51
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Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M. Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201702904] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Miriam Sonntag
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Bernd Simon
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ); Forschungszentrum Jülich GmbH; Lichtenbergstr. 1 85748 Garching Germany
| | - Arie Geerlof
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Frank Gabel
- Univ. Grenoble Alpes; CEA, CNRS, IBS; 38000 Grenoble France
- Institut Laue-Langevin (ILL); Avenue des Martyrs 38042 Grenoble France
| | - Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
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52
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Abstract
Efficient viral gene expression is threatened by cellular stress response programmes that rapidly reprioritize the translation machinery in response to varied environmental assaults, including virus infection. This results in inhibition of bulk synthesis of housekeeping proteins and causes the aggregation of messenger ribonucleoprotein complexes into cytoplasmic foci that are known as stress granules, which can entrap viral mRNAs. There is accumulating evidence for the antiviral nature of stress granules, which is supported by the discovery of many viral factors that interfere with stress granule formation and/or function. This Review focuses on recent advances in our understanding of the role of translation inhibition and stress granules in antiviral immune responses.
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53
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Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 471] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
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Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
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54
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Tumor protein D52 expression is post-transcriptionally regulated by T-cell intercellular antigen (TIA) 1 and TIA-related protein via mRNA stability. Biochem J 2017; 474:1669-1687. [PMID: 28298474 DOI: 10.1042/bcj20160942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/09/2017] [Accepted: 03/15/2017] [Indexed: 12/13/2022]
Abstract
Although tumor protein D52 (TPD52) family proteins were first identified nearly 20 years ago, their molecular regulatory mechanisms remain unclear. Therefore, we investigated the post-transcriptional regulation of TPD52 family genes. An RNA immunoprecipitation (RIP) assay showed the potential binding ability of TPD52 family mRNAs to several RNA-binding proteins, and an RNA degradation assay revealed that TPD52 is subject to more prominent post-transcriptional regulation than are TPD53 and TPD54. We subsequently focused on the 3'-untranslated region (3'-UTR) of TPD52 as a cis-acting element in post-transcriptional gene regulation. Several deletion mutants of the 3'-UTR of TPD52 mRNA were constructed and ligated to the 3'-end of a reporter green fluorescence protein gene. An RNA degradation assay revealed that a minimal cis-acting region, located in the 78-280 region of the 5'-proximal region of the 3'-UTR, stabilized the reporter mRNA. Biotin pull-down and RIP assays revealed specific binding of the region to T-cell intracellular antigen 1 (TIA-1) and TIA-1-related protein (TIAR). Knockdown of TIA-1/TIAR decreased not only the expression, but also the stability of TPD52 mRNA; it also decreased the expression and stability of the reporter gene ligated to the 3'-end of the 78-280 fragment. Stimulation of transforming growth factor-β and epidermal growth factor decreased the binding ability of these factors, resulting in decreased mRNA stability. These results indicate that the 78-280 fragment and TIA-1/TIAR concordantly contribute to mRNA stability as a cis-acting element and trans-acting factor(s), respectively. Thus, we here report the specific interactions between these elements in the post-transcriptional regulation of the TPD52 gene.
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55
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Moschall R, Gaik M, Medenbach J. Promiscuity in post-transcriptional control of gene expression: Drosophila sex-lethal and its regulatory partnerships. FEBS Lett 2017; 591:1471-1488. [PMID: 28391641 PMCID: PMC5488161 DOI: 10.1002/1873-3468.12652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/08/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
The Drosophila RNA‐binding protein Sex‐lethal (Sxl) is a potent post‐transcriptional regulator of gene expression that controls female development. It regulates the expression of key factors involved in sex‐specific differences in morphology, behavior, and dosage compensation. Functional Sxl protein is only expressed in female flies, where it binds to U‐rich RNA motifs present in its target mRNAs to regulate their fate. Sxl is a very versatile regulator that, by shuttling between the nucleus and the cytoplasm, can regulate almost all aspects of post‐transcriptional gene expression including RNA processing, nuclear export, and translation. For these functions, Sxl employs multiple interactions to either antagonize RNA‐processing factors or to recruit various coregulators, thus allowing it to establish a female‐specific gene expression pattern. Here, we summarize the current knowledge about Sxl function and review recent mechanistic and structural studies that further our understanding of how such a seemingly ‘simple’ RNA‐binding protein can exert this plethora of different functions.
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Affiliation(s)
| | - Monika Gaik
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Germany
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56
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Mourão A, Bonnal S, Soni K, Warner L, Bordonné R, Valcárcel J, Sattler M. Structural basis for the recognition of spliceosomal SmN/B/B' proteins by the RBM5 OCRE domain in splicing regulation. eLife 2016; 5:14707. [PMID: 27894420 PMCID: PMC5127646 DOI: 10.7554/elife.14707] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 11/01/2016] [Indexed: 12/18/2022] Open
Abstract
The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95, Caspase-2 and AID. An OCRE (OCtamer REpeat of aromatic residues) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U4/U6.U5 tri-snRNP. We show that the RBM5 OCRE domain adopts a unique β–sheet fold. NMR and biochemical experiments demonstrate that the OCRE domain directly binds to the proline-rich C-terminal tail of the essential snRNP core proteins SmN/B/B’. The NMR structure of an OCRE-SmN peptide complex reveals a specific recognition of poly-proline helical motifs in SmN/B/B’. Mutation of conserved aromatic residues impairs binding to the Sm proteins in vitro and compromises RBM5-mediated alternative splicing regulation of FAS/CD95. Thus, RBM5 OCRE represents a poly-proline recognition domain that mediates critical interactions with the C-terminal tail of the spliceosomal SmN/B/B’ proteins in FAS/CD95 alternative splicing regulation. The information required to produce proteins is encoded within genes. In the first step of creating a protein, its gene is “transcribed” to form a pre-messenger RNA molecule (called pre-mRNA for short). Both the gene and the pre-mRNA contain regions called exons that code for protein, and regions called introns that do not. The pre-mRNA therefore undergoes a process called splicing to remove the introns and join the exons together into a final mRNA molecule that is “translated” to make the protein. Many pre-mRNAs can be spliced in several different ways to include different combinations of exons in the final mRNA molecule. This process of “alternative splicing” allows different versions of a protein to be produced from the same gene. Changes that alter the pattern of alternative splicing in a cell affect various cellular and developmental processes and have been linked to diseases such as cancer. The pre-mRNA transcribed from a gene called FAS can be alternatively spliced so that it either does or does not contain an exon that enables the protein to embed itself in the cell membrane. The protein produced from mRNA that includes this exon generates a cell response that leads to cell death. By contrast, protein produced from mRNA that lacks this exon is released from cells and promotes their survival. A splicing factor called RBM5 promotes the removal of this exon from FAS pre-mRNA. RBM5 binds to some of the proteins that make up the molecular machine that splices pre-mRNA molecules. Mourão, Bonnal, Soni, Warner et al. have now used a technique called nuclear magnetic resonance spectroscopy to solve the three-dimensional structure formed when RBM5 binds to one of these proteins, called SmN. Further experiments introduced specific mutations to the proteins to investigate their effects in human cells. This revealed that mutations that impaired the association between RBM5 and SmN compromised the activity of RBM5 to regulate the alternative splicing of FAS pre-mRNA molecules. Future research could examine how RBM5 associates with pre-mRNAs and other components of the splicing machinery, and investigate whether proteins that are closely related to RBM5 act in similar ways.
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Affiliation(s)
- André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Garching, Germany
| | - Sophie Bonnal
- Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Centre de Regulació Genòmica, Barcelona, Spain
| | - Komal Soni
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Garching, Germany
| | - Lisa Warner
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Garching, Germany
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Université de Montpellier, Montpellier, France
| | - Juan Valcárcel
- Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Centre de Regulació Genòmica, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Garching, Germany
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57
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The increasing diversity of functions attributed to the SAFB family of RNA-/DNA-binding proteins. Biochem J 2016; 473:4271-4288. [DOI: 10.1042/bcj20160649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins play a central role in cellular metabolism by orchestrating the complex interactions of coding, structural and regulatory RNA species. The SAFB (scaffold attachment factor B) proteins (SAFB1, SAFB2 and SAFB-like transcriptional modulator, SLTM), which are highly conserved evolutionarily, were first identified on the basis of their ability to bind scaffold attachment region DNA elements, but attention has subsequently shifted to their RNA-binding and protein–protein interactions. Initial studies identified the involvement of these proteins in the cellular stress response and other aspects of gene regulation. More recently, the multifunctional capabilities of SAFB proteins have shown that they play crucial roles in DNA repair, processing of mRNA and regulatory RNA, as well as in interaction with chromatin-modifying complexes. With the advent of new techniques for identifying RNA-binding sites, enumeration of individual RNA targets has now begun. This review aims to summarise what is currently known about the functions of SAFB proteins.
