilasi A, Pocsfalvi G, Burgio G, Corona D, Palumbo Piccionello A, Zummo G, Bulone D, Conway de Macario E, Macario AJL, San Biagio PL, Cappello F. Human Hsp60 with its mitochondrial import signal occurs in solution as heptamers and tetradecamers remarkably stable over a wide range of concentrations. PLoS One 2014; 9:e97657. [PMID: 24830947 PMCID: PMC4022648 DOI: 10.1371/journal.pone.0097657] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/21/2014] [Indexed: 11/23/2022] Open
Abstract
It has been established that Hsp60 can accumulate in the cytosol in various pathological conditions, including cancer and chronic inflammatory diseases. Part or all of the cytosolic Hsp60 could be naïve, namely, bear the mitochondrial import signal (MIS), but neither the structure nor the in solution oligomeric organization of this cytosolic molecule has still been elucidated. Here we present a detailed study of the structure and self-organization of naïve cytosolic Hsp60 in solution. Results were obtained by different biophysical methods (light and X ray scattering, single molecule spectroscopy and hydrodynamics) that all together allowed us to assay a wide range of concentrations of Hsp60. We found that Naïve Hsp60 in aqueous solution is assembled in very stable heptamers and tetradecamers at all concentrations assayed, without any trace of monomer presence.
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Affiliation(s)
- Silvia Vilasi
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Rita Carrotta
- Institute of Biophysics, National Research Council, Palermo, Italy
| | | | - Claudia Campanella
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
| | - Fabio Librizzi
- Institute of Biophysics, National Research Council, Palermo, Italy
| | | | | | - Antonella Marino Gammazza
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences and National Interuniversity Consortium for the Physical Sciences of Matter, Marche Polytechnic University, Ancona, Italy
| | - Annalisa Vilasi
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - Gabriella Pocsfalvi
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - Giosalba Burgio
- Department of biological chemical and pharmaceutical sciences and technologies, University of Palermo, Palermo, Italy
| | - Davide Corona
- Department of biological chemical and pharmaceutical sciences and technologies, University of Palermo, Palermo, Italy
| | - Antonio Palumbo Piccionello
- Institute of Biophysics, National Research Council, Palermo, Italy
- Department of biological chemical and pharmaceutical sciences and technologies, University of Palermo, Palermo, Italy
| | - Giovanni Zummo
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Donatella Bulone
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Everly Conway de Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, and Institute of Marine and Environmental Technology, Columbus Center, Baltimore, Maryland, United States of America
| | - Alberto J. L. Macario
- Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, and Institute of Marine and Environmental Technology, Columbus Center, Baltimore, Maryland, United States of America
| | | | - Francesco Cappello
- Institute of Biophysics, National Research Council, Palermo, Italy
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
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7
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Kuzmanov A, Karina EI, Kirienko NV, Fay DS. The conserved PBAF nucleosome-remodeling complex mediates the response to stress in Caenorhabditis elegans. Mol Cell Biol 2014; 34:1121-35. [PMID: 24421384 PMCID: PMC3958046 DOI: 10.1128/mcb.01502-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/12/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022] Open
Abstract
To adapt to stress, cells must undergo major changes in their gene expression profiles. We have previously described a largely uncharacterized stress response pathway in Caenorhabditis elegans that acts through an evolutionarily conserved motif, termed ESRE, for ethanol and stress response element. We characterize here the requirements for ESRE gene expression and show that the ESRE network is regulated by a conserved SWI/SNF family nucleosome remodeling complex termed PBAF. Depletion of PBAF subunits SWSN-7/BAF200 and PBRM-1/BAF180 results in decreased expression of ESRE genes and increased sensitivity to thermal stress. When overexpressed, SWSN-7/BAF200 and PBRM-1/BAF180 led to increased ESRE transcription, enhanced thermotolerance, and induction of a nuclear ESRE-binding activity. Our data support a model in which PBAF is recruited by an ESRE-binding protein to genomic ESRE sites. We also show that the closely related SWI/SNF complex, BAF, which regulates stress induction through DAF-16/FOXO, does not contribute to ESRE gene expression or bind directly to ESRE sites. To our knowledge, this is the first report demonstrating direct and specific regulation of a stress response network by the PBAF nucleosome-remodeling complex in vivo in metazoa. In addition, we show that PBAF cooperates with the histone demethylase, JMJC-1/NO66, to promote expression of ESRE genes following stress.
