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DeSimone AM, Pakula A, Lek A, Emerson CP. Facioscapulohumeral Muscular Dystrophy. Compr Physiol 2017; 7:1229-1279. [PMID: 28915324 DOI: 10.1002/cphy.c160039] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Facioscapulohumeral Muscular Dystrophy is a common form of muscular dystrophy that presents clinically with progressive weakness of the facial, scapular, and humeral muscles, with later involvement of the trunk and lower extremities. While typically inherited as autosomal dominant, facioscapulohumeral muscular dystrophy (FSHD) has a complex genetic and epigenetic etiology that has only recently been well described. The most prevalent form of the disease, FSHD1, is associated with the contraction of the D4Z4 microsatellite repeat array located on a permissive 4qA chromosome. D4Z4 contraction allows epigenetic derepression of the array, and possibly the surrounding 4q35 region, allowing misexpression of the toxic DUX4 transcription factor encoded within the terminal D4Z4 repeat in skeletal muscles. The less common form of the disease, FSHD2, results from haploinsufficiency of the SMCHD1 gene in individuals carrying a permissive 4qA allele, also leading to the derepression of DUX4, further supporting a central role for DUX4. How DUX4 misexpression contributes to FSHD muscle pathology is a major focus of current investigation. Misexpression of other genes at the 4q35 locus, including FRG1 and FAT1, and unlinked genes, such as SMCHD1, has also been implicated as disease modifiers, leading to several competing disease models. In this review, we describe recent advances in understanding the pathophysiology of FSHD, including the application of MRI as a research and diagnostic tool, the genetic and epigenetic disruptions associated with the disease, and the molecular basis of FSHD. We discuss how these advances are leading to the emergence of new approaches to enable development of FSHD therapeutics. © 2017 American Physiological Society. Compr Physiol 7:1229-1279, 2017.
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Affiliation(s)
- Alec M DeSimone
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Anna Pakula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA
| | - Angela Lek
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Kumar S, Gomez EC, Chalabi-Dchar M, Rong C, Das S, Ugrinova I, Gaume X, Monier K, Mongelard F, Bouvet P. Integrated analysis of mRNA and miRNA expression in HeLa cells expressing low levels of Nucleolin. Sci Rep 2017; 7:9017. [PMID: 28827664 PMCID: PMC5567140 DOI: 10.1038/s41598-017-09353-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023] Open
Abstract
Nucleolin is an essential protein that plays important roles in the regulation of cell cycle and cell proliferation. Its expression is up regulated in many cancer cells but its molecular functions are not well characterized. Nucleolin is present in the nucleus where it regulates gene expression at the transcriptional and post-transcriptional levels. Using HeLa cells depleted in nucleolin we performed an mRNA and miRNA transcriptomics analysis to identify biological pathways involving nucleolin. Bioinformatic analysis strongly points to a role of nucleolin in lipid metabolism, and in many signaling pathways. Down regulation of nucleolin is associated with lower level of cholesterol while the amount of fatty acids is increased. This could be explained by the decreased and mis-localized expression of the transcription factor SREBP1 and the down-regulation of enzymes involved in the beta-oxidation and degradation of fatty acids. Functional classification of the miRNA-mRNA target genes revealed that deregulated miRNAs target genes involved in apoptosis, proliferation and signaling pathways. Several of these deregulated miRNAs have been shown to control lipid metabolism. This integrated transcriptomic analysis uncovers new unexpected roles for nucleolin in metabolic regulation and signaling pathways paving the way to better understand the global function of nucleolin within the cell.
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Affiliation(s)
- Sanjeev Kumar
- BioCOS Life Sciences Private Limited, AECS Layout, B-Block, Singasandra Hosur Road SAAMI Building, 851/A, 3rd Floor, Bengaluru, Karnataka, India.
| | - Elizabhet Cruz Gomez
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
| | - Mounira Chalabi-Dchar
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
| | - Cong Rong
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Iva Ugrinova
- Institute of Molecular Biology "Acad. Roumen Tsanev" Bulgarian Academy of Sciences "Acad. G Bonchev str. bl. 21, 1113, Sofia, Bulgaria
| | - Xavier Gaume
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Karine Monier
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
| | - Fabien Mongelard
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Philippe Bouvet
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS, 5286, Centre Léon Bérard, Lyon, France.
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France.
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Tsekrekou M, Stratigi K, Chatzinikolaou G. The Nucleolus: In Genome Maintenance and Repair. Int J Mol Sci 2017; 18:ijms18071411. [PMID: 28671574 PMCID: PMC5535903 DOI: 10.3390/ijms18071411] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 11/16/2022] Open
Abstract
The nucleolus is the subnuclear membrane-less organelle where rRNA is transcribed and processed and ribosomal assembly occurs. During the last 20 years, however, the nucleolus has emerged as a multifunctional organelle, regulating processes that go well beyond its traditional role. Moreover, the unique organization of rDNA in tandem arrays and its unusually high transcription rates make it prone to unscheduled DNA recombination events and frequent RNA:DNA hybrids leading to DNA double strand breaks (DSBs). If not properly repaired, rDNA damage may contribute to premature disease onset and aging. Deregulation of ribosomal synthesis at any level from transcription and processing to ribosomal subunit assembly elicits a stress response and is also associated with disease onset. Here, we discuss how genome integrity is maintained within nucleoli and how such structures are functionally linked to nuclear DNA damage response and repair giving an emphasis on the newly emerging roles of the nucleolus in mammalian physiology and disease.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece.
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Crete, Greece.
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece.
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Crete, Greece.
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece.
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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Wu M, Wei W, Chen J, Cong R, Shi T, Bouvet P, Li J, Wong J, Du JX. Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins. SCIENCE CHINA. LIFE SCIENCES 2017; 60:138-151. [PMID: 28194553 DOI: 10.1007/s11427-016-0413-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 01/09/2017] [Indexed: 02/03/2023]
Abstract
Histone methylation is believed to provide binding sites for specific reader proteins, which translate histone code into biological function. Here we show that a family of acidic domain-containing proteins including nucleophosmin (NPM1), pp32, SET/TAF1β, nucleolin (NCL) and upstream binding factor (UBF) are novel H3K4me2-binding proteins. These proteins exhibit a unique pattern of interaction with methylated H3K4, as their binding is stimulated by H3K4me2 and inhibited by H3K4me1 and H3K4me3. These proteins contain one or more acidic domains consisting mainly of aspartic and/or glutamic residues that are necessary for preferential binding of H3K4me2. Furthermore, we demonstrate that the acidic domain with sufficient length alone is capable of binding H3K4me2 in vitro and in vivo. NPM1, NCL and UBF require their acidic domains for association with and transcriptional activation of rDNA genes. Interestingly, by defining acidic domain as a sequence with at least 20 acidic residues in 50 continuous amino acids, we identified 655 acidic domain-containing protein coding genes in the human genome and Gene Ontology (GO) analysis showed that many of the acidic domain proteins have chromatin-related functions. Our data suggest that acidic domain is a novel histone binding motif that can differentially read the status of H3K4 methylation and is broadly present in chromatin-associated proteins.
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Affiliation(s)
- Meng Wu
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiwei Chen
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, 69364, France
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, 69364, France
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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Buschbeck M, Hake SB. Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 2017; 18:299-314. [DOI: 10.1038/nrm.2016.166] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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57
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Reddy BA, Jeronimo C, Robert F. Recent Perspectives on the Roles of Histone Chaperones in Transcription Regulation. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40610-017-0049-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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58
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Zhang P, Branson OE, Freitas MA, Parthun MR. Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability. BMC BIOCHEMISTRY 2016; 17:18. [PMID: 27716023 PMCID: PMC5045598 DOI: 10.1186/s12858-016-0074-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND There are 11 variants of linker histone H1 in mammalian cells. Beyond their shared abilities to stabilize and condense chromatin, the H1 variants have been found to have non-redundant functions, the mechanisms of which are not fully understood. Like core histones, there are both replication-dependent and replication-independent linker histone variants. The histone chaperones and other factors that regulate linker histone dynamics in the cell are largely unknown. In particular, it is not known whether replication-dependent and replication-independent linker histones interact with distinct or common sets of proteins. To better understand linker histone dynamics and assembly, we used chromatography and mass spectrometry approaches to identify proteins that are associated with replication-dependent and replication-independent H1 variants. We then used a variety of in vivo analyses to validate the functional relevance of identified interactions. RESULTS We identified proteins that bind to all linker histone variants and proteins that are specific for only one class of variant. The factors identified include histone chaperones, transcriptional regulators, RNA binding proteins and ribosomal proteins. The nuclear pore complex protein Tpr, which was found to associate with only replication-dependent linker histones, specifically promoted their stability. CONCLUSION Replication-dependent and replication-independent linker histone variants can interact with both common and distinct sets of proteins. Some of these factors are likely to function as histone chaperones while others may suggest novel links between linker histones and RNA metabolism. The nuclear pore complex protein Tpr specifically interacts with histone H1.1 and H1.2 but not H1x and can regulate the stability of these replication-dependent linker histones.
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Affiliation(s)
- Pei Zhang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
| | - Owen E. Branson
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Michael A. Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Mark R. Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
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Scott DD, Oeffinger M. Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol 2016; 94:419-432. [PMID: 27673355 DOI: 10.1139/bcb-2016-0068] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
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Affiliation(s)
- Daniel D Scott
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
| | - Marlene Oeffinger
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
- c Département de biochimie et médecine moléculaire, Faculté de Médecine, Université de Montréal, QC H3T 1J4, Canada
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Aizawa M, Sugimoto N, Watanabe S, Yoshida K, Fujita M. Nucleosome assembly and disassembly activity of GRWD1, a novel Cdt1-binding protein that promotes pre-replication complex formation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2739-2748. [PMID: 27552915 DOI: 10.1016/j.bbamcr.2016.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023]
Abstract
GRWD1 was previously identified as a novel Cdt1-binding protein that possesses histone-binding and nucleosome assembly activities and promotes MCM loading, probably by maintaining chromatin openness at replication origins. However, the molecular mechanisms underlying these activities remain unknown. We prepared reconstituted mononucleosomes from recombinant histones and a DNA fragment containing a nucleosome positioning sequence, and investigated the effects of GRWD1 on them. GRWD1 could disassemble these preformed mononucleosomes in vitro in an ATP-independent manner. Thus, our data suggest that GRWD1 facilitates removal of H2A-H2B dimers from nucleosomes, resulting in formation of hexasomes. The activity was compromised by deletion of the acidic domain, which is required for efficient histone binding. In contrast, nucleosome assembly activity of GRWD1 was not affected by deletion of the acidic domain. In HeLa cells, the acidic domain of GRWD1 was necessary to maintain chromatin openness and promote MCM loading at replication origins. Taken together, our results suggest that GRWD1 promotes chromatin fluidity by influencing nucleosome structures, e.g., by transient eviction of H2A-H2B, and thereby promotes efficient MCM loading at replication origins.