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58
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Alternative splicing and cell survival: from tissue homeostasis to disease. Cell Death Differ 2016; 23:1919-1929. [PMID: 27689872 DOI: 10.1038/cdd.2016.91] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/26/2016] [Accepted: 07/15/2016] [Indexed: 12/17/2022] Open
Abstract
Most human genes encode multiple mRNA variants and protein products through alternative splicing of exons and introns during pre-mRNA processing. In this way, alternative splicing amplifies enormously the coding potential of the human genome and represents a powerful evolutionary resource. Nonetheless, the plasticity of its regulation is prone to errors and defective splicing underlies a large number of inherited and sporadic diseases, including cancer. One key cellular process affected by alternative splicing is the programmed cell death or apoptosis. Many apoptotic genes encode for splice variants having opposite roles in cell survival. This regulation modulates cell and tissue homeostasis and is implicated in both developmental and pathological processes. Furthermore, recent evidence has also unveiled splicing-mediated regulation of genes involved in autophagy, another essential process for tissue homeostasis. In this review, we highlight some of the best-known examples of alternative splicing events involved in cell survival. Emphasis is given to the role of this regulation in human cancer and in the response to chemotherapy, providing examples of how alternative splicing of apoptotic genes can be exploited therapeutically.
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59
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Tak H, Eun JW, Kim J, Park SJ, Kim C, Ji E, Lee H, Kang H, Cho DH, Lee K, Kim W, Nam SW, Lee EK. T-cell-restricted intracellular antigen 1 facilitates mitochondrial fragmentation by enhancing the expression of mitochondrial fission factor. Cell Death Differ 2016; 24:49-58. [PMID: 27612012 DOI: 10.1038/cdd.2016.90] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 07/06/2016] [Accepted: 07/25/2016] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial morphology is dynamically regulated by the formation of small fragmented units or interconnected mitochondrial networks, and this dynamic morphological change is a pivotal process in normal mitochondrial function. In the present study, we identified a novel regulator responsible for the regulation of mitochondrial dynamics. An assay using CHANG liver cells stably expressing mitochondrial-targeted yellow fluorescent protein (mtYFP) and a group of siRNAs revealed that T-cell intracellular antigen protein-1 (TIA-1) affects mitochondrial morphology by enhancing mitochondrial fission. The function of TIA-1 in mitochondrial dynamics was investigated through various biological approaches and expression analysis in human specimen. Downregulation of TIA-1-enhanced mitochondrial elongation, whereas ectopic expression of TIA-1 resulted in mitochondria fragmentation. In addition, TIA-1 increased mitochondrial activity, including the rate of ATP synthesis and oxygen consumption. Further, we identified mitochondrial fission factor (MFF) as a direct target of TIA-1, and showed that TIA-1 promotes mitochondrial fragmentation by enhancing MFF translation. TIA-1 null cells had a decreased level of MFF and less mitochondrial Drp1, a critical factor for mitochondrial fragmentation, thereby enhancing mitochondrial elongation. Taken together, our results indicate that TIA-1 is a novel factor that facilitates mitochondrial dynamics by enhancing MFF expression and contributes to mitochondrial dysfunction.
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Affiliation(s)
- Hyosun Tak
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Jung Woo Eun
- Department of Pathology, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Jihye Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - So Jung Park
- Department of East-West Medical Science, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - Chongtae Kim
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Eunbyul Ji
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Heejin Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Hoin Kang
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Dong-Hyung Cho
- Department of East-West Medical Science, Graduate School of East-West Medical Science, Kyung Hee University, Yongin, South Korea
| | - Kyungbun Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Suk Woo Nam
- Department of Pathology, The Catholic University of Korea College of Medicine, Seoul, South Korea.,Cancer Evolution Research Center, The Catholic University of Korea College of Medicine, Seoul, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, South Korea.,Cancer Evolution Research Center, The Catholic University of Korea College of Medicine, Seoul, South Korea.,Institute for Aging and Metabolic Disease, The Catholic University of Korea College of Medicine, Seoul, South Korea
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60
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A Structure-free Method for Quantifying Conformational Flexibility in proteins. Sci Rep 2016; 6:29040. [PMID: 27358108 PMCID: PMC4928179 DOI: 10.1038/srep29040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022] Open
Abstract
All proteins sample a range of conformations at physiologic temperatures and this inherent flexibility enables them to carry out their prescribed functions. A comprehensive understanding of protein function therefore entails a characterization of protein flexibility. Here we describe a novel approach for quantifying a protein’s flexibility in solution using small-angle X-ray scattering (SAXS) data. The method calculates an effective entropy that quantifies the diversity of radii of gyration that a protein can adopt in solution and does not require the explicit generation of structural ensembles to garner insights into protein flexibility. Application of this structure-free approach to over 200 experimental datasets demonstrates that the methodology can quantify a protein’s disorder as well as the effects of ligand binding on protein flexibility. Such quantitative descriptions of protein flexibility form the basis of a rigorous taxonomy for the description and classification of protein structure.
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61
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Julien P, Miñana B, Baeza-Centurion P, Valcárcel J, Lehner B. The complete local genotype-phenotype landscape for the alternative splicing of a human exon. Nat Commun 2016; 7:11558. [PMID: 27161764 PMCID: PMC4866304 DOI: 10.1038/ncomms11558] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/08/2016] [Indexed: 01/21/2023] Open
Abstract
The properties of genotype–phenotype landscapes are crucial for understanding evolution but are not characterized for most traits. Here, we present a >95% complete local landscape for a defined molecular function—the alternative splicing of a human exon (FAS/CD95 exon 6, involved in the control of apoptosis). The landscape provides important mechanistic insights, revealing that regulatory information is dispersed throughout nearly every nucleotide in an exon, that the exon is more robust to the effects of mutations than its immediate neighbours in genotype space, and that high mutation sensitivity (evolvability) will drive the rapid divergence of alternative splicing between species unless it is constrained by selection. Moreover, the extensive epistasis in the landscape predicts that exonic regulatory sequences may diverge between species even when exon inclusion levels are functionally important and conserved by selection. Genotype–phenotype landscapes are an important characteristic for understanding the evolution of traits. Here the authors construct the local landscape for the alternative splicing of FAS/CD95 exon 6, revealing the regulation of splicing and the evolution of regulatory information between species.
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Affiliation(s)
- Philippe Julien
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Belén Miñana
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.,Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Pablo Baeza-Centurion
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Juan Valcárcel
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.,Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Ben Lehner
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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62
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Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-related/like protein (TIAR/TIAL1) are 2 proteins discovered in 1991 as components of cytotoxic T lymphocyte granules. They act in the nucleus as regulators of transcription and pre-mRNA splicing. In the cytoplasm, TIA1 and TIAR regulate and/or modulate the location, stability and/or translation of mRNAs. As knowledge of the different genes regulated by these proteins and the cellular/biological programs in which they are involved increases, it is evident that these antigens are key players in human physiology and pathology. This review will discuss the latest developments in the field, with physiopathological relevance, that point to novel roles for these regulators in the molecular and cell biology of higher eukaryotes.
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Affiliation(s)
- Carmen Sánchez-Jiménez
- a Centro de Biología Molecular Severo Ochoa; Consejo Superior de Investigaciones Científicas; Universidad Autónoma de Madrid (CSIC/UAM); C/Nicolás Cabrera 1 ; Madrid , Spain
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63
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Huelgas-Morales G, Silva-García CG, Salinas LS, Greenstein D, Navarro RE. The Stress Granule RNA-Binding Protein TIAR-1 Protects Female Germ Cells from Heat Shock in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2016; 6:1031-47. [PMID: 26865701 PMCID: PMC4825639 DOI: 10.1534/g3.115.026815] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/07/2016] [Indexed: 01/25/2023]
Abstract
In response to stressful conditions, eukaryotic cells launch an arsenal of regulatory programs to protect the proteome. One major protective response involves the arrest of protein translation and the formation of stress granules, cytoplasmic ribonucleoprotein complexes containing the conserved RNA-binding proteins TIA-1 and TIAR. The stress granule response is thought to preserve mRNA for translation when conditions improve. For cells of the germline-the immortal cell lineage required for sexual reproduction-protection from stress is critically important for perpetuation of the species, yet how stress granule regulatory mechanisms are deployed in animal reproduction is incompletely understood. Here, we show that the stress granule protein TIAR-1 protects the Caenorhabditis elegans germline from the adverse effects of heat shock. Animals containing strong loss-of-function mutations in tiar-1 exhibit significantly reduced fertility compared to the wild type following heat shock. Analysis of a heat-shock protein promoter indicates that tiar-1 mutants display an impaired heat-shock response. We observed that TIAR-1 was associated with granules in the gonad core and oocytes during several stressful conditions. Both gonad core and oocyte granules are dynamic structures that depend on translation; protein synthesis inhibitors altered their formation. Nonetheless, tiar-1 was required for the formation of gonad core granules only. Interestingly, the gonad core granules did not seem to be needed for the germ cells to develop viable embryos after heat shock. This suggests that TIAR-1 is able to protect the germline from heat stress independently of these structures.