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Affiliation(s)
- Aleksandra Kuzmanov
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, USA
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8
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Regulation of ISWI chromatin remodelling activity. Chromosoma 2014; 123:91-102. [PMID: 24414837 DOI: 10.1007/s00412-013-0447-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 12/22/2022]
Abstract
The packaging of the eukaryotic genome into chromatin facilitates the storage of the genetic information within the nucleus, but prevents the access to the underlying DNA sequences. Structural changes in chromatin are mediated by several mechanisms. Among them, ATP-dependent remodelling complexes belonging to ISWI family provides one of the best examples that eukaryotic cells evolved to finely regulate these changes. ISWI-containing complexes use the energy derived from ATP hydrolysis to rearrange nucleosomes on chromatin in order to favour specific nuclear reactions. The combination of regulatory nuclear factors associated with the ATPase subunit as well as its modulation by specific histone modifications, specializes the nuclear function of each ISWI-containing complex. Here we review the different ways by which ISWI enzymatic activity can be modulated and regulated in the nucleus of eukaryotic cells.
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9
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Neguembor MV, Xynos A, Onorati MC, Caccia R, Bortolanza S, Godio C, Pistoni M, Corona DF, Schotta G, Gabellini D. FSHD muscular dystrophy region gene 1 binds Suv4-20h1 histone methyltransferase and impairs myogenesis. J Mol Cell Biol 2013; 5:294-307. [DOI: 10.1093/jmcb/mjt018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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10
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Yajima M, Fairbrother WG, Wessel GM. ISWI contributes to ArsI insulator function in development of the sea urchin. Development 2012; 139:3613-22. [PMID: 22949616 DOI: 10.1242/dev.081828] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Insulators are genomic elements that regulate transcriptional activity by forming chromatin boundaries. Various DNA insulators have been identified or are postulated in many organisms, and the paradigmatic CTCF-dependent insulators are perhaps the best understood and most widespread in function. The diversity of DNA insulators is, however, understudied, especially in the context of embryonic development, when many new gene territories undergo transitions in functionality. Here we report the functional analysis of the arylsulfatase insulator (ArsI) derived from the sea urchin, which has conserved insulator activity throughout the many metazoans tested, but for which the molecular mechanism of function is unknown. Using a rapid in vivo assay system and a high-throughput mega-shift assay, we identified a minimal region in ArsI that is responsible for its insulator function. We discovered a small set of proteins specifically bound to the minimal ArsI region, including ISWI, a known chromatin-remodeling protein. During embryogenesis, ISWI was found to interact with select ArsI sites throughout the genome, and when inactivated led to misregulation of select gene expression, loss of insulator activity and aberrant morphogenesis. These studies reveal a mechanistic basis for ArsI function in the gene regulatory network of early development.
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Affiliation(s)
- Mamiko Yajima
- MCB Department, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA.