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Affiliation(s)
- Masahiro Aizawa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Shinya Watanabe
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan.
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Frau-Méndez MA, Fernández-Vega I, Ansoleaga B, Blanco Tech R, Carmona Tech M, Antonio Del Rio J, Zerr I, Llorens F, José Zarranz J, Ferrer I. Fatal familial insomnia: mitochondrial and protein synthesis machinery decline in the mediodorsal thalamus. Brain Pathol 2016; 27:95-106. [PMID: 27338255 DOI: 10.1111/bpa.12408] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/16/2016] [Indexed: 11/29/2022] Open
Abstract
The expression of subunits of mitochondrial respiratory complexes and components of the protein synthesis machinery from the nucleolus to the ribosome was analyzed in the mediodorsal thalamus in seven cases of fatal familial insomnia (FFI) compared with age-matched controls. NDUFB8 (complex I subunit), SDHB (complex II subunit), UQCRC2 (complex III subunit), COX2 (complex IV subunit), and ATP50 (complex V subunit) expression levels, as revealed by western blotting, were reduced in FFI. Voltage-dependent anion channel (VDAC) and ATP5H were also reduced due to the marked depopulation of neurons. In contrast, a marked increase in superoxide dismutase 2 (SOD2) was found in reactive astrocytes thus suggesting that astrocytes are key factors in oxidative stress responses. The histone-binding chaperones nucleolin and nucleoplasmin 3, and histone H3 di-methylated K9 were markedly reduced together with a decrease in the expression of protein transcription elongation factor eEF1A. These findings show severe impairment in the expression of crucial components of mitochondrial function and protein synthesis in parallel with neuron loss in mediodorsal thalamus at terminal stages of FFI. Therapeutic measures must be taken long before the appearance of clinical symptoms to prevent the devastating effects of FFI.
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Affiliation(s)
- Margalida A Frau-Méndez
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - Iván Fernández-Vega
- Department of Neuropathology, Pathology Department, University Hospital Araba, Álava, Brain Bank Araba University Hospital, Basque Biobank for Research (O+eHun), Spain
| | - Belén Ansoleaga
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - Rosa Blanco Tech
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain.,Department of Neuropathology, Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Spain
| | - Margarita Carmona Tech
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain.,Department of Neuropathology, Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Spain
| | - Jose Antonio Del Rio
- Department of Neuropathology, Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Spain.,Department of Cell Biology, Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Inga Zerr
- Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Franc Llorens
- Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Juan José Zarranz
- Neurology Department, University Hospital Cruces, University of the Basque Country, Bizkaia, Spain
| | - Isidro Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain.,Department of Neuropathology, Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Spain
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Charles Richard JL, Shukla MS, Menoni H, Ouararhni K, Lone IN, Roulland Y, Papin C, Ben Simon E, Kundu T, Hamiche A, Angelov D, Dimitrov S. FACT Assists Base Excision Repair by Boosting the Remodeling Activity of RSC. PLoS Genet 2016; 12:e1006221. [PMID: 27467129 PMCID: PMC4965029 DOI: 10.1371/journal.pgen.1006221] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/06/2016] [Indexed: 01/14/2023] Open
Abstract
FACT, in addition to its role in transcription, is likely implicated in both transcription-coupled nucleotide excision repair and DNA double strand break repair. Here, we present evidence that FACT could be directly involved in Base Excision Repair and elucidate the chromatin remodeling mechanisms of FACT during BER. We found that, upon oxidative stress, FACT is released from transcription related protein complexes to get associated with repair proteins and chromatin remodelers from the SWI/SNF family. We also showed the rapid recruitment of FACT to the site of damage, coincident with the glycosylase OGG1, upon the local generation of oxidized DNA. Interestingly, FACT facilitates uracil-DNA glycosylase in the removal of uracil from nucleosomal DNA thanks to an enhancement in the remodeling activity of RSC. This discloses a novel property of FACT wherein it has a co-remodeling activity and strongly enhances the remodeling capacity of the chromatin remodelers. Altogether, our data suggest that FACT may acts in concert with RSC to facilitate excision of DNA lesions during the initial step of BER. In the nucleus, DNA is packaged into chromatin. The repeating unit of chromatin, the nucleosome, consists of a histone octamer around which DNA is wrapped into two superhelical turns. The nucleosome is a barrier for various nuclear processes which require access to DNA. To repair lesions on DNA, this barrier has to be overcome by either nucleosome remodeling or by histone eviction. Here we present evidence that FACT, a protein known to be involved in transcription, is also involved in BER, by boosting nucleosome remodeling. Upon in vivo oxidized DNA lesion induction, FACT exhibits a BER-like protein behavior, and it is recruited to the sites of DNA damages. In vitro experiments show that FACT boosts the remodeling activity of the chromatin remodeler RSC and is implicated in DNA repair. The presence of FACT greatly facilitates the removal of uracil from nucleosomal, but not from naked DNA, in a RSC-mediated reaction. Taken collectively, our in vitro and in vivo data reveal a role of FACT in BER by helping the remodeling of chromatin at the sites of lesions.
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Affiliation(s)
- John Lalith Charles Richard
- Université Joseph Fourier-Grenoble 1, INSERM Institut Albert Bonniot U823, Site Santé, Grenoble, France
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, LBMC CNRS/ENSL/UCBL UMR5239 & Institut NeuroMyoGène–INMG CNRS/UCBL UMR5310, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Manu Shubhdarshan Shukla
- Université Joseph Fourier-Grenoble 1, INSERM Institut Albert Bonniot U823, Site Santé, Grenoble, France
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, LBMC CNRS/ENSL/UCBL UMR5239 & Institut NeuroMyoGène–INMG CNRS/UCBL UMR5310, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Hervé Menoni
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, LBMC CNRS/ENSL/UCBL UMR5239 & Institut NeuroMyoGène–INMG CNRS/UCBL UMR5310, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Khalid Ouararhni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Parc d’Innovation, Illkirch, France
| | - Imtiaz Nisar Lone
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, LBMC CNRS/ENSL/UCBL UMR5239 & Institut NeuroMyoGène–INMG CNRS/UCBL UMR5310, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Yohan Roulland
- Université Joseph Fourier-Grenoble 1, INSERM Institut Albert Bonniot U823, Site Santé, Grenoble, France
| | - Christophe Papin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Parc d’Innovation, Illkirch, France
| | - Elsa Ben Simon
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, LBMC CNRS/ENSL/UCBL UMR5239 & Institut NeuroMyoGène–INMG CNRS/UCBL UMR5310, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Tapas Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Ali Hamiche
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Parc d’Innovation, Illkirch, France
- * E-mail: (AH); (DA); (SD)
| | - Dimitar Angelov
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, LBMC CNRS/ENSL/UCBL UMR5239 & Institut NeuroMyoGène–INMG CNRS/UCBL UMR5310, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (AH); (DA); (SD)
| | - Stefan Dimitrov
- Université Joseph Fourier-Grenoble 1, INSERM Institut Albert Bonniot U823, Site Santé, Grenoble, France
- * E-mail: (AH); (DA); (SD)
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Terrier O, Carron C, De Chassey B, Dubois J, Traversier A, Julien T, Cartet G, Proust A, Hacot S, Ressnikoff D, Lotteau V, Lina B, Diaz JJ, Moules V, Rosa-Calatrava M. Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication. Sci Rep 2016; 6:29006. [PMID: 27373907 PMCID: PMC4931502 DOI: 10.1038/srep29006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/09/2016] [Indexed: 01/18/2023] Open
Abstract
Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells and these replicated genomes (vRNPs) are then exported from the nucleus to the cytoplasm and plasma membrane before budding. To achieve this export, influenza viruses hijack the host cell export machinery. However, the complete mechanisms underlying this hijacking remain not fully understood. We have previously shown that influenza viruses induce a marked alteration of the nucleus during the time-course of infection and notably in the nucleolar compartment. In this study, we discovered that a major nucleolar component, called nucleolin, is required for an efficient export of vRNPs and viral replication. We have notably shown that nucleolin interacts with the viral nucleoprotein (NP) that mainly constitutes vRNPs. Our results suggest that this interaction could allow vRNPs to "catch" the host cell export machinery, a necessary step for viral replication.
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Affiliation(s)
- Olivier Terrier
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Coralie Carron
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Benoît De Chassey
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Julia Dubois
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Aurélien Traversier
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Thomas Julien
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Gaëlle Cartet
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Anaïs Proust
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Sabine Hacot
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France and Université de Lyon, Lyon, France
| | - Denis Ressnikoff
- CIQLE, Centre d’imagerie quantitative Lyon-Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bruno Lina
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Hospices Civils de Lyon, Laboratory of Virology, Lyon, France
| | - Jean-Jacques Diaz
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France and Université de Lyon, Lyon, France
| | - Vincent Moules
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Manuel Rosa-Calatrava
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
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Pieraccioli M, Nicolai S, Antonov A, Somers J, Malewicz M, Melino G, Raschellà G. ZNF281 contributes to the DNA damage response by controlling the expression of XRCC2 and XRCC4. Oncogene 2016; 35:2592-601. [PMID: 26300006 DOI: 10.1038/onc.2015.320] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/02/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022]
Abstract
ZNF281 is a zinc-finger factor involved in the control of cellular stemness and epithelial-mesenchymal transition (EMT). Here, we report that ZNF281 expression increased after genotoxic stress caused by DNA-damaging drugs. Comet assays demonstrated that DNA repair was delayed in cells silenced for the expression of ZNF281 and treated with etoposide. Furthermore, the expression of 10 DNA damage response genes was downregulated in cells treated with etoposide and silenced for ZNF281. In line with this finding, XRCC2 and XRCC4, two genes that take part in homologous recombination and non-homologous end joining, respectively, were transcriptionally activated by ZNF281 through a DNA-binding-dependent mechanism, as demonstrated by luciferase assays and Chromatin crosslinking ImmunoPrecipitation experiments. c-Myc, which also binds to the promoters of XRCC2 and XRCC4, was unable to promote their transcription or to modify ZNF281 activity. Of interest, bioinformatic analysis of 1971 breast cancer patients disclosed a significant correlation between the expression of ZNF281 and that of XRCC2. In summary, our data highlight, for the first time, the involvement of ZNF281 in the cellular response to genotoxic stress through the control exercised on the expression of genes that act in different repair mechanisms.