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Affiliation(s)
- Gabriela Huelgas-Morales
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Carlos Giovanni Silva-García
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Laura S Salinas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - David Greenstein
- Department of Genetics, Cell Biology and Development, University of Minnesota Minneapolis, 55455 Minnesota
| | - Rosa E Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
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64
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Arimoto-Matsuzaki K, Saito H, Takekawa M. TIA1 oxidation inhibits stress granule assembly and sensitizes cells to stress-induced apoptosis. Nat Commun 2016; 7:10252. [PMID: 26738979 PMCID: PMC4729832 DOI: 10.1038/ncomms10252] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/20/2015] [Indexed: 12/24/2022] Open
Abstract
Cytoplasmic stress granules (SGs) are multimolecular aggregates of stalled translation pre-initiation complexes that prevent the accumulation of misfolded proteins, and that are formed in response to certain types of stress including ER stress. SG formation contributes to cell survival not only by suppressing translation but also by sequestering some apoptosis regulatory factors. Because cells can be exposed to various stresses simultaneously in vivo, the regulation of SG assembly under multiple stress conditions is important but unknown. Here we report that reactive oxygen species (ROS) such as H2O2 oxidize the SG-nucleating protein TIA1, thereby inhibiting SG assembly. Thus, when cells are confronted with a SG-inducing stress such as ER stress caused by protein misfolding, together with ROS-induced oxidative stress, they cannot form SGs, resulting in the promotion of apoptosis. We demonstrate that the suppression of SG formation by oxidative stress may underlie the neuronal cell death seen in neurodegenerative diseases. Cytoplasmic stress granules (SG) are intracellular aggregates that suppress translation and sequester apoptosis regulatory factors. Here the authors show that reactive oxygen species oxidise the SG-nucleating protein TIA1, preventing SG formation and promoting apoptosis in the presence of additional stress.
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Affiliation(s)
- Kyoko Arimoto-Matsuzaki
- Division of Molecular Cell Signaling, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Haruo Saito
- Division of Molecular Cell Signaling, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Huertas CS, Carrascosa LG, Bonnal S, Valcárcel J, Lechuga LM. Quantitative evaluation of alternatively spliced mRNA isoforms by label-free real-time plasmonic sensing. Biosens Bioelectron 2015; 78:118-125. [PMID: 26599481 DOI: 10.1016/j.bios.2015.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/16/2015] [Accepted: 11/09/2015] [Indexed: 12/12/2022]
Abstract
Alternative splicing of mRNA precursors enables cells to generate different protein outputs from the same gene depending on their developmental or homeostatic status. Its deregulation is strongly linked to disease onset and progression. Current methodologies for monitoring alternative splicing demand elaborate procedures and often present difficulties in discerning between closely related isoforms, e.g. due to cross-hybridization during their detection. Herein, we report a general methodology using a Surface Plasmon Resonance (SPR) biosensor for label-free monitoring of alternative splicing events in real-time, without any cDNA synthesis or PCR amplification requirements. We applied this methodology to RNA isolated from HeLa cells for the quantification of alternatively spliced isoforms of the Fas gene, involved in cancer progression through regulation of programmed cell death. We demonstrate that our methodology is isoform-specific, with virtually no cross-hybridization, achieving limits of detection (LODs) in the picoMolar (pM) range. Similar results were obtained for the detection of the BCL-X gene mRNA isoforms. The results were independently validated by RT-qPCR, with excellent concordance in the determination of isoform ratios. The simplicity and robustness of this biosensor technology can greatly facilitate the exploration of alternative splicing biomarkers in disease diagnosis and therapy.
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Affiliation(s)
- César S Huertas
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - L G Carrascosa
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - S Bonnal
- Centre de Regulació Genòmica and The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - J Valcárcel
- Centre de Regulació Genòmica and The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Spain
| | - L M Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain.
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66
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Heck MV, Azizov M, Stehning T, Walter M, Kedersha N, Auburger G. Dysregulated expression of lipid storage and membrane dynamics factors in Tia1 knockout mouse nervous tissue. Neurogenetics 2015; 15:135-44. [PMID: 24659297 PMCID: PMC3994287 DOI: 10.1007/s10048-014-0397-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/03/2014] [Indexed: 12/13/2022]
Abstract
During cell stress, the transcription and translation of immediate early genes are prioritized, while most other messenger RNAs (mRNAs) are stored away in stress granules or degraded in processing bodies (P-bodies). TIA-1 is an mRNA-binding protein that needs to translocate from the nucleus to seed the formation of stress granules in the cytoplasm. Because other stress granule components such as TDP-43, FUS, ATXN2, SMN, MAPT, HNRNPA2B1, and HNRNPA1 are crucial for the motor neuron diseases amyotrophic lateral sclerosis (ALS)/spinal muscular atrophy (SMA) and for the frontotemporal dementia (FTD), here we studied mouse nervous tissue to identify mRNAs with selective dependence on Tia1 deletion. Transcriptome profiling with oligonucleotide microarrays in comparison of spinal cord and cerebellum, together with independent validation in quantitative reverse transcriptase PCR and immunoblots demonstrated several strong and consistent dysregulations. In agreement with previously reported TIA1 knock down effects, cell cycle and apoptosis regulators were affected markedly with expression changes up to +2-fold, exhibiting increased levels for Cdkn1a, Ccnf, and Tprkb vs. decreased levels for Bid and Inca1 transcripts. Novel and surprisingly strong expression alterations were detected for fat storage and membrane trafficking factors, with prominent +3-fold upregulations of Plin4, Wdfy1, Tbc1d24, and Pnpla2 vs. a −2.4-fold downregulation of Cntn4 transcript, encoding an axonal membrane adhesion factor with established haploinsufficiency. In comparison, subtle effects on the RNA processing machinery included up to 1.2-fold upregulations of Dcp1b and Tial1. The effect on lipid dynamics factors is noteworthy, since also the gene deletion of Tardbp (encoding TDP-43) and Atxn2 led to fat metabolism phenotypes in mouse. In conclusion, genetic ablation of the stress granule nucleator TIA-1 has a novel major effect on mRNAs encoding lipid homeostasis factors in the brain, similar to the fasting effect.
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Affiliation(s)
- Melanie Vanessa Heck
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Mekhman Azizov
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Tanja Stehning
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076 Tübingen, Germany
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Smith 652, One Jimmy Fund Way, Boston, MA 02115 USA
| | - Georg Auburger
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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67
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Ge D, Han L, Huang S, Peng N, Wang P, Jiang Z, Zhao J, Su L, Zhang S, Zhang Y, Kung H, Zhao B, Miao J. Identification of a novel MTOR activator and discovery of a competing endogenous RNA regulating autophagy in vascular endothelial cells. Autophagy 2015; 10:957-71. [PMID: 24879147 DOI: 10.4161/auto.28363] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MTOR, a central regulator of autophagy, is involved in cancer and cardiovascular and neurological diseases. Modulating the MTOR signaling balance could be of great significance for numerous diseases. No chemical activators of MTOR have been found, and the urgent challenge is to find novel MTOR downstream components. In previous studies, we found a chemical small molecule, 3-benzyl-5-((2-nitrophenoxy) methyl)-dihydrofuran-2(3H)-one (3BDO), that inhibited autophagy in human umbilical vein endothelial cells (HUVECs) and neuronal cells. Here, we found that 3BDO activated MTOR by targeting FKBP1A (FK506-binding protein 1A, 12 kDa). We next used 3BDO to detect novel factors downstream of the MTOR signaling pathway. Activation of MTOR by 3BDO increased the phosphorylation of TIA1 (TIA1 cytotoxic granule-associated RNA binding protein/T-cell-restricted intracellular antigen-1). Finally, we used gene microarray, RNA interference, RNA-ChIP assay, bioinformatics, luciferase reporter assay, and other assays and found that 3BDO greatly decreased the level of a long noncoding RNA (lncRNA) derived from the 3' untranslated region (3'UTR) of TGFB2, known as FLJ11812. TIA1 was responsible for processing FLJ11812. Further experiments results showed that FLJ11812 could bind with MIR4459 targeting ATG13 (autophagy-related 13), and ATG13 protein level was decreased along with 3BDO-decreased FLJ11812 level. Here, we provide a new activator of MTOR, and our findings highlight the role of the lncRNA in autophagy.