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11
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Campanella C, Bucchieri F, Merendino AM, Fucarino A, Burgio G, Corona DFV, Barbieri G, David S, Farina F, Zummo G, de Macario EC, Macario AJL, Cappello F. The odyssey of Hsp60 from tumor cells to other destinations includes plasma membrane-associated stages and Golgi and exosomal protein-trafficking modalities. PLoS One 2012; 7:e42008. [PMID: 22848686 PMCID: PMC3405006 DOI: 10.1371/journal.pone.0042008] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 07/02/2012] [Indexed: 11/18/2022] Open
Abstract
Background In a previous work we showed for the first time that human tumor cells secrete Hsp60 via exosomes, which are considered immunologically active microvesicles involved in tumor progression. This finding raised questions concerning the route followed by Hsp60 to reach the exosomes, its location in them, and whether Hsp60 can be secreted also via other mechanisms, e.g., by the Golgi. We addressed these issues in the work presented here. Principal Findings We found that Hsp60 localizes in the tumor cell plasma membrane, is associated with lipid rafts, and ends up in the exosomal membrane. We also found evidence that Hsp60 localizes in the Golgi apparatus and its secretion is prevented by an inhibitor of this organelle. Conclusions/Significance We propose a multistage process for the translocation of Hsp60 from the inside to the outside of the cell that includes a combination of protein traffic pathways and, ultimately, presence of the chaperonin in the circulating blood. The new information presented should help in designing future strategies for research and for developing diagnostic-monitoring means useful in clinical oncology.
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Affiliation(s)
- Claudia Campanella
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia, Palermo, Italy
| | - Fabio Bucchieri
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia, Palermo, Italy
| | - Anna M. Merendino
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
| | - Alberto Fucarino
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
| | - Giosalba Burgio
- Dipartimento STEMBIO, University of Palermo, Palermo, Italy
- Dulbecco Telethon Institute, Palermo, Italy
| | - Davide F. V. Corona
- Dipartimento STEMBIO, University of Palermo, Palermo, Italy
- Dulbecco Telethon Institute, Palermo, Italy
| | - Giovanna Barbieri
- Istituto di Biomedicina e Immunologia Molecolare, C.N.R., Palermo, Italy
| | - Sabrina David
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
| | - Felicia Farina
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
| | - Giovanni Zummo
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
| | - Everly Conway de Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, and IMET, Baltimore, Maryland, United States of America
| | - Alberto J. L. Macario
- Istituto Euro-Mediterraneo di Scienza e Tecnologia, Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, and IMET, Baltimore, Maryland, United States of America
| | - Francesco Cappello
- Dipartimento BIONEC, Sezione di Anatomia Umana, University of Palermo, Palermo, Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia, Palermo, Italy
- * E-mail:
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12
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Yip DJ, Corcoran CP, Alvarez-Saavedra M, DeMaria A, Rennick S, Mears AJ, Rudnicki MA, Messier C, Picketts DJ. Snf2l regulates Foxg1-dependent progenitor cell expansion in the developing brain. Dev Cell 2012; 22:871-8. [PMID: 22516202 DOI: 10.1016/j.devcel.2012.01.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 01/21/2023]
Abstract
Balancing progenitor cell self-renewal and differentiation is essential for brain development and is regulated by the activity of chromatin remodeling complexes. Nevertheless, linking chromatin changes to specific pathways that control cortical histogenesis remains a challenge. Here we identify a genetic interaction between the chromatin remodeler Snf2l and Foxg1, a key regulator of neurogenesis. Snf2l mutant mice exhibit forebrain hypercellularity arising from increased Foxg1 expression, increased progenitor cell expansion, and delayed differentiation. We demonstrate that Snf2l binds to the Foxg1 locus at midneurogenesis and that the phenotype is rescued by reducing Foxg1 dosage, thus revealing that Snf2l and Foxg1 function antagonistically to regulate brain size.