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Affiliation(s)
- M Pieraccioli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - S Nicolai
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - A Antonov
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - J Somers
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - M Malewicz
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - G Melino
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
| | - G Raschellà
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
- Radiation Biology and Human Health Unit, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) Research Center Casaccia, Rome, Italy
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65
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Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
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Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
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66
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Hernández-Ortega K, Garcia-Esparcia P, Gil L, Lucas JJ, Ferrer I. Altered Machinery of Protein Synthesis in Alzheimer's: From the Nucleolus to the Ribosome. Brain Pathol 2015; 26:593-605. [PMID: 26512942 DOI: 10.1111/bpa.12335] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 10/22/2015] [Indexed: 12/17/2022] Open
Abstract
Ribosomes and protein synthesis have been reported to be altered in the cerebral cortex at advanced stages of Alzheimer's disease (AD). Modifications in the hippocampus with disease progression have not been assessed. Sixty-seven cases including middle-aged (MA) and AD stages I-VI were analyzed. Nucleolar chaperones nucleolin, nucleophosmin and nucleoplasmin 3, and upstream binding transcription factor RNA polymerase I gene (UBTF) mRNAs are abnormally regulated and their protein levels reduced in AD. Histone modifications dimethylated histone H3K9 (H3K9me2) and acetylated histone H3K12 (H3K12ac) are decreased in CA1. Nuclear tau declines in CA1 and dentate gyrus (DG), and practically disappears in neurons with neurofibrillary tangles. Subunit 28 ribosomal RNA (28S rRNA) expression is altered in CA1 and DG in AD. Several genes encoding ribosomal proteins are abnormally regulated and protein levels of translation initiation factors eIF2α, eIF3η and eIF5, and elongation factor eEF2, are altered in the CA1 region in AD. These findings show alterations in the protein synthesis machinery in AD involving the nucleolus, nucleus and ribosomes in the hippocampus in AD some of them starting at first stages (I-II) preceding neuron loss. These changes may lie behind reduced numbers of dendritic branches and reduced synapses of CA1 and DG neurons which cause hippocampal atrophy.
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Affiliation(s)
- Karina Hernández-Ortega
- Institute of Neuropathology, Service of Pathologic Anatomy, IDIBELL-Bellvitge University Hospital, University of Barcelona, Hospitalet de Llobregat, Spain.,Neuropathology, CIBERNED (Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas), Madrid, Spain
| | - Paula Garcia-Esparcia
- Institute of Neuropathology, Service of Pathologic Anatomy, IDIBELL-Bellvitge University Hospital, University of Barcelona, Hospitalet de Llobregat, Spain.,Neuropathology, CIBERNED (Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas), Madrid, Spain
| | - Laura Gil
- Department of Genetics, Medical School, Alfonso X el Sabio University (UAX), Villanueva de la Cañada; Centro de Investigaciones Biologicas (CIB), CSIC, Madrid, Spain
| | - José J Lucas
- Neuropathology, CIBERNED (Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas), Madrid, Spain.,Department of Molecular Biology, Center for Molecular Biology "Severo Ochoa" (CBMSO) CSIC/UAM, Madrid, 28049, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Service of Pathologic Anatomy, IDIBELL-Bellvitge University Hospital, University of Barcelona, Hospitalet de Llobregat, Spain.,Neuropathology, CIBERNED (Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas), Madrid, Spain
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67
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Garcia-Esparcia P, Hernández-Ortega K, Koneti A, Gil L, Delgado-Morales R, Castaño E, Carmona M, Ferrer I. Altered machinery of protein synthesis is region- and stage-dependent and is associated with α-synuclein oligomers in Parkinson's disease. Acta Neuropathol Commun 2015; 3:76. [PMID: 26621506 PMCID: PMC4666041 DOI: 10.1186/s40478-015-0257-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/14/2015] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Parkinson's disease (PD) is characterized by the accumulation of abnormal α-synuclein in selected regions of the brain following a gradient of severity with disease progression. Whether this is accompanied by globally altered protein synthesis is poorly documented. The present study was carried out in PD stages 1-6 of Braak and middle-aged (MA) individuals without alterations in brain in the substantia nigra, frontal cortex area 8, angular gyrus, precuneus and putamen. RESULTS Reduced mRNA expression of nucleolar proteins nucleolin (NCL), nucleophosmin (NPM1), nucleoplasmin 3 (NPM3) and upstream binding transcription factor (UBF), decreased NPM1 but not NPM3 nucleolar protein immunostaining in remaining neurons; diminished 18S rRNA, 28S rRNA; reduced expression of several mRNAs encoding ribosomal protein (RP) subunits; and altered protein levels of initiation factor eIF3 and elongation factor eEF2 of protein synthesis was found in the substantia nigra in PD along with disease progression. Although many of these changes can be related to neuron loss in the substantia nigra, selective alteration of certain factors indicates variable degree of vulnerability of mRNAs, rRNAs and proteins in degenerating sustantia nigra. NPM1 mRNA and 18S rRNA was increased in the frontal cortex area 8 at stage 5-6; modifications were less marked and region-dependent in the angular gyrus and precuneus. Several RPs were abnormally regulated in the frontal cortex area 8 and precuneus, but only one RP in the angular gyrus, in PD. Altered levels of eIF3 and eIF1, and decrease eEF1A and eEF2 protein levels were observed in the frontal cortex in PD. No modifications were found in the putamen at any time of the study except transient modifications in 28S rRNA and only one RP mRNA at stages 5-6. These observations further indicate marked region-dependent and stage-dependent alterations in the cerebral cortex in PD. Altered solubility and α-synuclein oligomer formation, assessed in total homogenate fractions blotted with anti-α-synuclein oligomer-specific antibody, was demonstrated in the substantia nigra and frontal cortex, but not in the putamen, in PD. Dramatic increase in α-synuclein oligomers was also seen in fluorescent-activated cell sorter (FACS)-isolated nuclei in the frontal cortex in PD. CONCLUSIONS Altered machinery of protein synthesis is altered in the substantia nigra and cerebral cortex in PD being the frontal cortex area 8 more affected than the angular gyrus and precuneus; in contrast, pathways of protein synthesis are apparently preserved in the putamen. This is associated with the presence of α-synuclein oligomeric species in total homogenates; substantia nigra and frontal cortex are enriched, albeit with different band patterns, in α-synuclein oligomeric species, whereas α-synuclein oligomers are not detected in the putamen.
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Affiliation(s)
- Paula Garcia-Esparcia
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Karina Hernández-Ortega
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Anusha Koneti
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Laura Gil
- Department of Genetics, Medical School, Alfonso X el Sabio University, Villanueva de la Cañada, Madrid, Spain
| | - Raul Delgado-Morales
- Cancer Epigenetics and Biology Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ester Castaño
- Biology-Bellvitge Unit, Scientific and Technological Centers-University of Barcelona (CCiTUB), Hospitalet de Llobregat, Barcelona, Spain
| | - Margarita Carmona
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain.
- Institute of Neuropathology, Service of Pathologic Anatomy, Bellvitge University Hospital, carrer Feixa Llarga s/n, 08907, Hospitalet de Llobregat, Spain.
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68
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Bhatia S, Reister S, Mahotka C, Meisel R, Borkhardt A, Grinstein E. Control of AC133/CD133 and impact on human hematopoietic progenitor cells through nucleolin. Leukemia 2015; 29:2208-20. [PMID: 26183533 DOI: 10.1038/leu.2015.146] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 01/01/2023]
Abstract
AC133 is a prominent surface marker of CD34+ and CD34- hematopoietic stem/progenitor cell (HSPC) subsets. AC133+ HSPCs contain high progenitor cell activity and are capable of hematopoietic reconstitution. Furthermore, AC133 is used for prospective isolation of tumor-initiating cells in several hematological malignancies. Nucleolin is a multifunctional factor of growing and cancer cells, which is aberrantly active in certain hematological neoplasms, and serves as a candidate molecular target for cancer therapy. Nucleolin is involved in gene transcription and RNA metabolism and is prevalently expressed in HSPCs, as opposed to differentiated hematopoietic tissue. The present study dissects nucleolin-mediated activation of surface AC133 and its cognate gene CD133, via specific interaction of nucleolin with the tissue-dependent CD133 promoter P1, as a mechanism that crucially contributes to AC133 expression in CD34+ HSPCs. In mobilized peripheral blood (MPB)-derived HSPCs, nucleolin elevates colony-forming unit (CFU) frequencies and enriches granulocyte-macrophage CFUs. Furthermore, nucleolin amplifies long-term culture-initiating cells and also promotes long-term, cytokine-dependent maintenance of hematopoietic progenitor cells. Active β-catenin, active Akt and Bcl-2 levels in MPB-derived HSPCs are nucleolin-dependent, and effects of nucleolin on these cells partially rely on β-catenin activity. The study provides new insights into molecular network relevant to stem/progenitor cells in normal and malignant hematopoiesis.