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Affiliation(s)
- Di Ge
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Lei Han
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - ShuYa Huang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Nan Peng
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - PengChong Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Zheng Jiang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Jing Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Le Su
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - ShangLi Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research; Chinese Ministry of Education and Chinese Ministry of Health; Shandong University Qilu Hospital; Jinan, China
| | - HsiangFu Kung
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China; Institute of Pathology and Southwest Cancer Center; Third Military Medical University; Chongqing, China
| | - BaoXiang Zhao
- Institute of Organic Chemistry; School of Chemistry and Chemical Engineering; Shandong University; Jinan, China
| | - JunYing Miao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research; Chinese Ministry of Education and Chinese Ministry of Health; Shandong University Qilu Hospital; Jinan, China
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68
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Cruz-Gallardo I, Del Conte R, Velázquez-Campoy A, García-Mauriño SM, Díaz-Moreno I. A Non-Invasive NMR Method Based on Histidine Imidazoles to Analyze the pH-Modulation of Protein-Nucleic Acid Interfaces. Chemistry 2015; 21:7588-95. [PMID: 25846236 DOI: 10.1002/chem.201405538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 02/19/2015] [Indexed: 12/20/2022]
Abstract
A useful (2) J(N-H) coupling-based NMR spectroscopic approach is proposed to unveil, at the molecular level, the contribution of the imidazole groups of histidines from RNA/DNA-binding proteins on the modulation of binding to nucleic acids by pH. Such protonation/deprotonation events have been monitored on the single His96 located at the second RNA/DNA recognition motif (RRM2) of T-cell intracellular antigen-1 (TIA-1) protein. The pKa values of the His96 ionizable groups were substantially higher in the complexes with short U-rich RNA and T-rich DNA oligonucleotides than those of the isolated TIA-1 RRM2. Herein, the methodology applied to determine changes in pKa of histidine side chains upon DNA/RNA binding, gives valuable information to understand the pH effect on multidomain DNA/RNA-binding proteins that shuttle among different cellular compartments.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Instituto de Bioquímica Vegetal y Fotosíntesis cicCartuja, Universidad de Sevilla - CSIC, Avenida Américo Vespucio 49, 41092 Sevilla (Spain)
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69
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Sánchez-Jiménez C, Ludeña MD, Izquierdo JM. T-cell intracellular antigens function as tumor suppressor genes. Cell Death Dis 2015; 6:e1669. [PMID: 25741594 PMCID: PMC4385921 DOI: 10.1038/cddis.2015.43] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/16/2014] [Accepted: 01/19/2015] [Indexed: 12/12/2022]
Abstract
Knockdown of T-cell intracellular antigens TIA1 and TIAR in transformed cells triggers cell proliferation and tumor growth. Using a tetracycline-inducible system, we report here that an increased expression of TIA1 or TIAR in 293 cells results in reduced rates of cell proliferation. Ectopic expression of these proteins abolish endogenous TIA1 and TIAR levels via the regulation of splicing of their pre-mRNAs, and partially represses global translation in a phospho-eukaryotic initiation factor 2 alpha-dependent manner. This is accompanied by cell cycle arrest at G1/S and cell death through caspase-dependent apoptosis and autophagy. Genome-wide profiling illustrates a selective upregulation of p53 signaling pathway-related genes. Nude mice injected with doxycycline-inducible cells expressing TIA1 or TIAR retard, or even inhibit, growth of xenotumors. Remarkably, low expressions of TIA1 and TIAR correlate with poor prognosis in patients with lung squamous cell carcinoma. These findings strongly support the concept that TIA proteins act as tumor suppressor genes.
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Affiliation(s)
- C Sánchez-Jiménez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera 1, Madrid, Spain
| | - M D Ludeña
- Facultad de Medicina, Departamento de Biología Celular y Patología, Universidad de Salamanca-Hospital Universitario de Salamanca, C/ Paseo de San Vicente 58-182, Salamanca, Spain
| | - J M Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera 1, Madrid, Spain
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70
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Liu W, Lin YT, Yan XL, Ding YL, Wu YL, Chen WN, Lin X. Hepatitis B virus core protein inhibits Fas-mediated apoptosis of hepatoma cells via regulation of mFas/FasL and sFas expression. FASEB J 2014; 29:1113-23. [PMID: 25466893 DOI: 10.1096/fj.14-263822] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hepatitis B virus core protein (HBc) has been implicated in hepatocarcinogenesis through several mechanisms. Resistance of hepatitis B virus (HBV)-infected hepatocytes to apoptosis is considered one of the major contributors to the progression of chronic hepatitis to cirrhosis and ultimately to hepatocellular carcinoma. The Fas receptor/ligand (Fas/FasL) system plays a prominent role in hepatocyte death during HBV infection. Here we report that HBc mediates resistance of hepatoma cells to agonistic anti-Fas antibody (CH11)-induced apoptosis. When HBc was introduced into human hepatoma cells, the cells became resistant to CH11 cytotoxicity in a p53-dependent manner. HBc significantly down-regulated the expression of p53, total Fas, and membrane-bound Fas at the mRNA and protein levels and reduced FasL mRNA expression. In contrast, HBc up-regulated the expression of soluble forms of Fas by increasing Fas alternative mRNA splicing. Mechanistically, HBc-mediated Fas alternative mRNA splicing was associated with up-regulation of polypyrimidine tract-binding protein 1 and down-regulation of Fas-activated serine/threonine kinase. These results indicated that HBc may prevent hepatocytes from Fas-induced apoptosis by the dual effects of reducing the expression of the proapoptotic form of Fas and enhancing the expression of the antiapoptotic form of the receptor, which may contribute to the survival and persistence of infected hepatocytes during chronic infection.
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Affiliation(s)
- Wei Liu
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
| | - Yan-Ting Lin
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
| | - Xiao-Li Yan
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
| | - Ya-Lan Ding
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
| | - Yun-Li Wu
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
| | - Wan-Nan Chen
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
| | - Xu Lin
- *Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Minhou, China; and Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Minhou, China
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71
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Núñez M, Sánchez-Jiménez C, Alcalde J, Izquierdo JM. Long-term reduction of T-cell intracellular antigens reveals a transcriptome associated with extracellular matrix and cell adhesion components. PLoS One 2014; 9:e113141. [PMID: 25405991 PMCID: PMC4236147 DOI: 10.1371/journal.pone.0113141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 10/23/2014] [Indexed: 12/31/2022] Open
Abstract
Knockdown of T-cell intracellular antigens TIA1 and TIAR contributes to a cellular phenotype characterised by uncontrolled proliferation and tumorigenesis. Massive-scale poly(A+) RNA sequencing of TIA1 or TIAR-knocked down HeLa cells reveals transcriptome signatures comprising genes and functional categories potentially able to modulate several aspects of membrane dynamics associated with extracellular matrix and focal/cell adhesion events. The transcriptomic heterogeneity is the result of differentially expressed genes and RNA isoforms generated by alternative splicing and/or promoter usage. These results suggest a role for TIA proteins in the regulation and/or modulation of cellular homeostasis related to focal/cell adhesion, extracellular matrix and membrane and cytoskeleton dynamics.
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Affiliation(s)
- Mario Núñez
- Centro de Biología Molecular ‘Severo Ochoa’, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - Carmen Sánchez-Jiménez
- Centro de Biología Molecular ‘Severo Ochoa’, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - José Alcalde
- Centro de Biología Molecular ‘Severo Ochoa’, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular ‘Severo Ochoa’, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
- * E-mail:
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72
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Tessier SN, Audas TE, Wu CW, Lee S, Storey KB. The involvement of mRNA processing factors TIA-1, TIAR, and PABP-1 during mammalian hibernation. Cell Stress Chaperones 2014; 19:813-25. [PMID: 24590458 PMCID: PMC4389841 DOI: 10.1007/s12192-014-0505-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/10/2023] Open
Abstract
Mammalian hibernators survive low body temperatures, ischemia-reperfusion, and restricted nutritional resources via global reductions in energy-expensive cellular processes and selective increases in stress pathways. Consequently, studies that analyze hibernation uncover mechanisms which balance metabolism and support survival by enhancing stress tolerance. We hypothesized processing factors that influence messenger ribonucleic acid (mRNA) maturation and translation may play significant roles in hibernation. We characterized the amino acid sequences of three RNA processing proteins (T cell intracellular antigen 1 (TIA-1), TIA1-related (TIAR), and poly(A)-binding proteins (PABP-1)) from thirteen-lined ground squirrels (Ictidomys tridecemlineatus), which all displayed a high degree of sequence identity with other mammals. Alternate Tia-1 and TiaR gene variants were found in the liver with higher expression of isoform b versus a in both cases. The localization of RNA-binding proteins to subnuclear structures was assessed by immunohistochemistry and confirmed by subcellular fractionation; TIA-1 was identified as a major component of subnuclear structures with up to a sevenfold increase in relative protein levels in the nucleus during hibernation. By contrast, there was no significant difference in the relative protein levels of TIARa/TIARb in the nucleus, and a decrease was observed for TIAR isoforms in cytoplasmic fractions of torpid animals. Finally, we used solubility tests to analyze the formation of reversible aggregates that are associated with TIA-1/R function during stress; a shift towards the soluble fraction (TIA-1a, TIA-1b) was observed during hibernation suggesting enhanced protein aggregation was not present during torpor. The present study identifies novel posttranscriptional regulatory mechanisms that may play a role in reducing translational rates and/or mRNA processing under unfavorable environmental conditions.
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Affiliation(s)
- Shannon N. Tessier
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Timothy E. Audas
- />Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - Cheng-Wei Wu
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Stephen Lee
- />Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - Kenneth B. Storey
- />Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
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Huang S, Liu N, Li H, Zhao J, Su L, Zhang Y, Zhang S, Zhao B, Miao J. TIA1 interacts with annexin A7 in regulating vascular endothelial cell autophagy. Int J Biochem Cell Biol 2014; 57:115-22. [PMID: 25461769 DOI: 10.1016/j.biocel.2014.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/27/2014] [Accepted: 10/09/2014] [Indexed: 01/11/2023]
Abstract
T-cell intracellular antigen-1 (TIA1) is a DNA/RNA binding protein broadly expressed in eukaryotic cells, participating in multiple aspects of cellular metabolism. TIA1 phosphorylation was related with cell apoptosis and its RNA binding activity, however, the regulator and other functions of TIA1 phosphorylation were very little known. To find the modulator of TIA1 phosphorylation, we performed yeast two-hybrid screening and identified annexin A7 (ANXA7) as an interaction protein of TIA1. Recent study showed that a small molecule ABO could directly target ANXA7 and inhibit ANXA7 activity and its targets' phosphorylation. As a GTPase, ANXA7 was speculated to modulate TIA1 phosphorylation. Our results showed that ABO treatment promoted the interaction between TIA1 and ANXA7, and then greatly inhibited phosphorylation of TIA1 in HUVECs. Further results showed that ABO-increased interaction between ANXA7 and TIA1 significantly promoted the processing of a pro-autophagic factor FLJ11812 and the expression of ATG13. Moreover, we found that ABO increased TIA1 protein level, co-localization of ANXA7 and TIA1, and ATG13 expression in the aortic endothelium of apoE(-/-) mice. These data highlighted the new role of TIA1 phosphorylation in autophagy.