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Affiliation(s)
- Darren J Yip
- Regenerative Medicine Program, Ottawa Hospital Research Institute, and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
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13
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Burgio G, Cipressa F, Ingrassia AMR, Cenci G, Corona DFV. The histone deacetylase Rpd3 regulates the heterochromatin structure of Drosophila telomeres. J Cell Sci 2011; 124:2041-8. [DOI: 10.1242/jcs.078261] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Telomeres are specialized structures at the end of eukaryotic chromosomes that are required to preserve genome integrity, chromosome stability and nuclear architecture. Telomere maintenance and function are established epigenetically in several eukaryotes. However, the exact chromatin enzymatic modifications regulating telomere homeostasis are poorly understood. In Drosophila melanogaster, telomere length and stability are maintained through the retrotransposition of specialized telomeric sequences and by the specific loading of protecting capping proteins, respectively. Here, we show that the loss of the essential and evolutionarily conserved histone deacetylase Rpd3, the homolog of mammalian HDAC1, causes aberrant telomeric fusions on polytene chromosome ends. Remarkably, these telomere fusion defects are associated with a marked decrease of histone H4 acetylation, as well as an accumulation of heterochromatic epigenetic marks at telomeres, including histone H3K9 trimethylation and the heterochromatic protein HP2. Our work suggests that Drosophila telomere structure is epigenetically regulated by the histone deacetylase Rpd3.
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Affiliation(s)
- Giosalba Burgio
- Istituto Telethon Dulbecco, c/o STEMBIO, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
- Università degli Studi di Palermo–Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari – Sezione di Biologia Cellulare, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
| | - Francesca Cipressa
- Dipartimento di Biologia di Base ed Applicata, Università dell'Aquila, 67100 Coppito, L'Aquila, Italy
| | - Antonia Maria Rita Ingrassia
- Istituto Telethon Dulbecco, c/o STEMBIO, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
- Università degli Studi di Palermo–Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari – Sezione di Biologia Cellulare, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
| | - Giovanni Cenci
- Dipartimento di Biologia di Base ed Applicata, Università dell'Aquila, 67100 Coppito, L'Aquila, Italy
| | - Davide F. V. Corona
- Istituto Telethon Dulbecco, c/o STEMBIO, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
- Università degli Studi di Palermo–Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari – Sezione di Biologia Cellulare, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
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14
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Onorati MC, Lazzaro S, Mallik M, Ingrassia AMR, Carreca AP, Singh AK, Chaturvedi DP, Lakhotia SC, Corona DFV. The ISWI chromatin remodeler organizes the hsrω ncRNA-containing omega speckle nuclear compartments. PLoS Genet 2011; 7:e1002096. [PMID: 21637796 PMCID: PMC3102753 DOI: 10.1371/journal.pgen.1002096] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/06/2011] [Indexed: 12/23/2022] Open
Abstract
The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their associated ncRNAs, are emerging as important components of gene regulatory networks, although their functional connections have remained poorly defined. Here we provide multiple lines of evidence showing that the hsrω ncRNA interacts in vivo and in vitro with ISWI, regulating its ATPase activity. Remarkably, we found that the organization of nucleoplasmic omega speckles depends on ISWI function. Our findings highlight a novel role for chromatin remodelers in organization of nucleoplasmic compartments, providing the first example of interaction between an ATP-dependent chromatin remodeler and a large ncRNA. Chromatin structure and function are regulated by the concerted activity of covalent modifiers of chromatin, nucleosome remodeling factors, and several emerging classes of non-coding RNAs. ISWI is an evolutionarily conserved ATP-dependent chromatin remodeler playing essential roles in chromosome condensation, gene expression, and DNA replication. ISWI activity has been involved in a variety of nuclear functions including telomere silencing, stem cell renewal, neural morphogenesis, and epigenetic reprogramming. Using an in vivo assay to identify factors regulating ISWI activity in the model system Drosophila melanogaster, we recovered a genetic interaction between ISWI and hsrω. The hsrω gene encodes multiple non-coding RNAs (ncRNAs), of which the >10 kb nuclear hsrω-n RNA, with functional homolog in mammals, is essential for the assembly and organization of hnRNP-containing nucleoplasmic omega speckles. These special nuclear compartments play essential roles in the storage/sequestration of hnRNP family and other proteins, thus playing important roles in mRNA maturation and other regulatory processes. Here we show that the hsrω-n ncRNA interacts in vivo and in vitro with ISWI to directly regulate its ATPase activity. We also provide in vivo data showing that omega speckle nuclear organization depends on ISWI function, highlighting a novel role for chromatin remodelers in nuclear speckles organization.