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Affiliation(s)
- S Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - S Reister
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - C Mahotka
- Institute of Pathology, Heinrich Heine University, Düsseldorf, Germany
| | - R Meisel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - A Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - E Grinstein
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
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Experimental analysis of hFACT action during Pol II transcription in vitro. Methods Mol Biol 2015; 1276:315-26. [PMID: 25665573 DOI: 10.1007/978-1-4939-2392-2_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
FACT (facilitates chromatin transcription) is a histone chaperone that facilitates transcription through chromatin and promotes histone recovery during transcription. Here, we describe a highly purified experimental system that recapitulates many important properties of transcribed chromatin and the key aspects of hFACT action during this process in vitro. We present the protocols describing how to prepare different forms of nucleosomes, including intact nucleosome, covalently conjugated nucleosome, nucleosome missing one of the two H2A/2B dimers (hexasome) and tetrasome (a nucleosome missing both H2A/2B dimers). These complexes allow analysis of various aspects of FACT's function. These approaches and other methods described below can also be applied to the study of other chromatin remodelers and chromatin-targeted factors.
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70
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Tosoni E, Frasson I, Scalabrin M, Perrone R, Butovskaya E, Nadai M, Palù G, Fabris D, Richter SN. Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription. Nucleic Acids Res 2015; 43:8884-97. [PMID: 26354862 PMCID: PMC4605322 DOI: 10.1093/nar/gkv897] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 01/26/2023] Open
Abstract
Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy.
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Affiliation(s)
- Elena Tosoni
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Dan Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
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71
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Berger CM, Gaume X, Bouvet P. The roles of nucleolin subcellular localization in cancer. Biochimie 2015; 113:78-85. [PMID: 25866190 DOI: 10.1016/j.biochi.2015.03.023] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/29/2015] [Indexed: 01/10/2023]
Abstract
Nucleolin (NCL) is one of the most abundant non ribosomal protein of the nucleolus where it plays a central role in polymerase I transcription. NCL is also found outside of the nucleolus, in the nucleoplasm, cytoplasm as well as on the cell membrane. It acts in all cell compartments to control cellular homeostasis and therefore each cellular pool of NCL can play a different role in cancer development. NCL overexpression and its increased localization at the cell membrane is a common feature of several tumor cells. In cancer cells, NCL overexpression influences cell survival, proliferation and invasion through its action on different cellular pathways. In this review, we describe how the multiple functions of NCL that are associated to its multiple cellular localization can participate to the development of cancer.
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Affiliation(s)
- Caroline Madeleine Berger
- Département de Biologie, Master Biosciences, ENS de Lyon, Lyon, France; Ecole Normale Supérieure de Lyon, Laboratoire Joliot-Curie, CNRS USR 3010, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Xavier Gaume
- Ecole Normale Supérieure de Lyon, Laboratoire Joliot-Curie, CNRS USR 3010, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon, Laboratoire Joliot-Curie, CNRS USR 3010, 46 allée d'Italie, 69364 Lyon Cedex 7, France.
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72
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Saningong AD, Bayer P. Human DNA-binding peptidyl-prolyl cis/trans isomerase Par14 is cell cycle dependently expressed and associates with chromatin in vivo. BMC BIOCHEMISTRY 2015; 16:4. [PMID: 25645591 PMCID: PMC4327958 DOI: 10.1186/s12858-015-0033-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/15/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Par14, a member of the parvulin family of peptidyl-prolyl cis-trans isomerases that is involved in rRNA processing, microtubule formation and the glucose metabolism and has been suggested to play a role in chromatin remodeling on basis of sequence and structural identities to HMG proteins. Par14 is enriched in the nucleus and binds to double-stranded DNA in vitro. RESULTS By means of sub-nuclear biochemical fractionations, we demonstrate that cellular Par14 is associated with chromatin 3-fold higher than with the nuclear matrix in vivo. Par14 is released from the chromatin fraction after treatment with DNase I and elutes at high NaCl concentrations from the nucleic acid-binding fraction. Using qRT-PCR and western blotting we demonstrate that Par14 is up-regulated during the S and G2/M phases in synchronised human foreskin fibroblasts cells. CONCLUSION In the light of our results, Par14 can be described as an endogenous non-histone chromatin protein, which binds DNA in vivo. We propose that Par14 is involved in a DNA-dependent activity such as transcription.
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Affiliation(s)
- Akuma D Saningong
- Department of Structural and Medicinal Biochemistry, Center of Medical Biotechnology, Universität Duisburg-Essen, Room S03 S01 A35, Universitätsstr. 1-5, 45141, Essen, Germany.
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Center of Medical Biotechnology, Universität Duisburg-Essen, Room S03 S01 A35, Universitätsstr. 1-5, 45141, Essen, Germany.
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73
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Durut N, Sáez-Vásquez J. Nucleolin: dual roles in rDNA chromatin transcription. Gene 2015; 556:7-12. [PMID: 25225127 DOI: 10.1016/j.gene.2014.09.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023]
Abstract
Nucleolin is a major nucleolar protein conserved in all eukaryotic organisms. It is a multifunctional protein involved in different cellular aspects like chromatin organization and stability, DNA and RNA metabolism, assembly of ribonucleoprotein complexes, cytokinesis, cell proliferation and stress response. The multifunctionality of nucleolin is linked to its tripartite structure, post-translational modifications and its ability of shuttling from and to the nucleolus/nucleoplasm and cytoplasm. Nucleolin has been now studied for many years and its activities and properties have been described in a number of excellent reviews. Here, we overview the role of nucleolin in RNA polymerase I (RNAPI) transcription and describe recent results concerning its functional interaction with rDNA chromatin organization. For a long time, nucleolin has been associated with rRNA gene expression and pre-rRNA processing. However, the functional connection between nucleolin and active versus inactive rRNA genes is still not fully understood. Novel evidence indicates that the nucleolin protein might be required for controlling the transcriptional ON/OFF states of rDNA chromatin in both mammals and plants.
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Affiliation(s)
- Nathalie Durut
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France; Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France; Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France.
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74
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Gurard-Levin ZA, Quivy JP, Almouzni G. Histone chaperones: assisting histone traffic and nucleosome dynamics. Annu Rev Biochem 2015; 83:487-517. [PMID: 24905786 DOI: 10.1146/annurev-biochem-060713-035536] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The functional organization of eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. Histone chaperones, which are proteins that escort histones throughout their cellular life, are key actors in all facets of histone metabolism; they regulate the supply and dynamics of histones at chromatin for its assembly and disassembly. Histone chaperones can also participate in the distribution of histone variants, thereby defining distinct chromatin landscapes of importance for genome function, stability, and cell identity. Here, we discuss our current knowledge of the known histone chaperones and their histone partners, focusing on histone H3 and its variants. We then place them into an escort network that distributes these histones in various deposition pathways. Through their distinct interfaces, we show how they affect dynamics during DNA replication, DNA damage, and transcription, and how they maintain genome integrity. Finally, we discuss the importance of histone chaperones during development and describe how misregulation of the histone flow can link to disease.
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Affiliation(s)
- Zachary A Gurard-Levin
- Institut Curie, Centre de Recherche; CNRS UMR 3664; Equipe Labellisée, Ligue contre le Cancer; and Université Pierre et Marie Curie, Paris F-75248, France;
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75
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Ishibashi N, Kitakura S, Terakura S, Machida C, Machida Y. Protein encoded by oncogene 6b from Agrobacterium tumefaciens has a reprogramming potential and histone chaperone-like activity. FRONTIERS IN PLANT SCIENCE 2014; 5:572. [PMID: 25389429 PMCID: PMC4211554 DOI: 10.3389/fpls.2014.00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/05/2014] [Indexed: 05/31/2023]
Abstract
Crown gall tumors are formed mainly by actions of a group of genes in the T-DNA that is transferred from Agrobacterium tumefaciens and integrated into the nuclear DNA of host plants. These genes encode enzymes for biosynthesis of auxin and cytokinin in plant cells. Gene 6b in the T-DNA affects tumor morphology and this gene alone is able to induce small tumors on certain plant species. In addition, unorganized calli are induced from leaf disks of tobacco that are incubated on phytohormone-free media; shooty teratomas, and morphologically abnormal plants, which might be due to enhanced competence of cell division and meristematic states, are regenerated from the calli. Thus, the 6b gene appears to stimulate a reprogramming process in plants. To uncover mechanisms behind this process, various approaches including the yeast-two-hybrid system have been exploited and histone H3 was identified as one of the proteins that interact with 6b. It has been also demonstrated that 6b acts as a histone H3 chaperon in vitro and affects the expression of various genes related to cell division competence and the maintenance of meristematic states. We discuss current views on a role of 6b protein in tumorigenesis and reprogramming in plants.
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Affiliation(s)
- Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
| | - Saeko Kitakura
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
- Graduate School of Bioscience and Biotechnology, Chubu UniversityKasugai, Japan
| | - Shinji Terakura
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu UniversityKasugai, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
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76
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Xiao S, Caglar E, Maldonado P, Das D, Nadeem Z, Chi A, Trinité B, Li X, Saxena A. Induced expression of nucleolin phosphorylation-deficient mutant confers dominant-negative effect on cell proliferation. PLoS One 2014; 9:e109858. [PMID: 25313645 PMCID: PMC4196967 DOI: 10.1371/journal.pone.0109858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/08/2014] [Indexed: 11/25/2022] Open
Abstract
Nucleolin (NCL) is a major nucleolar phosphoprotein that has pleiotropic effects on cell proliferation and is elevated in a variety of tumors. NCL is highly phosphorylated at the N-terminus by two major kinases: interphase casein kinase 2 (CK2) and mitotic cyclin-dependent kinase 1 (CDK1). Earlier we demonstrated that a NCL-mutant that is partly defective in undergoing phosphorylation by CK2 inhibits chromosomal replication through its interactions with Replication Protein A, mimicking the cellular response to DNA damage. We further delineated that the N-terminus of NCL associates with Hdm2, the most common E3 ubiquitin ligase of p53. We reported that NCL antagonizes Hdm2 to stabilize p53 and stimulates p53 transcriptional activity. Although NCL-phosphorylation by CK2 and ribosomal DNA transcription are closely coordinated during interphase, the role of NCL phosphorylation in regulating cell proliferation remains unexplored. We have therefore engineered unique human cells that specifically induce expression of NCL-wild type (WT) or a phosphorylation-deficient NCL-mutant, 6/S*A where all the six CK2 consensus serine sites residing in the N-terminus NCL were mutated to alanine. Here we show that this NCL-mutant is defective in undergoing phosphorylation by CK2. We also demonstrate that NCL-phosphorylation by CK2 is required through the S-phase progression in cell cycle and hence proliferation. Induced expression of NCL with mutated CK2 phosphorylation sites stabilizes p53, results in higher expression of Bcl2 (B-cell lymphoma 2) homology 3 (BH3)-only apoptotic markers and causes a dominant-negative effect on cell viability. Our unique cellular system thus provides the first evidential support to delineate phospho-specific functions of NCL on cell proliferation.