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Affiliation(s)
- Shuya Huang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Ning Liu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Haiying Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jing Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Le Su
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Shandong University Qilu Hospital, Jinan 250012, China
| | - Shangli Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Baoxiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Junying Miao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Shandong University Qilu Hospital, Jinan 250012, China.
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74
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Genome-wide profiling reveals a role for T-cell intracellular antigens TIA1 and TIAR in the control of translational specificity in HeLa cells. Biochem J 2014; 461:43-50. [PMID: 24927121 DOI: 10.1042/bj20140227] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TIA (T-cell intracellular antigens)-knockdown HeLa cells show an increase in ribosomes and translational machinery components. This increase correlates with specific changes in translationally up-regulated mRNAs involved in cell-cycle progression and DNA repair, as shown in polysomal profiling analysis. Our data support the hypothesis that a concerted activation of both global and selective translational rates leads to the transition to a more proliferative status in TIA-knockdown HeLa cells.
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75
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Paronetto M, Bernardis I, Volpe E, Bechara E, Sebestyén E, Eyras E, Valcárcel J. Regulation of FAS Exon Definition and Apoptosis by the Ewing Sarcoma Protein. Cell Rep 2014; 7:1211-26. [DOI: 10.1016/j.celrep.2014.03.077] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 02/16/2014] [Accepted: 03/31/2014] [Indexed: 12/18/2022] Open
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76
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Carrascoso I, Sánchez-Jiménez C, Izquierdo JM. Long-term reduction of T-cell intracellular antigens leads to increased beta-actin expression. Mol Cancer 2014; 13:90. [PMID: 24766723 PMCID: PMC4113145 DOI: 10.1186/1476-4598-13-90] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The permanent down-regulated expression of T-cell intracellular antigen (TIA) proteins in HeLa cells improves cytoskeleton-mediated functions such as cell proliferation and tumor growth. METHODS Making use of human and mouse cells with knocked down/out expression of T-cell intracellular antigen 1 (TIA1) and/or TIA1 related/like (TIAR/TIAL1) proteins and classical RNA (e.g. reverse transcription-quantitative polymerase chain reaction, polysomal profiling analysis using sucrose gradients, immunoblotting, immunoprecipitation, electrophoretic mobility shift assays, ultraviolet light crosslinking and poly (A+) test analysis) and cellular (e.g. immunofluorescence microscopy and quimeric mRNA transfections) biology methods, we have analyzed the regulatory role of TIA proteins in the post-transcriptional modulation of beta-actin (ACTB) mRNA. RESULTS Our observations show that the acquisition of above cellular capacities is concomitant with increased expression levels of the actin beta subunit (ACTB) protein. Regulating TIA abundance does not modify ACTB mRNA levels, however, an increase of ACTB mRNA translation is observed. This regulatory capacity of TIA proteins is linked to the ACTB mRNA 3'-untranslated region (3'-UTR), where these proteins could function as RNA binding proteins. The expression of GFP from a chimeric reporter containing human ΑCΤΒ 3'-UTR recapitulates the translational control found by the endogenous ACTB mRNA in the absence of TIA proteins. Additionally, murine embryonic fibroblasts (MEF) knocked out for TIA1 rise mouse ACTB protein expression compared to the controls. Once again steady-state levels of mouse ACTB mRNA remained unchanged. CONCLUSIONS Collectively, these results suggest that TIA proteins can function as long-term regulators of the ACTB mRNA metabolism in mouse and human cells.
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Affiliation(s)
| | | | - José M Izquierdo
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, DP 28049 Madrid, Spain.
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Cruz-Gallardo I, Aroca Á, Gunzburg MJ, Sivakumaran A, Yoon JH, Angulo J, Persson C, Gorospe M, Karlsson BG, Wilce JA, Díaz-Moreno I. The binding of TIA-1 to RNA C-rich sequences is driven by its C-terminal RRM domain. RNA Biol 2014; 11:766-76. [PMID: 24824036 DOI: 10.4161/rna.28801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
T-cell intracellular antigen-1 (TIA-1) is a key DNA/RNA binding protein that regulates translation by sequestering target mRNAs in stress granules (SG) in response to stress conditions. TIA-1 possesses three RNA recognition motifs (RRM) along with a glutamine-rich domain, with the central domains (RRM2 and RRM3) acting as RNA binding platforms. While the RRM2 domain, which displays high affinity for U-rich RNA sequences, is primarily responsible for interaction with RNA, the contribution of RRM3 to bind RNA as well as the target RNA sequences that it binds preferentially are still unknown. Here we combined nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) techniques to elucidate the sequence specificity of TIA-1 RRM3. With a novel approach using saturation transfer difference NMR (STD-NMR) to quantify protein-nucleic acids interactions, we demonstrate that isolated RRM3 binds to both C- and U-rich stretches with micromolar affinity. In combination with RRM2 and in the context of full-length TIA-1, RRM3 significantly enhanced the binding to RNA, particularly to cytosine-rich RNA oligos, as assessed by biotinylated RNA pull-down analysis. Our findings provide new insight into the role of RRM3 in regulating TIA-1 binding to C-rich stretches, that are abundant at the 5' TOPs (5' terminal oligopyrimidine tracts) of mRNAs whose translation is repressed under stress situations.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
| | - Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
| | - Menachem J Gunzburg
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Andrew Sivakumaran
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Je-Hyun Yoon
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program; NIH; Baltimore, MD USA
| | - Jesús Angulo
- Instituto de Investigaciones Químicas; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain; School of Pharmacy; University of East Anglia; Norwich Research Park; Norwich, UK
| | - Cecilia Persson
- Swedish NMR Centre; University of Gothenburg; Gothenburg, Sweden
| | - Myriam Gorospe
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program; NIH; Baltimore, MD USA
| | - B Göran Karlsson
- Swedish NMR Centre; University of Gothenburg; Gothenburg, Sweden
| | - Jacqueline A Wilce
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
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Wuillemin N, Terracciano L, Beltraminelli H, Schlapbach C, Fontana S, Krähenbühl S, Pichler WJ, Yerly D. T cells infiltrate the liver and kill hepatocytes in HLA-B(∗)57:01-associated floxacillin-induced liver injury. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1677-82. [PMID: 24731753 DOI: 10.1016/j.ajpath.2014.02.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 02/20/2014] [Accepted: 02/25/2014] [Indexed: 01/06/2023]
Abstract
Drug-induced liver injury is a major safety issue. It can cause severe disease and is a common cause of the withdrawal of drugs from the pharmaceutical market. Recent studies have identified the HLA-B(∗)57:01 allele as a risk factor for floxacillin (FLUX)-induced liver injury and have suggested a role for cytotoxic CD8(+) T cells in the pathomechanism of liver injury caused by FLUX. This study aimed to confirm the importance of FLUX-reacting cytotoxic lymphocytes in the pathomechanism of liver injury and to dissect the involved mechanisms of cytotoxicity. IHC staining of a liver biopsy from a patient with FLUX-induced liver injury revealed periportal inflammation and the infiltration of cytotoxic CD3(+) CD8(+) lymphocytes into the liver. The infiltration of cytotoxic lymphocytes into the liver of a patient with FLUX-induced liver injury demonstrates the importance of FLUX-reacting T cells in the underlying pathomechanism. Cytotoxicity of FLUX-reacting T cells from 10 HLA-B(∗)57:01(+) healthy donors toward autologous target cells and HLA-B(∗)57:01-transduced hepatocytes was analyzed in vitro. Cytotoxicity of FLUX-reacting T cells was concentration dependent and required concentrations in the range of peak serum levels after FLUX administration. Killing of target cells was mediated by different cytotoxic mechanisms. Our findings emphasize the role of the adaptive immune system and especially of activated drug-reacting T cells in human leukocyte antigen-associated, drug-induced liver injury.
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Affiliation(s)
- Natascha Wuillemin
- Clinic for Rheumatology and Clinical Immunology/Allergology, University Hospital of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Luigi Terracciano
- Division of Molecular Pathology Division, Institute of Pathology, University Hospital of Basel, Basel, Switzerland
| | | | | | - Stefano Fontana
- Regional Blood Transfusion Service, Swiss Red Cross, Bern, Switzerland
| | - Stephan Krähenbühl
- Division of Clinical Pharmacology and Toxicology, University Hospital of Basel, Basel, Switzerland
| | - Werner J Pichler
- Clinic for Rheumatology and Clinical Immunology/Allergology, University Hospital of Bern, Bern, Switzerland.
| | - Daniel Yerly
- Clinic for Rheumatology and Clinical Immunology/Allergology, University Hospital of Bern, Bern, Switzerland
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79
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Wang I, Hennig J, Jagtap PKA, Sonntag M, Valcárcel J, Sattler M. Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1. Nucleic Acids Res 2014; 42:5949-66. [PMID: 24682828 PMCID: PMC4027183 DOI: 10.1093/nar/gku193] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.