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Affiliation(s)
- Maria C. Onorati
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Sandra Lazzaro
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Moushami Mallik
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Antonia M. R. Ingrassia
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Anna P. Carreca
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Anand K. Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Deo Prakash Chaturvedi
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Subhash C. Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Davide F. V. Corona
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
- * E-mail:
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15
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Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI. EMBO J 2011; 30:1766-77. [PMID: 21448136 DOI: 10.1038/emboj.2011.98] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 02/25/2011] [Indexed: 12/22/2022] Open
Abstract
The evolutionarily conserved ATP-dependent nucleosome remodelling factor ISWI can space nucleosomes affecting a variety of nuclear processes. In Drosophila, loss of ISWI leads to global transcriptional defects and to dramatic alterations in higher-order chromatin structure, especially on the male X chromosome. In order to understand if chromatin condensation and gene expression defects, observed in ISWI mutants, are directly correlated with ISWI nucleosome spacing activity, we conducted a genome-wide survey of ISWI binding and nucleosome positioning in wild-type and ISWI mutant chromatin. Our analysis revealed that ISWI binds both genic and intergenic regions. Remarkably, we found that ISWI binds genes near their promoters causing specific alterations in nucleosome positioning at the level of the Transcription Start Site, providing an important insights in understanding ISWI role in higher eukaryote transcriptional regulation. Interestingly, differences in nucleosome spacing, between wild-type and ISWI mutant chromatin, tend to accumulate on the X chromosome for all ISWI-bound genes analysed. Our study shows how in higher eukaryotes the activity of the evolutionarily conserved nucleosome remodelling factor ISWI regulates gene expression and chromosome organization genome-wide.
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The Putzig-NURF nucleosome remodeling complex is required for ecdysone receptor signaling and innate immunity in Drosophila melanogaster. Genetics 2011; 188:127-39. [PMID: 21385730 DOI: 10.1534/genetics.111.127795] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Putzig (Pzg) was originally identified as being an integral component of the TRF2/DREF complex in Drosophila melanogaster, thereby regulating the transcriptional activation of replication-related genes. In a DREF-independent manner, Pzg was shown to mediate Notch target gene activation. This function of Pzg entails an association with the nucleosome remodeling factor complex NURF, which directly binds the ecdysone receptor EcR and coregulates targets of the EcR via the NURF-specific subunit Nurf-301. In contrast, Nurf-301 acts as a negative regulator of JAK/STAT signaling. Here, we provide evidence to show that Pzg is fundamental for these functions of NURF, apart from the regulation of Notch signaling activity. A jump-out mutagenesis provided us with a pzg null mutant displaying early larval lethality, defects in growth, and molting accompanied by aberrant feeding behavior. We show that Pzg is associated with EcR in vivo and required for the transcriptional induction of EcR target genes, whereas reduced ecdysteroid levels imply a NURF-independent function of Pzg. Moreover, pzg interferes with JAK/STAT-signaling activity by acting as a corepressor of Ken. Lamellocyte differentiation was consistently affected in a JAK/STAT mutant background and the expression level of defense response genes was elevated in pzg mutants, leading to the formation of melanotic tumors. Our results suggest that Pzg acts as an important partner of NURF in the regulation of EcR and JAK/STAT signaling.