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Affiliation(s)
- Shu Xiao
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
| | - Elif Caglar
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
| | - Priscilla Maldonado
- New York University School of Medicine, New York, New York, United States of America
| | - Dibash Das
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
| | - Zaineb Nadeem
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
| | - Angela Chi
- Great Neck South High School, Great Neck, New York, United States of America
| | - Benjamin Trinité
- New York University College of Dentistry, New York, New York, United States of America
| | - Xin Li
- New York University College of Dentistry, New York, New York, United States of America
| | - Anjana Saxena
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
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77
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Wang W, Luo J, Xiang F, Liu X, Jiang M, Liao L, Hu J. Nucleolin down-regulation is involved in ADP-induced cell cycle arrest in S phase and cell apoptosis in vascular endothelial cells. PLoS One 2014; 9:e110101. [PMID: 25290311 PMCID: PMC4188626 DOI: 10.1371/journal.pone.0110101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 09/16/2014] [Indexed: 01/20/2023] Open
Abstract
High concentration of extracellular ADP has been reported to induce cell apoptosis, but the molecular mechanisms remain not fully elucidated. In this study, we found by serendipity that ADP treatment of human umbilical vein endothelial cells (HUVEC) and human aortic endothelial cells (HAEC) down-regulated the protein level of nucleolin in a dose- and time-dependent manner. ADP treatment did not decrease the transcript level of nucloelin, suggesting that ADP might induce nucleolin protein degradation. HUVEC and HAEC expressed ADP receptor P2Y13 receptor, but did not express P2Y1 or P2Y12 receptors. However, P2Y1, 12, 13 receptor antagonists MRS2179, PSB0739, MRS2211 did not inhibit ADP-induced down-regulation of nucleolin. Moreover, MRS2211 itself down-regulated nucleolin protein level. In addition, 2-MeSADP, an agonist for P2Y1, 12 and 13 receptors, did not down-regulate nucleolin protein. These results suggested that ADP-induced nucleolin down-regulation was not due to the activation of P2Y1, 12, or 13 receptors. We also found that ADP treatment induced cell cycle arrest in S phase, cell apoptosis and cell proliferation inhibition via nucleolin down-regulation. The over-expression of nucleolin by gene transfer partly reversed ADP-induced cell cycle arrest, cell apoptosis and cell proliferation inhibition. Furthermore, ADP sensitized HUVEC to cisplatin-induced cell death by the down-regulation of Bcl-2 expression. Taken together, we found, for the first time to our knowledge, a novel mechanism by which ADP regulates cell proliferation by induction of cell cycle arrest and cell apoptosis via targeting nucelolin.
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MESH Headings
- Adenosine Diphosphate/analogs & derivatives
- Adenosine Diphosphate/pharmacology
- Antineoplastic Agents/pharmacology
- Aorta/cytology
- Aorta/drug effects
- Aorta/metabolism
- Apoptosis/drug effects
- Azo Compounds/pharmacology
- Cell Line
- Cell Proliferation/drug effects
- Cisplatin/pharmacology
- Dose-Response Relationship, Drug
- Endothelial Cells/cytology
- Endothelial Cells/drug effects
- Endothelial Cells/metabolism
- Gene Expression Regulation
- Human Umbilical Vein Endothelial Cells/cytology
- Human Umbilical Vein Endothelial Cells/drug effects
- Human Umbilical Vein Endothelial Cells/metabolism
- Humans
- Monocytes/cytology
- Monocytes/drug effects
- Monocytes/metabolism
- Phosphoproteins/antagonists & inhibitors
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Primary Cell Culture
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Purinergic Agonists/pharmacology
- Purinergic Antagonists/pharmacology
- Pyridoxal Phosphate/analogs & derivatives
- Pyridoxal Phosphate/pharmacology
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Purinergic P2/genetics
- Receptors, Purinergic P2/metabolism
- Receptors, Purinergic P2Y1/deficiency
- Receptors, Purinergic P2Y1/genetics
- Receptors, Purinergic P2Y12/deficiency
- Receptors, Purinergic P2Y12/genetics
- S Phase Cell Cycle Checkpoints/drug effects
- S Phase Cell Cycle Checkpoints/genetics
- Signal Transduction
- Thionucleotides/pharmacology
- Nucleolin
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Affiliation(s)
- Wenmeng Wang
- Department of Internal Medicine, Hunan Armed Police Force's Hospital, Changsha, Hunan, China
- Medical Research Center, Changsha Central Hospital, Changsha, Hunan, China
| | - Junqing Luo
- Department of Internal Medicine, Hunan Armed Police Force's Hospital, Changsha, Hunan, China
| | - Fang Xiang
- Department of Internal Medicine, Hunan Armed Police Force's Hospital, Changsha, Hunan, China
| | - Xueting Liu
- Medical Research Center, Changsha Central Hospital, Changsha, Hunan, China
| | - Manli Jiang
- Medical Research Center, Changsha Central Hospital, Changsha, Hunan, China
| | - Lingjuan Liao
- Medical Research Center, Changsha Central Hospital, Changsha, Hunan, China
| | - Jinyue Hu
- Medical Research Center, Changsha Central Hospital, Changsha, Hunan, China
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78
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DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
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79
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Shen N, Yan F, Pang J, Wu LC, Al-Kali A, Litzow MR, Liu S. A nucleolin-DNMT1 regulatory axis in acute myeloid leukemogenesis. Oncotarget 2014; 5:5494-509. [PMID: 25015109 PMCID: PMC4170608 DOI: 10.18632/oncotarget.2131] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 06/24/2014] [Indexed: 12/15/2022] Open
Abstract
Nucleolin overexpression and DNA hypermethylation have been implicated in cancer pathogenesis, but whether and how these aberrations cooperate in controlling leukemia cell fate remains elusive. Here, we provide the first mechanistic insights into the role of nucleolin in leukemogenesis through creating a DNA hypermethylation profile in leukemia cells. We found that, in leukemia patients, nucleolin levels are significantly elevated and nucleolin overexpression strongly associates with DNMT upregulation and shorter survival. Enforced nucleolin expression augmented leukemia cell proliferation, whereas nucleolin dysfunction by RNA interference and inhibitory molecule AS1411 blocked leukemia cell clonogenic potential in vitro and impaired tumorigenesis in vivo. Mechanistic investigations showed that nucleolin directly activates NFκB signaling, and NFκB activates its downstream effector, DNA methylation machinery. Indeed, nucleolin overexpression increased NFκB phosphorylation and upregulated DNMT1 that is followed by DNA demethylation; by contrast, nucleolin dysfunction dephosphorylated NFκB and abrogated DNMT1 expression, which resulted in decreased global DNA methylation, restored p15INK4B expression and DNA hypomethylation on p15INK4B promoter. Notably, NFκB inactivation diminished, whereas NFκB overexpression enhanced DNMT1 promoter activity and endogenous DNMT1 expression. Collectively, our studies identify nucleolin as an unconventional epigenetic regulator in leukemia cells and demonstrate nucleolin-NFκB-DNMT1 axis as a new molecular pathway underlying AML leukemogenesis.
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Affiliation(s)
- Na Shen
- The Hormel Institute, University of Minnesota, Austin, MN
| | - Fei Yan
- The Hormel Institute, University of Minnesota, Austin, MN
| | - Jiuxia Pang
- The Hormel Institute, University of Minnesota, Austin, MN
| | - Lai-Chu Wu
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | - Shujun Liu
- The Hormel Institute, University of Minnesota, Austin, MN
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80
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Smith CL, Matheson TD, Trombly DJ, Sun X, Campeau E, Han X, Yates JR, Kaufman PD. A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli. Mol Biol Cell 2014; 25:2866-81. [PMID: 25057015 PMCID: PMC4161520 DOI: 10.1091/mbc.e14-05-1029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin assembly factor-1 contains a separable domain unrelated to histone deposition, which provides a previously unrecognized ability to maintain nucleolar protein and chromosome associations. Chromatin assembly factor-1 (CAF-1) is a three-subunit protein complex conserved throughout eukaryotes that deposits histones during DNA synthesis. Here we present a novel role for the human p150 subunit in regulating nucleolar macromolecular interactions. Acute depletion of p150 causes redistribution of multiple nucleolar proteins and reduces nucleolar association with several repetitive element–containing loci. Of note, a point mutation in a SUMO-interacting motif (SIM) within p150 abolishes nucleolar associations, whereas PCNA or HP1 interaction sites within p150 are not required for these interactions. In addition, acute depletion of SUMO-2 or the SUMO E2 ligase Ubc9 reduces α-satellite DNA association with nucleoli. The nucleolar functions of p150 are separable from its interactions with the other subunits of the CAF-1 complex because an N-terminal fragment of p150 (p150N) that cannot interact with other CAF-1 subunits is sufficient for maintaining nucleolar chromosome and protein associations. Therefore these data define novel functions for a separable domain of the p150 protein, regulating protein and DNA interactions at the nucleolus.