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Affiliation(s)
- Iren Wang
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Miriam Sonntag
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
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80
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Maticzka D, Lange SJ, Costa F, Backofen R. GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol 2014; 15:R17. [PMID: 24451197 PMCID: PMC4053806 DOI: 10.1186/gb-2014-15-1-r17] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 01/22/2014] [Indexed: 12/01/2022] Open
Abstract
We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstrating that the modeled binding preferences conform to the literature, and showcase the biological relevance and two applications of GraphProt models. First, estimated binding affinities correlate with experimental measurements. Second, predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not. Computational binding models, such as those provided by GraphProt, are essential for predicting RBP binding sites and affinities in all tissues. GraphProt is freely available at http://www.bioinf.uni-freiburg.de/Software/GraphProt.
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81
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Hudig D, Hunter KW, Diamond WJ, Redelman D. Properties of human blood monocytes. II. Monocytes from healthy adults are highly heterogeneous within and among individuals. CYTOMETRY PART B-CLINICAL CYTOMETRY 2013; 86:121-34. [PMID: 24327358 DOI: 10.1002/cyto.b.21141] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/17/2013] [Accepted: 10/18/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND Human blood monocytes are known to include subsets defined by the expression of CD14 and CD16 but otherwise are often assumed to be relatively homogeneous. However, we had observed additional heterogeneity that led us to a more extensive examination of monocytes. METHODS Blood samples from 200 healthy adults without known immunological abnormalities were examined by analysis with a hematology analyzer and by flow cytometry (FCM) to determine leukocyte differential counts, to identify subsets and to measure expression of monocyte-associated molecules. RESULTS The estimated cell counts of monocytes, neutrophils, total lymphocytes, and T cells all varied to a similar extent, that is, ±30-35%. The fractions of monocyte subsets defined by CD14 and CD16 or by CD163 expression also varied among individuals. FCM examinations showed that all the monocyte-associated molecules that were examined varied in expression in this increasing order-CD244, CD4, CD38, CD91, CD11b, toll-like receptor 2 (TLR2), TIA-1, CD14 (on CD14(Br+) cells), CD86, CD80, HLA-DQ, CD33, and HLA-DR. CONCLUSIONS Human blood monocytes are heterogeneous among healthy adults with respect to cell counts, subsets, and the levels of expression of monocyte-associated molecules. An increase in the "non-classical" (CD14(Lo/Neg) /CD16(+) ) monocyte subset or in the expression of CD11b or TLR2 have known diagnostic/prognostic implications. CD244 and CD4 have well-defined functions on lymphocytes but perform unknown activities on monocytes although their expression appears more narrowly controlled. Together, these data suggest that monocytes should be more extensively examined in both clinical and basic contexts.
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Affiliation(s)
- Dorothy Hudig
- Department of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada, 89557
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82
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Sánchez-Jiménez C, Izquierdo JM. T-cell intracellular antigen (TIA)-proteins deficiency in murine embryonic fibroblasts alters cell cycle progression and induces autophagy. PLoS One 2013; 8:e75127. [PMID: 24086455 PMCID: PMC3782481 DOI: 10.1371/journal.pone.0075127] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/09/2013] [Indexed: 02/03/2023] Open
Abstract
Mice lacking either T-cell intracellular antigen 1 (TIA1) or TIA1 related/like protein (TIAR/TIAL1) show high rates of embryonic lethality, suggesting a relevant role for these proteins during embryonic development. However, intrinsic molecular and cellular consequences of either TIA1 or TIAR deficiency remain poorly defined. By using genome-wide expression profiling approach, we demonstrate that either TIA1 or TIAR inactivation broadly alter normal development-associated signalling pathways in murine embryonic fibroblasts (MEF). Indeed, these analyses highlighted alterations of cytokine-cytokine and ECM-receptor interactions and Wnt, MAPK, TGF-beta dependent signalling pathways. Consistent with these results, TIA1 and TIAR knockout (KO) MEF show reduced rates of cell proliferation, cell cycle progression delay and increased cell size. Furthermore, TIA-proteins deficiency also caused metabolic deficiencies, increased ROS levels and DNA damage, promoting a gentle rise of cell death. Concomitantly, high rates of autophagy were detected in both TIA1 and TIAR KO MEF with induction of the formation of autophagosomes, as evidenced by the up-regulation of the LC3B protein, and autolysosomes, measured by colocalization of LC3B and LAMP1, as a survival mechanism attempt. Taken together, these observations support that TIA proteins orchestrate a transcriptome programme to activate specific developmental decisions. This program is likely to contribute to mouse physiology starting at early stages of the embryonic development. TIA1/TIAR might function as cell sensors to maintain homeostasis and promote adaptation/survival responses to developmental stress.
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Affiliation(s)
- Carmen Sánchez-Jiménez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
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83
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Álvarez E, Castelló A, Carrasco L, Izquierdo JM. Poliovirus 2A protease triggers a selective nucleo-cytoplasmic redistribution of splicing factors to regulate alternative pre-mRNA splicing. PLoS One 2013; 8:e73723. [PMID: 24066065 PMCID: PMC3774746 DOI: 10.1371/journal.pone.0073723] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/30/2013] [Indexed: 12/31/2022] Open
Abstract
Poliovirus protease 2A (2Apro) obstructs host gene expression by reprogramming transcriptional and post-transcriptional regulatory events during infection. Here we demonstrate that expression of 2Apro induces a selective nucleo-cytoplasm translocation of several important RNA binding proteins and splicing factors. Subcellular fractionation studies, together with immunofluorescence microscopy revealed an asymmetric distribution of HuR and TIA1/TIAR in 2Apro expressing cells, which modulates splicing of the human Fas exon 6. Consistent with this result, knockdown of HuR or overexpression of TIA1/TIAR, leads to Fas exon 6 inclusion in 2Apro-expressing cells. Therefore, poliovirus 2Apro can target alternative pre-mRNA splicing by regulating protein shuttling between the nucleus and the cytoplasm.
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Affiliation(s)
- Enrique Álvarez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- * E-mail: (EA); (JMI)
| | - Alfredo Castelló
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Luis Carrasco
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- * E-mail: (EA); (JMI)
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84
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Silva-García CG, Estela Navarro R. The C. elegans TIA-1/TIAR homolog TIAR-1 is required to induce germ cell apoptosis. Genesis 2013; 51:690-707. [PMID: 23913578 DOI: 10.1002/dvg.22418] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 11/11/2022]
Abstract
In Caenorhabditis elegans, physiological germ cell apoptosis eliminates more than half of the cells in the hermaphrodite gonad to support gamete quality and germline homeostasis by a still unidentified mechanism. External factors can also affect germ cell apoptosis. The BH3-only protein EGL-1 induces germ cell apoptosis when animals are exposed to pathogens or agents that produce DNA damage. DNA damage-induced apoptosis also requires the nematode p53 homolog CEP-1. Previously, we found that heat shock, oxidative, and osmotic stresses induce germ cell apoptosis through an EGL-1 and CEP-1 independent mechanism that requires the MAPKK pathway. However, we observed that starvation increases germ cell apoptosis by an unknown pathway. Searching for proteins that participate in stress-induced apoptosis, we found the RNA-binding protein TIAR-1 (a homolog of the mammalian TIA-1/TIAR family of proteins). Here, we show that TIAR-1 in C. elegans is required to induce apoptosis in the germline under several conditions. We also show that TIAR-1 acts downstream of CED-9 (a BCL2 homolog) to induce apoptosis under stress conditions, and apparently does not seem to regulate ced-4 or ced-3 mRNAs accumulation directly. TIAR-1 is expressed ubiquitously in the cytoplasm of the soma as well as the germline, where it sometimes associates with P granules. We show that animals lacking TIAR-1 expression are temperature sensitive sterile due to oogenesis and spermatogenesis defects. Our work shows that TIAR-1 is required for proper germline function and demonstrates that this protein is important to induce germ cell apoptosis under several conditions.
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Affiliation(s)
- Carlos Giovanni Silva-García
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
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85
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Cruz-Gallardo I, Aroca Á, Persson C, Karlsson BG, Díaz-Moreno I. RNA binding of T-cell intracellular antigen-1 (TIA-1) C-terminal RNA recognition motif is modified by pH conditions. J Biol Chem 2013; 288:25986-25994. [PMID: 23902765 DOI: 10.1074/jbc.m113.489070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
T-cell intracellular antigen-1 (TIA-1) is a DNA/RNA-binding protein that regulates critical events in cell physiology by the regulation of pre-mRNA splicing and mRNA translation. TIA-1 is composed of three RNA recognition motifs (RRMs) and a glutamine-rich domain and binds to uridine-rich RNA sequences through its C-terminal RRM2 and RRM3 domains. Here, we show that RNA binding mediated by either isolated RRM3 or the RRM23 construct is controlled by slight environmental pH changes due to the protonation/deprotonation of TIA-1 RRM3 histidine residues. The auxiliary role of the C-terminal RRM3 domain in TIA-1 RNA recognition is poorly understood, and this work provides insight into its binding mechanisms.