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Di Stefano L, Walker JA, Burgio G, Corona DFV, Mulligan P, Näär AM, Dyson NJ. Functional antagonism between histone H3K4 demethylases in vivo. Genes Dev 2011; 25:17-28. [PMID: 21205864 DOI: 10.1101/gad.1983711] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Dynamic regulation of histone modifications is critical during development, and aberrant activity of chromatin-modifying enzymes has been associated with diseases such as cancer. Histone demethylases have been shown to play a key role in eukaryotic gene transcription; however, little is known about how their activities are coordinated in vivo to regulate specific biological processes. In Drosophila, two enzymes, dLsd1 (Drosophila ortholog of lysine-specific demethylase 1) and Lid (little imaginal discs), demethylate histone H3 at Lys 4 (H3K4), a residue whose methylation is associated with actively transcribed genes. Our studies show that compound mutation of Lid and dLsd1 results in increased H3K4 methylation levels. However, unexpectedly, Lid mutations strongly suppress dLsd1 mutant phenotypes. Investigation of the basis for this antagonism revealed that Lid opposes the functions of dLsd1 and the histone methyltransferase Su(var)3-9 in promoting heterochromatin spreading at heterochromatin-euchromatin boundaries. Moreover, our data reveal a novel role for dLsd1 in Notch signaling in Drosophila, and a complex network of interactions between dLsd1, Lid, and Notch signaling at euchromatic genes. These findings illustrate the complexity of functional interplay between histone demethylases in vivo, providing insights into the epigenetic regulation of heterochromatin/euchromatin boundaries by Lid and dLsd1 and showing their involvement in Notch pathway-specific control of gene expression in euchromatin.
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Affiliation(s)
- Luisa Di Stefano
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
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18
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Osipov SA, Preobrazhenskaya OV, Karpov VL. Chromatin structure and transcription regulation in Saccharomyces cerevisiae. Mol Biol 2010. [DOI: 10.1134/s0026893310060026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Ellison-Zelski SJ, Alarid ET. Maximum growth and survival of estrogen receptor-alpha positive breast cancer cells requires the Sin3A transcriptional repressor. Mol Cancer 2010; 9:263. [PMID: 20920219 PMCID: PMC2956731 DOI: 10.1186/1476-4598-9-263] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 09/29/2010] [Indexed: 11/16/2022] Open
Abstract
Background Sin3A is an evolutionarily conserved transcriptional repressor which regulates gene expression as part of the multi-protein Sin3 repressive complex. It functions as a scaffold upon which proteins with enzymatic activity dock, including chromatin modifying histone deacetylases. Although regulation of transcription by Sin3A has been studied in detail, little is understood about the function of Sin3A in cancer cells. We previously showed that Sin3A is expressed in breast cancer cells and is a repressor of estrogen receptor-alpha (ERα, ESR1) gene expression. Here, we expand our previous studies to elucidate the function of Sin3A in the control of gene expression and growth of breast cancer cells. Results Analysis of gene expression following knockdown of Sin3A revealed changes in both basal and regulated gene transcription. Genes of known importance in breast cancer and estrogen signaling, including ERBB2, PGR, MYC, CLU, and NCOA2, were among those identified as Sin3A-responsive. The mechanism of Sin3A action varied among genes and was found to be mediated through both HDAC1/2 -dependent and -independent activities. Loss of Sin3A inhibited breast cancer cell growth by increasing apoptosis without affecting cell cycle progression. Analysis of both ERα-positive and ERα-negative cell lines revealed that the effects of Sin3A on growth were cell-type specific, as Sin3A expression promoted maximum growth of only the ERα-positive cells, and, notably, Sin3A protein itself was increased by estrogen. Further gene expression experiments revealed that Sin3A repressed expression of key apoptotic genes, including TRAIL, TRAILR1, CASP10, and APAF1, in ERα-positive, but not ERα-negative, cell lines, which could provide a mechanistic explanation for cell-type differences in growth. Conclusions This study identifies Sin3A as a regulator of gene expression, survival, and growth in ERα-positive breast cancer cells. Sin3A regulates the transcription of genes involved in breast cancer and apoptosis and acts through multiple mechanisms not limited to histone deacetylase function. These findings reveal previously undescribed functions of Sin3A in breast cancer and provide evidence for an important role of this transcriptional repressor in ERα-positive tumor cell growth.