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Affiliation(s)
- Corey L Smith
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Timothy D Matheson
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daniel J Trombly
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiaoming Sun
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Eric Campeau
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xuemei Han
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Paul D Kaufman
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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81
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Durut N, Abou-Ellail M, Pontvianne F, Das S, Kojima H, Ukai S, de Bures A, Comella P, Nidelet S, Rialle S, Merret R, Echeverria M, Bouvet P, Nakamura K, Sáez-Vásquez J. A duplicated NUCLEOLIN gene with antagonistic activity is required for chromatin organization of silent 45S rDNA in Arabidopsis. THE PLANT CELL 2014; 26:1330-44. [PMID: 24668745 PMCID: PMC4001387 DOI: 10.1105/tpc.114.123893] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 05/19/2023]
Abstract
In plants as well as in animals, hundreds to thousands of 45S rRNA gene copies localize in Nucleolus Organizer Regions (NORs), and the activation or repression of specific sets of rDNA depends on epigenetic mechanisms. Previously, we reported that the Arabidopsis thaliana nucleolin protein NUC1, an abundant and evolutionarily conserved nucleolar protein in eukaryotic organisms, is required for maintaining DNA methylation levels and for controlling the expression of specific rDNA variants in Arabidopsis. Interestingly, in contrast with animal or yeast cells, plants contain a second nucleolin gene. Here, we report that Arabidopsis NUC1 and NUC2 nucleolin genes are both required for plant growth and survival and that NUC2 disruption represses flowering. However, these genes seem to be functionally antagonistic. In contrast with NUC1, disruption of NUC2 induces CG hypermethylation of rDNA and NOR association with the nucleolus. Moreover, NUC2 loss of function triggers major changes in rDNA spatial organization, expression, and transgenerational stability. Our analyses indicate that silencing of specific rRNA genes is mostly determined by the active or repressed state of the NORs and that nucleolin proteins play a key role in the developmental control of this process.
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Affiliation(s)
- Nathalie Durut
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Mohamed Abou-Ellail
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Sadhan Das
- École Normale Supérieure Lyon, CNRS,
Unité de Service et de Recherche 3010, Lyon 69364, France
| | - Hisae Kojima
- Graduate School of Bioagricultural Sciences, Nagoya
University, Nagoya 464-8601, Japan
| | - Seiko Ukai
- Graduate School of Bioagricultural Sciences, Nagoya
University, Nagoya 464-8601, Japan
| | - Anne de Bures
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Pascale Comella
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | | | | | - Remy Merret
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Manuel Echeverria
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Philippe Bouvet
- École Normale Supérieure Lyon, CNRS,
Unité de Service et de Recherche 3010, Lyon 69364, France
| | - Kenzo Nakamura
- Graduate School of Bioagricultural Sciences, Nagoya
University, Nagoya 464-8601, Japan
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
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82
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Li L, Zhang Z, Wang C, Miao L, Zhang J, Wang J, Jiao B, Zhao S. Quantitative proteomics approach to screening of potential diagnostic and therapeutic targets for laryngeal carcinoma. PLoS One 2014; 9:e90181. [PMID: 24587265 PMCID: PMC3937387 DOI: 10.1371/journal.pone.0090181] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/28/2014] [Indexed: 12/31/2022] Open
Abstract
To discover candidate biomarkers for diagnosis and detection of human laryngeal carcinoma and explore possible mechanisms of this cancer carcinogenesis, two-dimensional strong cation-exchange/reversed-phase nano-scale liquid chromatography/mass spectrometry analysis was used to identify differentially expressed proteins between the laryngeal carcinoma tissue and the adjacent normal tissue. As a result, 281 proteins with significant difference in expression were identified, and four differential proteins, Profilin-1 (PFN1), Nucleolin (NCL), Cytosolic non-specific dipeptidase (CNDP2) and Mimecan (OGN) with different subcellular localization were selectively validated. Semiquantitative RT-PCR and Western blotting were performed to detect the expression of the four proteins employing a large collection of human laryngeal carcinoma tissues, and the results validated the differentially expressed proteins identified by the proteomics. Furthermore, we knocked down PFN1 in immortalized human laryngeal squamous cell line Hep-2 cells and then the proliferation and metastasis of these transfected cells were measured. The results showed that PFN1 silencing inhibited the proliferation and affected the migration ability of Hep-2 cells, providing some new insights into the pathogenesis of PFN1 in laryngeal carcinoma. Altogether, our present data first time show that PFN1, NCL, CNDP2 and OGN are novel potential biomarkers for diagnosis and therapeutic targets for laryngeal carcinoma, and PFN1 is involved in the metastasis of laryngeal carcinoma.
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Affiliation(s)
- Li Li
- Department of Otolaryngology-Head and Neck Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhenwei Zhang
- Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
- Key Laboratory of Liver Disease, Center of Infectious Diseases, Guangzhou 458 Hospital, Guangzhou, China
| | - Chengyu Wang
- Department of Otolaryngology-Head and Neck Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Lei Miao
- Department of Pharmacology, School of Pharmacy and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jianpeng Zhang
- Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
- * E-mail: (BJ); (SZ); (JZ)
| | - Jiasen Wang
- Department of Otolaryngology-Head and Neck Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
- * E-mail: (BJ); (SZ); (JZ)
| | - Shuwei Zhao
- Department of Otolaryngology-Head and Neck Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
- * E-mail: (BJ); (SZ); (JZ)
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83
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Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ, Head SR, Duester G, Dong PDS, Rana TM. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 2014; 53:1005-19. [PMID: 24530304 DOI: 10.1016/j.molcel.2014.01.021] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/03/2013] [Accepted: 01/10/2014] [Indexed: 11/29/2022]
Abstract
Here, we generated a genome-scale shRNA library targeting long intergenic noncoding RNAs (lincRNAs) in the mouse. We performed an unbiased loss-of-function study in mouse embryonic stem cells (mESCs) and identified 20 lincRNAs involved in the maintenance of pluripotency. Among these, TUNA (Tcl1 Upstream Neuron-Associated lincRNA, or megamind) was required for pluripotency and formed a complex with three RNA-binding proteins (RBPs). The TUNA-RBP complex was detected at the promoters of Nanog, Sox2, and Fgf4, and knockdown of TUNA or the individual RBPs inhibited neural differentiation of mESCs. TUNA showed striking evolutionary conservation of both sequence- and CNS-restricted expression in vertebrates. Accordingly, knockdown of tuna in zebrafish caused impaired locomotor function, and TUNA expression in the brains of Huntington's disease patients was significantly associated with disease grade. Our results suggest that the lincRNA TUNA plays a vital role in pluripotency and neural differentiation of ESCs and is associated with neurological function of adult vertebrates.
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Affiliation(s)
- Nianwei Lin
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kung-Yen Chang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Zhonghan Li
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Keith Gates
- Program for Genetic Disease, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Zacharia A Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jason Dang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Danhua Zhang
- Program for Genetic Disease, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tianxu Han
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chao-Shun Yang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas J Cunningham
- Program for Development and Aging, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steven R Head
- The Scripps Research Institute, Microarray and NGS Core Facility, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gregg Duester
- Program for Development and Aging, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - P Duc Si Dong
- Program for Genetic Disease, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tariq M Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Pediatrics, Rady Children's Hospital San Diego and University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.
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84
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Chen YL, Liu CD, Cheng CP, Zhao B, Hsu HJ, Shen CL, Chiu SJ, Kieff E, Peng CW. Nucleolin is important for Epstein-Barr virus nuclear antigen 1-mediated episome binding, maintenance, and transcription. Proc Natl Acad Sci U S A 2014; 111:243-8. [PMID: 24344309 PMCID: PMC3890893 DOI: 10.1073/pnas.1321800111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is essential for EBV episome maintenance, replication, and transcription. These effects are mediated by EBNA1 binding to cognate oriP DNA, which comprise 20 imperfect copies of a 30-bp dyad symmetry enhancer and an origin for DNA replication. To identify cell proteins essential for these EBNA1 functions, EBNA1 associated cell proteins were immune precipitated and analyzed by liquid chromatography-tandem mass spectrometry. Nucleolin (NCL) was identified to be EBNA1 associated. EBNA1's N-terminal 100 aa and NCL's RNA-binding domains were critical for EBNA1/NCL interaction. Lentivirus shRNA-mediated NCL depletion substantially reduced EBNA1 recruitment to oriP DNA, EBNA1-dependent transcription of an EBV oriP luciferase reporter, and EBV genome maintenance in lymphoblastoid cell lines. NCL RNA-binding domain K429 was critical for ATP and EBNA1 binding. NCL overexpression increased EBNA1 binding to oriP and transcription, whereas NCL K429A was deficient. Moreover, NCL silencing impaired lymphoblastoid cell line growth. These experiments reveal a surprisingly critical role for NCL K429 in EBNA1 episome maintenance and transcription, which may be a target for therapeutic intervention.
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Affiliation(s)
- Ya-Lin Chen
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
| | - Cheng-Der Liu
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
| | - Chi-Ping Cheng
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
| | - Bo Zhao
- Department of Medicine, Brigham and Women’s Hospital, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Hao-Jen Hsu
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
| | - Chih-Long Shen
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
| | - Shu-Jun Chiu
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
| | - Elliott Kieff
- Department of Medicine, Brigham and Women’s Hospital, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Chih-wen Peng
- Department of Life Sciences, Tzu-Chi University, Hualien 97004, Taiwan; and
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85
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Cong R, Das S, Douet J, Wong J, Buschbeck M, Mongelard F, Bouvet P. macroH2A1 histone variant represses rDNA transcription. Nucleic Acids Res 2014; 42:181-92. [PMID: 24071584 PMCID: PMC3874179 DOI: 10.1093/nar/gkt863] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 01/21/2023] Open
Abstract
The regulation of ribosomal DNA transcription is an important step for the control of cell growth. Epigenetic marks such as DNA methylation and posttranslational modifications of canonical histones have been involved in this regulation, but much less is known about the role of histone variants. In this work, we show that the histone variant macroH2A1 is present on the promoter of methylated rDNA genes. The inhibition of the expression of macroH2A1 in human HeLa and HepG2 cells and in a mouse ES cell line resulted in an up to 5-fold increase of pre-rRNA levels. This increased accumulation of pre-rRNA is accompanied by an increase of the loading of RNA polymerase I and UBF on the rDNA without any changes in the number of active rDNA genes. The inhibition of RNA polymerase I transcription by actinomycin D or by knocking down nucleolin, induces the recruitment of macroH2A1 on the rDNA and the relocalization of macroH2A1 in the nucleolus. Interestingly, the inhibition of rDNA transcription induced by nucleolin depletion is alleviated by the inactivation of macroH2A1. These results demonstrate that macroH2A1 is a new factor involved in the regulation of rDNA transcription.