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Affiliation(s)
- Isabel Cruz-Gallardo
- From the Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), 41092 Seville, Spain and
| | - Ángeles Aroca
- From the Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), 41092 Seville, Spain and
| | - Cecilia Persson
- the Swedish NMR Centre, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - B Göran Karlsson
- the Swedish NMR Centre, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Irene Díaz-Moreno
- From the Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), 41092 Seville, Spain and.
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86
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Cléry A, Sinha R, Anczuków O, Corrionero A, Moursy A, Daubner GM, Valcárcel J, Krainer AR, Allain FHT. Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition. Proc Natl Acad Sci U S A 2013; 110:E2802-11. [PMID: 23836656 PMCID: PMC3725064 DOI: 10.1073/pnas.1303445110] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine (SR) proteins, one of the major families of alternative-splicing regulators in Eukarya, have two types of RNA-recognition motifs (RRMs): a canonical RRM and a pseudo-RRM. Although pseudo-RRMs are crucial for activity of SR proteins, their mode of action was unknown. By solving the structure of the human SRSF1 pseudo-RRM bound to RNA, we discovered a very unusual and sequence-specific RNA-binding mode that is centered on one α-helix and does not involve the β-sheet surface, which typically mediates RNA binding by RRMs. Remarkably, this mode of binding is conserved in all pseudo-RRMs tested. Furthermore, the isolated pseudo-RRM is sufficient to regulate splicing of about half of the SRSF1 target genes tested, and the bound α-helix is a pivotal element for this function. Our results strongly suggest that SR proteins with a pseudo-RRM frequently regulate splicing by competing with, rather than recruiting, spliceosome components, using solely this unusual RRM.
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Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Rahul Sinha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Anna Corrionero
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | - Ahmed Moursy
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Gerrit M. Daubner
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Juan Valcárcel
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | | | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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87
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Far upstream element-binding protein 1 and RNA secondary structure both mediate second-step splicing repression. Proc Natl Acad Sci U S A 2013; 110:E2687-95. [PMID: 23818605 DOI: 10.1073/pnas.1310607110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Splicing of mRNA precursors consists of two steps that are almost invariably tightly coupled to facilitate efficient generation of spliced mRNA. However, we described previously a splicing substrate that is completely blocked after the first step. We have now investigated the basis for this unusual second-step inhibition and unexpectedly elucidated two independent mechanisms. One involves a stem-loop structure located downstream of the 3'splice site, and the other involves an exonic splicing silencer (ESS) situated 3' to the structure. Both elements contribute to the second-step block in vitro and also cause exon skipping in vivo. Importantly, we identified far upstream element-binding protein 1 (FUBP1), a single-stranded DNA- and RNA-binding protein not previously implicated in splicing, as a strong ESS binding protein, and several assays implicate it in ESS function. We demonstrate using depletion/add-back experiments that FUBP1 acts as a second-step repressor in vitro and show by siRNA-mediated knockdown and overexpression assays that it modulates exon inclusion in vivo. Together, our results provide additional insights into splicing control, and identify FUBP1 as a splicing regulator.
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88
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Schwer B, Chang J, Shuman S. Structure-function analysis of the 5' end of yeast U1 snRNA highlights genetic interactions with the Msl5*Mud2 branchpoint-binding complex and other spliceosome assembly factors. Nucleic Acids Res 2013; 41:7485-500. [PMID: 23754852 PMCID: PMC3753624 DOI: 10.1093/nar/gkt490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Yeast pre-mRNA splicing initiates via formation of a complex comprising U1 snRNP bound at the 5' splice site (5'SS) and the Msl5•Mud2 heterodimer engaged at the branchpoint (BP). Here, we present a mutational analysis of the U1 snRNA, which shows that although enlarging the 5' leader between the TMG cap and the (3)ACUUAC(8) motif that anneals to the 5'SS is tolerated, there are tight constraints on the downstream spacer between (3)ACUUAC(8) and helix 1 of the U1 fold. We exploit U1 alleles with 5' extensions, variations in the (3)ACUUAC(8) motif, downstream mutations and a longer helix 1 to discover new intra-snRNP synergies with U1 subunits Nam8 and Mud1 and the trimethylguanosine (TMG) cap. We describe novel mutations in U1 snRNA that bypass the essentiality of the DEAD-box protein Prp28. Structure-guided mutagenesis of Msl5 distinguished four essential amino acids that contact the BP sequence from nine other BP-binding residues that are inessential. We report new synthetic genetic interactions of the U1 snRNP with Msl5 and Mud2 and with the nuclear cap-binding subunit Cbc2. Our results fortify the idea that spliceosome assembly can occur via distinct genetically buffered microscopic pathways involving cross-intron-bridging interactions of the U1 snRNP•5'SS complex with the Mud2•Msl5•BP complex.
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Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, NY 10065, USA and Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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89
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Melamed Z, Levy A, Ashwal-Fluss R, Lev-Maor G, Mekahel K, Atias N, Gilad S, Sharan R, Levy C, Kadener S, Ast G. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Mol Cell 2013; 50:869-81. [PMID: 23747012 DOI: 10.1016/j.molcel.2013.05.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/25/2013] [Accepted: 04/30/2013] [Indexed: 12/16/2022]
Abstract
The initial step in microRNA (miRNA) biogenesis requires processing of the precursor miRNA (pre-miRNA) from a longer primary transcript. Many pre-miRNAs originate from introns, and both a mature miRNA and a spliced RNA can be generated from the same transcription unit. We have identified a mechanism in which RNA splicing negatively regulates the processing of pre-miRNAs that overlap exon-intron junctions. Computational analysis identified dozens of such pre-miRNAs, and experimental validation demonstrated competitive interaction between the Microprocessor complex and the splicing machinery. Tissue-specific alternative splicing regulates maturation of one such miRNA, miR-412, resulting in effects on its targets that code a protein network involved in neuronal cell death processes. This mode of regulation specifically controls maturation of splice-site-overlapping pre-miRNAs but not pre-miRNAs located completely within introns or exons of the same transcript. Our data present a biological role of alternative splicing in regulation of miRNA biogenesis.
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Affiliation(s)
- Ze'ev Melamed
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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90
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Dreumont N, Séraphin B. Rapid screening of yeast mutants with reporters identifies new splicing phenotypes. FEBS J 2013; 280:2712-26. [PMID: 23560879 DOI: 10.1111/febs.12277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 11/29/2022]
Abstract
Nuclear precursor mRNA splicing requires the stepwise assembly of a large complex, the spliceosome. Recent large-scale analyses, including purification of splicing complexes, high-throughput genetic screens and interactomic studies, have linked numerous factors to this dynamic process, including a well-defined core conserved from yeast to human. Intriguingly, despite extensive studies, no splicing defects were reported for some of the corresponding yeast mutants. To resolve this paradox, we screened a collection of viable yeast strains carrying mutations in splicing-related factors with a set of reporters including artificial constructs carrying competing splice sites. Previous analyses have indeed demonstrated that this strategy identifies yeast factors able to regulate alternative splicing and whose properties are conserved in human cells. The method, sensitive to subtle defects, revealed new splicing phenotypes for most analyzed factors such as the Urn1 protein. Interestingly, a mutant of PRP8 specifically lacking an N-terminal proline-rich region stimulated the splicing of a reporter containing competing branchpoint/3' splice site regions. Thus, using appropriate reporters, yeast can be used to quickly delineate the effect of various factors on splicing and identify those with the propensity to regulate alternative splicing events.
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Affiliation(s)
- Natacha Dreumont
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67404 Illkirch, France
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91
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Martinez NM, Lynch KW. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev 2013; 253:216-36. [PMID: 23550649 PMCID: PMC3621013 DOI: 10.1111/imr.12047] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most mammalian pre-mRNAs are alternatively spliced in a manner that alters the resulting open reading frame. Consequently, alternative pre-mRNA splicing provides an important RNA-based layer of protein regulation and cellular function. The ubiquitous nature of alternative splicing coupled with the advent of technologies that allow global interrogation of the transcriptome have led to an increasing awareness of the possibility that widespread changes in splicing patterns contribute to lymphocyte function during an immune response. Indeed, a few notable examples of alternative splicing have clearly been demonstrated to regulate T-cell responses to antigen. Moreover, several proteins key to the regulation of splicing in T cells have recently been identified. However, much remains to be done to truly identify the spectrum of genes that are regulated at the level of splicing in immune cells and to determine how many of these are controlled by currently known factors and pathways versus unknown mechanisms. Here, we describe the proteins, pathways, and mechanisms that have been shown to regulate alternative splicing in human T cells and discuss what is and is not known about the genes regulated by such factors. Finally, we highlight unifying themes with regards to the mechanisms and consequences of alternative splicing in the adaptive immune system and give our view of important directions for future studies.