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20
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Ji Y, Tulin AV. The roles of PARP1 in gene control and cell differentiation. Curr Opin Genet Dev 2010; 20:512-8. [PMID: 20591646 DOI: 10.1016/j.gde.2010.06.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/20/2010] [Accepted: 06/02/2010] [Indexed: 12/13/2022]
Abstract
Cell growth and differentiation during developmental processes require the activation of many inducible genes. However, eukaryotic chromatin, which consists of DNA and histones, becomes a natural barrier impeding access to the functional transcription machinery. To break through the chromatin barrier, eukaryotic organisms have evolved the strategy of using poly(ADP-ribose) polymerase 1 (PARP1) to modulate chromatin structure and initiate the steps leading to gene expression control. As a structural protein in chromatin, enzymatically silent PARP1 inhibits transcription by contributing to the condensation of chromatin, which creates a barrier against gene transcription. However, once activated by environmental stimuli and developmental signals, PARP1 can modify itself and other chromatin-associated proteins, thereby loosening chromatin to facilitate gene transcription. Here we discuss the roles of PARP1 in transcriptional control during development.
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Affiliation(s)
- Yingbiao Ji
- Epigenetics and Progenitor Cell Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States
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21
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Veraksa A. When peptides fly: advances in Drosophila proteomics. J Proteomics 2010; 73:2158-70. [PMID: 20580952 DOI: 10.1016/j.jprot.2010.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/11/2010] [Indexed: 10/25/2022]
Abstract
In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the current status of proteomics research in the fly. Areas that have seen major advances in recent years include efforts to map and catalog the Drosophila proteome and high-throughput as well as targeted studies to analyze protein-protein interactions and post-translational modifications. Stable isotope labeling of flies and other applications of quantitative proteomics have opened up new possibilities for functional analyses. It is clear that proteomics is becoming an indispensable tool in Drosophila systems biology research that adds a unique dimension to studying gene function.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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22
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The nucleosome remodeling factor ISWI functionally interacts with an evolutionarily conserved network of cellular factors. Genetics 2010; 185:129-40. [PMID: 20194965 DOI: 10.1534/genetics.110.114256] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ISWI is an evolutionarily conserved ATP-dependent chromatin remodeling factor playing central roles in DNA replication, RNA transcription, and chromosome organization. The variety of biological functions dependent on ISWI suggests that its activity could be highly regulated. Our group has previously isolated and characterized new cellular activities that positively regulate ISWI in Drosophila melanogaster. To identify factors that antagonize ISWI activity we developed a novel in vivo eye-based assay to screen for genetic suppressors of ISWI. Our screen revealed that ISWI interacts with an evolutionarily conserved network of cellular and nuclear factors that escaped previous genetic and biochemical analyses.
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23
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Pham CD, He X, Schnitzler GR. Divergent human remodeling complexes remove nucleosomes from strong positioning sequences. Nucleic Acids Res 2009; 38:400-13. [PMID: 19906705 PMCID: PMC2811002 DOI: 10.1093/nar/gkp1030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nucleosome positioning plays a major role in controlling the accessibility of DNA to transcription factors and other nuclear processes. Nucleosome positions after assembly are at least partially determined by the relative affinity of DNA sequences for the histone octamer. Nucleosomes can be moved, however, by a class of ATP dependent chromatin remodeling complexes. We recently showed that the human SWI/SNF remodeling complex moves nucleosomes in a sequence specific manner, away from nucleosome positioning sequences (NPSes). Here, we compare the repositioning specificity of five remodelers of diverse biological functions (hSWI/SNF, the SNF2h ATPase and the hACF, CHRAC and WICH complexes than each contain SNF2h) on 5S rDNA, MMTV and 601 NPS polynucleosomal templates. We find that all five remodelers act similarly to reduce nucleosome occupancy over the strongest NPSes, an effect that could directly contribute to the function of WICH in activating 5S rDNA transcription. While some differences were observed between complexes, all five remodelers were found to result in surprisingly similar nucleosome distributions. This suggests that remodeling complexes may share a conserved repositioning specificity, and that their divergent biological functions may largely arise from other properties conferred by complex-specific subunits.