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Affiliation(s)
- Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Julien Douet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Marcus Buschbeck
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fabien Mongelard
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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86
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Reddy D, Bhattacharya S, Gupta S. Histone Chaperones: Functions beyond Nucleosome Deposition. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/abb.2014.56064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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87
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Chang HW, Kulaeva OI, Shaytan AK, Kibanov M, Kuznedelov K, Severinov KV, Kirpichnikov MP, Clark DJ, Studitsky VM. Analysis of the mechanism of nucleosome survival during transcription. Nucleic Acids Res 2013; 42:1619-27. [PMID: 24234452 PMCID: PMC3919589 DOI: 10.1093/nar/gkt1120] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that is likely required for nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. To evaluate these predictions, we analysed transcription through a nucleosome by different, structurally related RNA polymerases and mutant yeast Pol II having different histone-interacting surfaces that presumably stabilize the Ø-loop. The height of the nucleosomal barrier to transcription and efficiency of nucleosome survival correlate with the net negative charges of the histone-interacting surfaces. Molecular modeling and analysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient Ø-loop formation and nucleosome survival are mediated by electrostatic interactions between the largest subunit of Pol II and core histones.
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Affiliation(s)
- Han-Wen Chang
- Department of Biochemistry and Molecular Biology, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA, School of Biology, Lomonosov Moscow State University, 119991 Leninskie gori, MSU, Bldg. 1, korpus 12, Moscow, Russia, Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA, Institute of Gene Biology, Russian Academy of Sciences, 1190334 34/5 Vavilova street, Moscow, Russia and Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, PO Box 3006, Rockville, MD 20847, USA
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88
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Goldstein M, Derheimer FA, Tait-Mulder J, Kastan MB. Nucleolin mediates nucleosome disruption critical for DNA double-strand break repair. Proc Natl Acad Sci U S A 2013; 110:16874-9. [PMID: 24082117 PMCID: PMC3801049 DOI: 10.1073/pnas.1306160110] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recruitment of DNA repair factors and modulation of chromatin structure at sites of DNA double-strand breaks (DSBs) is a complex and highly orchestrated process. We developed a system that can induce DSBs rapidly at defined endogenous sites in mammalian genomes and enables direct assessment of repair and monitoring of protein recruitment, egress, and modification at DSBs. The tight regulation of the system also permits assessments of relative kinetics and dependencies of events associated with cellular responses to DNA breakage. Distinct advantages of this system over focus formation/disappearance assays for assessing DSB repair are demonstrated. Using ChIP, we found that nucleosomes are partially disassembled around DSBs during nonhomologous end-joining repair in G1-arrested mammalian cells, characterized by a transient loss of the H2A/H2B histone dimer. Nucleolin, a protein with histone chaperone activity, interacts with RAD50 via its arginine-glycine rich domain and is recruited to DSBs rapidly in an MRE11-NBS1-RAD50 complex-dependent manner. Down-regulation of nucleolin abrogates the nucleosome disruption, the recruitment of repair factors, and the repair of the DSB, demonstrating the functional importance of nucleosome disruption in DSB repair and identifying a chromatin-remodeling protein required for the process. Interestingly, the nucleosome disruption that occurs during DSB repair in cycling cells differs in that both H2A/H2B and H3/H4 histone dimers are removed. This complete nucleosome disruption is also dependent on nucleolin and is required for recruitment of replication protein A to DSBs, a marker of DSB processing that is a requisite for homologous recombination repair.
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Affiliation(s)
- Michael Goldstein
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105; and
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710
| | | | | | - Michael B. Kastan
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105; and
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710
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89
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Han JH, Jung YJ, Lee HJ, Jung HS, Lee KO, Kang H. The RNA chaperone and protein chaperone activity of Arabidopsis glycine-rich RNA-binding protein 4 and 7 is determined by the propensity for the formation of high molecular weight complexes. Protein J 2013; 32:449-55. [PMID: 23912241 DOI: 10.1007/s10930-013-9504-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
RNA chaperones and protein chaperones are cellular proteins that can aid the correct folding of target RNAs and proteins, respectively. Although many proteins possessing RNA chaperone or protein chaperone activity have been demonstrated in diverse organisms, report evaluating the RNA chaperone and protein chaperone activity of a given protein is severely limited. Here, two glycine-rich RNA-binding proteins in Arabidopsis thaliana (AtGRPs), AtGRP7 exhibiting RNA chaperone activity and AtGRP4 exhibiting no RNA chaperone activity, were investigated for their protein chaperone activity. The heat-induced thermal aggregation of a substrate protein was significantly decreased with the addition of AtGRP4 depending on protein concentration, whereas the thermal aggregation of a substrate protein was further increased with the addition of AtGRP7, demonstrating that AtGRP4 but not AtGRP7 possesses protein chaperone activity. Size exclusion chromatography and electron microscopy analyses revealed that the formation of high molecular weight (HMW) complexes is closely related to the protein chaperone activity of AtGRP4. Importantly, the additional 25 amino acids at the N-terminus of AtGRP4 are crucial for HMW complex formation and protein chaperone activity. Taken together, these results show that the formation of HMW complexes is important for determining the RNA chaperone and protein chaperone activity of AtGRP4 and AtGRP7.
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Affiliation(s)
- Ji Hoon Han
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Kwangju, 500-757, Korea
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90
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Calkins AS, Iglehart JD, Lazaro JB. DNA damage-induced inhibition of rRNA synthesis by DNA-PK and PARP-1. Nucleic Acids Res 2013; 41:7378-86. [PMID: 23775790 PMCID: PMC3753630 DOI: 10.1093/nar/gkt502] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
RNA synthesis and DNA replication cease after DNA damage. We studied RNA synthesis using an in situ run-on assay and found ribosomal RNA (rRNA) synthesis was inhibited 24 h after UV light, gamma radiation or DNA cross-linking by cisplatin in human cells. Cisplatin led to accumulation of cells in S phase. Inhibition of the DNA repair proteins DNA-dependent protein kinase (DNA-PK) or poly(ADP-ribose) polymerase 1 (PARP-1) prevented the DNA damage-induced block of rRNA synthesis. However, DNA-PK and PARP-1 inhibition did not prevent the cisplatin-induced arrest of cell cycle in S phase, nor did it induce de novo BrdU incorporation. Loss of DNA-PK function prevented activation of PARP-1 and its recruitment to chromatin in damaged cells, suggesting regulation of PARP-1 by DNA-PK within a pathway of DNA repair. From these results, we propose a sequential activation of DNA-PK and PARP-1 in cells arrested in S phase by DNA damage causes the interruption of rRNA synthesis after DNA damage.
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Affiliation(s)
- Anne S Calkins
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA and Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
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91
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Posavec M, Timinszky G, Buschbeck M. Macro domains as metabolite sensors on chromatin. Cell Mol Life Sci 2013; 70:1509-24. [PMID: 23455074 PMCID: PMC11113152 DOI: 10.1007/s00018-013-1294-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/30/2022]
Abstract
How metabolism and epigenetics are molecularly linked and regulate each other is poorly understood. In this review, we will discuss the role of direct metabolite-binding to chromatin components and modifiers as a possible regulatory mechanism. We will focus on globular macro domains, which are evolutionarily highly conserved protein folds that can recognize NAD(+)-derived metabolites. Macro domains are found in histone variants, histone modifiers, and a chromatin remodeler among other proteins. Here we summarize the macro domain-containing chromatin proteins and the enzymes that generate relevant metabolites. Focusing on the histone variant macroH2A, we further discuss possible implications of metabolite binding for chromatin function.
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Affiliation(s)
- Melanija Posavec
- Institute for Predictive and Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona Spain
| | - Gyula Timinszky
- Butenandt Institute of Physiological Chemistry, Ludwig Maximilian University of Munich, Butenandtstrasse 5, 81377 Munich, Germany
| | - Marcus Buschbeck
- Institute for Predictive and Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona Spain
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92
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Abstract
Chromatin acts as an organizer and indexer of genomic DNA and is a highly dynamic and regulated structure with properties directly related to its constituent parts. Histone variants are abundant components of chromatin that replace canonical histones in a subset of nucleosomes, thereby altering nucleosomal characteristics. The present review focuses on the H2A variant histones, summarizing current knowledge of how H2A variants can introduce chemical and functional heterogeneity into chromatin, the positions that nucleosomes containing H2A variants occupy in eukaryotic genomes, and the regulation of these localization patterns.
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93
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Das S, Cong R, Shandilya J, Senapati P, Moindrot B, Monier K, Delage H, Mongelard F, Kumar S, Kundu TK, Bouvet P. Characterization of nucleolin K88 acetylation defines a new pool of nucleolin colocalizing with pre-mRNA splicing factors. FEBS Lett 2013; 587:417-24. [PMID: 23353999 DOI: 10.1016/j.febslet.2013.01.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/17/2012] [Accepted: 01/14/2013] [Indexed: 11/22/2022]
Abstract
Nucleolin is a multifunctional protein that carries several post-translational modifications. We characterized nucleolin acetylation and developed antibodies specific to nucleolin K88 acetylation. Using this antibody we show that nucleolin is acetylated in vivo and is not localized in the nucleoli, but instead is distributed throughout the nucleoplasm. Immunofluorescence studies indicate that acetylated nucleolin is co-localized with the splicing factor SC35 and partially with Y12. Acetylated nucleolin is expressed in all tested proliferating cell types. Our findings show that acetylation defines a new pool of nucleolin which support a role for nucleolin in the regulation of mRNA maturation and transcription by RNA polymerase II.