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Affiliation(s)
- Chuong D Pham
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
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24
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Abstract
The packaging of chromosomal DNA by nucleosomes condenses and organizes the genome, but occludes many regulatory DNA elements. However, this constraint also allows nucleosomes and other chromatin components to actively participate in the regulation of transcription, chromosome segregation, DNA replication, and DNA repair. To enable dynamic access to packaged DNA and to tailor nucleosome composition in chromosomal regions, cells have evolved a set of specialized chromatin remodeling complexes (remodelers). Remodelers use the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes. Here, we address many aspects of remodeler biology: their targeting, mechanism, regulation, shared and unique properties, and specialization for particular biological processes. We also address roles for remodelers in development, cancer, and human syndromes.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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25
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Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications. BMC Genomics 2009; 10:304. [PMID: 19586523 PMCID: PMC2713269 DOI: 10.1186/1471-2164-10-304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 07/08/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated. RESULTS In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy) compared with the presence of either one. CONCLUSION We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.
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26
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Sala A, La Rocca G, Burgio G, Kotova E, Di Gesù D, Collesano M, Ingrassia AMR, Tulin AV, Corona DFV. The nucleosome-remodeling ATPase ISWI is regulated by poly-ADP-ribosylation. PLoS Biol 2009; 6:e252. [PMID: 18922045 PMCID: PMC2567001 DOI: 10.1371/journal.pbio.0060252] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 09/09/2008] [Indexed: 12/22/2022] Open
Abstract
ATP-dependent nucleosome-remodeling enzymes and covalent modifiers of chromatin
set the functional state of chromatin. However, how these enzymatic activities
are coordinated in the nucleus is largely unknown. We found that the
evolutionary conserved nucleosome-remodeling ATPase ISWI and the poly-ADP-ribose
polymerase PARP genetically interact. We present evidence showing that ISWI is
target of poly-ADP-ribosylation. Poly-ADP-ribosylation counteracts ISWI function
in vitro and in vivo. Our work suggests that ISWI is a physiological target of
PARP and that poly-ADP-ribosylation can be a new, important post-translational
modification regulating the activity of ATP-dependent nucleosome remodelers. The ISWI protein is a highly conserved nucleosome remodeler that plays essential
roles in regulating chromosome structure, DNA replication, and gene expression.
The variety of functions associated with ISWI activity are probably connected to
the ability of other cellular factors to regulate its ATP-dependent
nucleosome-remodeling activity. We identified one factor—the poly-ADP-ribose
polymerase, PARP—that can counteract ISWI function. PARP is an abundant nuclear
protein that catalyzes the transfer of ADP-ribose units to specific proteins
involved in DNA repair, transcription, and chromatin structure. Our work
suggests that the activity of an ATP-dependent remodeler can be modulated by
poly-ADP-ribosylation in order to regulate chromatin function in vivo. Enzymes that mediate nucleosome remodeling and poly-ADP-ribosylation play
essential roles in the eukaryotic cell. A new study suggests a mechanism to
explain how two nuclear enzymes can coordinate their activities to regulate
chromatin structure and function.
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Affiliation(s)
- Anna Sala
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
| | - Gaspare La Rocca
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
| | - Giosalba Burgio
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di
Palermo, Palermo, Italy
| | - Elena Kotova
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
of America
| | - Dario Di Gesù
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di
Palermo, Palermo, Italy
| | - Marianna Collesano
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
| | | | - Alexei V Tulin
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
of America
| | - Davide F. V Corona
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di
Palermo, Palermo, Italy
- * To whom correspondence should be addressed. E-mail:
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