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Affiliation(s)
- Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, France
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94
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The chaperone like function of the nonhistone protein HMGB1. Biochem Biophys Res Commun 2013; 432:231-5. [PMID: 23402754 DOI: 10.1016/j.bbrc.2013.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 11/21/2022]
Abstract
Almost all essential nuclear processes as replication, repair, transcription and recombination require the chromatin template to be correctly unwound and than repackaged. The major strategy that the cell uses to overcome the nucleosome barrier is the proper removal of the histone octamer and subsequent deposition onto DNA. Important factors in this multi step phenomenon are the histone chaperones that can assemble nucleosome arrays in vitro in the absence of ATP. The nonhistone protein HMGB1 is a good candidate for a chaperone as its molecule consists of two DNA binding motives, Box's A and B, and a long nonstructured C tail highly negatively charged. HMGB1 protein is known as a nuclear "architectural" factor for its property to bind preferentially to distorted DNA structures and was reported to kink the double helix. Our experiments show that in the classical stepwise dialysis method for nucleosome assembly the addition of HMGB1 protein stimulates more than two times the formation of middle-positioned nucleosomes. The stimulation effect persists in dialysis free experiment when the reconstitution is possible only in the presence of a chaperone. The addition of HMGB1 protein strongly enhanced the formation of a nucleosome in a dose dependant manner. Our results show that the target of HMGB1 action as a chaperone is the DNA fragment not the histone octamer. One possible explanation for the stimulating effect of HMGB1 is the "architectural" property of the protein to associate with the middle of the DNA fragment and to kink it. The acquired V shaped DNA structure is probably conformationals more favorable to wrap around the prefolded histone octamer. We tested also the role of the post-synthetic acetylation for the chaperone function of HMGB1 protein. The presence of an acetyl groups at Lys 2 decreases strongly the stimulating effect of the protein in the stepwise salt dialysis experiment and the same tendency persisted in the dialysis free experiment.
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95
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Osakabe A, Tachiwana H, Takaku M, Hori T, Obuse C, Kimura H, Fukagawa T, Kurumizaka H. Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription. J Cell Sci 2013; 126:1323-32. [PMID: 23378026 DOI: 10.1242/jcs.112623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In eukaryotes, transcription occurs in the chromatin context with the assistance of histone-binding proteins, such as chromatin/nucleosome remodeling factors and histone chaperones. However, it is unclear how each remodeling factor or histone chaperone functions in transcription. Here, we identify a novel histone-binding protein, Spt2, in higher eukaryotes. Recombinant human Spt2 binds to histones and DNA, and promotes nucleosome assembly in vitro. Spt2 accumulates in nucleoli and interacts with RNA polymerase I in chicken DT40 cells, suggesting its involvement in ribosomal RNA transcription. Consistently, Spt2-deficient chicken DT40 cells are sensitive to RNA polymerase I inhibitors and exhibit decreased transcription activity, as shown by a transcription run-on assay. Domain analyses of Spt2 revealed that the C-terminal region, containing the region homologous to yeast Spt2, is responsible for histone binding, while the central region is essential for nucleolar localization and DNA binding. Based on these results, we conclude that vertebrate Spt2 is a novel histone chaperone with a separate DNA-binding domain that facilitates ribosomal DNA transcription through chromatin remodeling during transcription.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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96
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Kobayashi J, Fujimoto H, Sato J, Hayashi I, Burma S, Matsuura S, Chen DJ, Komatsu K. Nucleolin participates in DNA double-strand break-induced damage response through MDC1-dependent pathway. PLoS One 2012; 7:e49245. [PMID: 23145133 PMCID: PMC3492271 DOI: 10.1371/journal.pone.0049245] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 10/05/2012] [Indexed: 01/05/2023] Open
Abstract
H2AX is an important factor for chromatin remodeling to facilitate accumulation of DNA damage-related proteins at DNA double-strand break (DSB) sites. In order to further understand the role of H2AX in the DNA damage response (DDR), we attempted to identify H2AX-interacting proteins by proteomics analysis. As a result, we identified nucleolin as one of candidates. Here, we show a novel role of a major nucleolar protein, nucleolin, in DDR. Nucleolin interacted with γ-H2AX and accumulated to laser micro-irradiated DSB damage sites. Chromatin Immunoprecipitation assay also displayed the accumulation of nucleolin around DSB sites. Nucleolin-depleted cells exhibited repression of both ATM-dependent phosphorylation following exposure to γ-ray and subsequent cell cycle checkpoint activation. Furthermore, nucleolin-knockdown reduced HR and NHEJ activity and showed decrease in IR-induced chromatin accumulation of HR/NHEJ factors, agreeing with the delayed kinetics of γ-H2AX focus. Moreover, nucleolin-knockdown decreased MDC1-related events such as focus formation of 53 BP1, RNF168, phosphorylated ATM, and H2A ubiquitination. Nucleolin also showed FACT-like activity for DSB damage-induced histone eviction from chromatin. Taken together, nucleolin could promote both ATM-dependent cell cycle checkpoint and DSB repair by functioning in an MDC1-related pathway through its FACT-like function.
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Affiliation(s)
- Junya Kobayashi
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan.
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97
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Cong R, Das S, Ugrinova I, Kumar S, Mongelard F, Wong J, Bouvet P. Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription. Nucleic Acids Res 2012; 40:9441-54. [PMID: 22859736 PMCID: PMC3479187 DOI: 10.1093/nar/gks720] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 06/04/2012] [Accepted: 07/04/2012] [Indexed: 12/13/2022] Open
Abstract
Nucleolin is a multi-functional nucleolar protein that is required for ribosomal RNA gene (rRNA) transcription in vivo, but the mechanism by which nucleolin modulates RNA polymerase I (RNAPI) transcription is not well understood. Nucleolin depletion results in an increase in the heterochromatin mark H3K9me2 and a decrease in H4K12Ac and H3K4me3 euchromatin histone marks in rRNA genes. ChIP-seq experiments identified an enrichment of nucleolin in the ribosomal DNA (rDNA) coding and promoter region. Nucleolin is preferentially associated with unmethylated rRNA genes and its depletion leads to the accumulation of RNAPI at the beginning of the transcription unit and a decrease in UBF along the coding and promoter regions. Nucleolin is able to affect the binding of transcription termination factor-1 on the promoter-proximal terminator T0, thus inhibiting the recruitment of TIP5 and HDAC1 and the establishment of a repressive heterochromatin state. These results reveal the importance of nucleolin for the maintenance of the euchromatin state and transcription elongation of rDNA.
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Affiliation(s)
- Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Iva Ugrinova
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Sanjeev Kumar
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Fabien Mongelard
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Jiemin Wong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China and BioCOS Life Sciences Private Limited, Biotech Park, Electronics City, Phase-1, Bangalore 560100, India
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98
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Smolle M, Workman JL. Transcription-associated histone modifications and cryptic transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:84-97. [PMID: 22982198 DOI: 10.1016/j.bbagrm.2012.08.008] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/14/2012] [Accepted: 08/29/2012] [Indexed: 12/21/2022]
Abstract
Eukaryotic genomes are packaged into chromatin, a highly organized structure consisting of DNA and histone proteins. All nuclear processes take place in the context of chromatin. Modifications of either DNA or histone proteins have fundamental effects on chromatin structure and function, and thus influence processes such as transcription, replication or recombination. In this review we highlight histone modifications specifically associated with gene transcription by RNA polymerase II and summarize their genomic distributions. Finally, we discuss how (mis-)regulation of these histone modifications perturbs chromatin organization over coding regions and results in the appearance of aberrant, intragenic transcription. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Michaela Smolle
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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99
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Shang Y, Kakinuma S, Nishimura M, Kobayashi Y, Nagata K, Shimada Y. Interleukin-9 receptor gene is transcriptionally regulated by nucleolin in T-cell lymphoma cells. Mol Carcinog 2012; 51:619-27. [PMID: 21809393 DOI: 10.1002/mc.20834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/28/2011] [Accepted: 07/06/2011] [Indexed: 01/08/2023]
Abstract
Interleukin-9 (IL-9) is a multifunctional cytokine that not only has roles in immune and inflammatory responses but also is involved in growth-promoting and anti-apoptotic activities in multiple transformed cell lines, which suggests a potential role in tumorigenesis. Over-expression of the receptor of IL-9 (IL-9R) occurs in several types of human leukemias and in radiation-induced mouse T-cell lymphoma (TL). The molecular mechanism that regulates transcription of the IL-9R gene (Il9r) during leukemogenesis is, however, not well understood. Using a mouse TL cell line that has high expression of Il9r, we sought to dissect its promoter structure. Here we show that the active promoter for Il9r is located in the 5'-flanking AT-rich region. Chromatin immunoprecipitation showed the opening of chromatin structure of the promoter region coupled with nucleolin binding in vivo. Immunohistochemical analysis confirmed the increased localization of nucleolin in the nuclei of TL cells. These data indicate that increased expression of Il9r is associated with an increased binding of nucleolin, coupled with chromatin opening, to an AT-rich region in the 5'-flanking region of Il9r in TL cells.
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MESH Headings
- 5' Flanking Region/genetics
- AT Rich Sequence/genetics
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Western
- Cell Nucleus/metabolism
- Chromatin Immunoprecipitation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Immunohistochemistry
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Molecular Sequence Data
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Interleukin-9/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Cells, Cultured
- Nucleolin
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Affiliation(s)
- Yi Shang
- Experimental Radiobiology for Children's Health Research Group, Research Center for Radiation Protection, National Institute of Radiological Sciences, Inage-ku, Chiba, Japan
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100
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Stępiński D. Nucleolin level in plant root meristematic cells under chilling stress and recovery. Micron 2012; 43:870-5. [PMID: 22483616 DOI: 10.1016/j.micron.2012.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
Abstract
Nucleolin and its homologues are multifunctional proteins which reside mainly in nucleoli of yeast, animal and plant cells. Hence, they are generally implicated in many stages of ribosome biosynthesis. In this study nucleolin was identified in root meristematic cell nucleoli of soybean plants subjected to chilling stress, recovered after chilling and under control conditions with the use of the immunogold electron microscopy technique. Soybean nucleoli exhibited various metabolic activities under these conditions (Stępiński, 2004). Current studies showed that the level of nucleolin, expressed as a number of gold grains per μm(2), varied in particular subnucleolar regions in the soybean root meristematic cell nucleoli. Labeling density changed in these regions when plants were subjected to the given treatment. Most abundantly this protein was present in dense fibrillar component (DFC) around fibrillar centers (FCs) in the nucleoli of recovered plants, while in the nucleoli of stressed plants this region contained the lowest level of nucleolin. It can be supposed that nucleolin participates in ribosome biogenesis and its level is correlated with metabolic activity of soybean nucleoli - the more active nucleoli, the higher level of nucleolin and vice versa.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
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