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Affiliation(s)
- Nicole M Martinez
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, USA
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92
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Kim HS, Headey SJ, Yoga YMK, Scanlon MJ, Gorospe M, Wilce MCJ, Wilce JA. Distinct binding properties of TIAR RRMs and linker region. RNA Biol 2013; 10:579-89. [PMID: 23603827 PMCID: PMC3710364 DOI: 10.4161/rna.24341] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The RNA-binding protein TIAR is an mRNA-binding protein that acts as a translational repressor, particularly important under conditions of cellular stress. It binds to target mRNA and DNA via its RNA recognition motif (RRM) domains and is involved in both splicing regulation and translational repression via the formation of "stress granules." TIAR has also been shown to bind ssDNA and play a role in the regulation of transcription. Here we show, using surface plasmon resonance and nuclear magnetic resonance spectroscopy, specific roles of individual TIAR domains for high-affinity binding to RNA and DNA targets. We confirm that RRM2 of TIAR is the major RNA- and DNA-binding domain. However, the strong nanomolar affinity binding to U-rich RNA and T-rich DNA depends on the presence of the six amino acid residues found in the linker region C-terminal to RRM2. On its own, RRM1 shows preferred binding to DNA over RNA. We further characterize the interaction between RRM2 with the C-terminal extension and an AU-rich target RNA sequence using NMR spectroscopy to identify the amino acid residues involved in binding. We demonstrate that TIAR RRM2, together with its C-terminal extension, is the major contributor for the high-affinity (nM) interactions of TIAR with target RNA sequences.
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Affiliation(s)
- Henry S Kim
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
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93
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Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
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Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
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94
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Hackman P, Sarparanta J, Lehtinen S, Vihola A, Evilä A, Jonson PH, Luque H, Kere J, Screen M, Chinnery PF, Åhlberg G, Edström L, Udd B. Welander distal myopathy is caused by a mutation in the RNA-binding protein TIA1. Ann Neurol 2013; 73:500-9. [PMID: 23401021 DOI: 10.1002/ana.23831] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/14/2012] [Accepted: 11/30/2012] [Indexed: 12/11/2022]
Abstract
OBJECTIVE A study was undertaken to identify the molecular cause of Welander distal myopathy (WDM), a classic autosomal dominant distal myopathy. METHODS The genetic linkage was confirmed and defined by microsatellite and single nucleotide polymorphism haplotyping. The whole linked genomic region was sequenced with targeted high-throughput and Sanger sequencing, and coding transcripts were sequenced on the cDNA level. WDM muscle biopsies were studied by Western blotting and immunofluorescence microscopy. Splicing of TIA1 and its target genes in muscle and myoblast cultures was analyzed by reverse transcriptase polymerase chain reaction. Mutant TIA1 was characterized by cell biological studies on HeLa cells, including quantification of stress granules by high content analysis and fluorescence recovery after photobleaching (FRAP) experiments. RESULTS The linked haplotype at 2p13 was narrowed down to <806 kb. Sequencing by multiple methods revealed only 1 segregating coding mutation, c.1362 G>A (p.E384K) in the RNA-binding protein TIA1, a key component of stress granules. Immunofluorescence microscopy of WDM biopsies showed a focal increase of TIA1 in atrophic and vacuolated fibers. In HeLa cells, mutant TIA1 constructs caused a mild increase in stress granule abundance compared to wild type, and showed slower average fluorescence recovery in FRAP. INTERPRETATION WDM is caused by mutated TIA1 through a dominant pathomechanism probably involving altered stress granule dynamics.
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Affiliation(s)
- Peter Hackman
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
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95
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Sánchez-Jiménez C, Carrascoso I, Barrero J, Izquierdo JM. Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling. BMC Mol Biol 2013; 14:4. [PMID: 23387986 PMCID: PMC3600012 DOI: 10.1186/1471-2199-14-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 02/04/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND T-cell intracellular antigen (TIA) proteins function as regulators of cell homeostasis. These proteins control gene expression globally at multiple levels in response to dynamic regulatory changes and environmental stresses. Herein we identified a micro(mi)RNA signature associated to transiently TIA-depleted HeLa cells and analyzed the potential role of miRNAs combining genome-wide analysis data on mRNA and miRNA profiles. RESULTS Using high-throughput miRNA expression profiling, transient depletion of TIA-proteins in HeLa cells was observed to promote significant and reproducible changes affecting to a pool of up-regulated miRNAs involving miR-30b-3p, miR125a-3p, miR-193a-5p, miR-197-3p, miR-203a, miR-210, miR-371-5p, miR-373-5p, miR-483-5p, miR-492, miR-498, miR-503-5p, miR-572, miR-586, miR-612, miR-615-3p, miR-623, miR-625-5p, miR-629-5p, miR-638, miR-658, miR-663a, miR-671-5p, miR-769-3p and miR-744-5p. Some up-regulated and unchanged miRNAs were validated and previous results confirmed by reverse transcription and real time PCR. By target prediction of the miRNAs and combined analysis of the genome-wide expression profiles identified in TIA-depleted HeLa cells, we detected connections between up-regulated miRNAs and potential target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis suggest that target genes are related with biological processes associated to the regulation of DNA-dependent transcription, signal transduction and multicellular organismal development as well as with the enrichment of pathways involved in cancer, focal adhesion, regulation of actin cytoskeleton, endocytosis and MAPK and Wnt signaling pathways, respectively. When the collection of experimentally defined differentially expressed genes in TIA-depleted HeLa cells was intersected with potential target genes only 7 out of 68 (10%) up- and 71 out of 328 (22%) down-regulated genes were shared. GO and KEGG database analyses showed that the enrichment categories of biological processes and cellular pathways were related with innate immune response, signal transduction, response to interleukin-1, glomerular basement membrane development as well as neuroactive ligand-receptor interaction, endocytosis, lysosomes and apoptosis, respectively. CONCLUSION All this considered, these observations suggest that individual miRNAs could act as potential mediators of the epigenetic switch linking transcriptomic dynamics and cell phenotypes mediated by TIA proteins.
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Affiliation(s)
- Carmen Sánchez-Jiménez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
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96
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Ruirui K, Ray P, Yang M, Wen P, Zhu L, Liu J, Fushimi K, Kar A, Liu Y, He R, Kuo D, Wu JY. Alternative Pre-mRNA Splicing, Cell Death, and Cancer. Cancer Treat Res 2013; 158:181-212. [PMID: 24222359 DOI: 10.1007/978-3-642-31659-3_8] [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: 06/02/2023]
Abstract
Alternative splicing is one of the most powerful mechanisms for generating functionally distinct products from a single genetic loci and for fine-tuning gene activities at the post-transcriptional level. Alternative splicing plays important roles in regulating genes critical for cell death. These cell death genes encode death ligands, cell surface death receptors, intracellular death regulators, signal transduction molecules, and death executor enzymes such as caspases and nucleases. Alternative splicing of these genes often leads to the formation of functionally different products, some of which have antagonistic effects that are either cell death-promoting or cell death-preventing. Differential alternative splicing can affect expression, subcellular distribution, and functional activities of the gene products. Molecular defects in splicing regulation of cell death genes have been associated with cancer development and resistance to treatment. Studies using molecular, biochemical, and systems-based approaches have begun to reveal mechanisms underlying the regulation of alternative splicing of cell death genes. Systematic studies have begun to uncover the multi-level interconnected networks that regulate alternative splicing. A global picture of the complex mechanisms that regulate cell death genes at the pre-mRNA splicing level has thus begun to emerge.
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Affiliation(s)
- Kong Ruirui
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science, Beijing, China
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97
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Damgaard CK, Lykke-Andersen J. Regulation of ARE-mRNA Stability by Cellular Signaling: Implications for Human Cancer. Cancer Treat Res 2013; 158:153-80. [PMID: 24222358 DOI: 10.1007/978-3-642-31659-3_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During recent years, it has become clear that regulation of mRNA stability is an important event in the control of gene expression. The stability of a large class of mammalian mRNAs is regulated by AU-rich elements (AREs) located in the mRNA 3' UTRs. mRNAs with AREs are inherently labile but as a response to different cellular cues they can become either stabilized, allowing expression of a given gene, or further destabilized to silence their expression. These tightly regulated mRNAs include many that encode growth factors, proto-oncogenes, cytokines, and cell cycle regulators. Failure to properly regulate their stability can therefore lead to uncontrolled expression of factors associated with cell proliferation and has been implicated in several human cancers. A number of transfactors that recognize AREs and regulate the translation and degradation of ARE-mRNAs have been identified. These transfactors are regulated by signal transduction pathways, which are often misregulated in cancers. This chapter focuses on the function of ARE-binding proteins with an emphasis on their regulation by signaling pathways and the implications for human cancer.
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98
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Platteborze PL. The transcriptional effects of the vesicants lewisite and sulfur mustard on human epidermal keratinocytes. Toxicol Mech Methods 2012; 15:185-92. [PMID: 20021082 DOI: 10.1080/15376520590945603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Sulfur mustard (SM) injury is a complex process that begins with extensive alkylation of critical cellular components and culminates in cell death and skin vesication. The mechanism of toxicity is not well understood since SM broadly alkylates cellular nucleophiles. However, two events appear integral-the formation of DNA cross-links and the release of proteases into the extracellular matrix. To identify genes directly involved in vesication, the transcriptional profile of SM was compared to the vesicant lewisite (L). Similarly, to identify genes directly involved in DNA damage, the transcriptional profile of SM was compared to the genotoxic agent cisplatin (c-Pt). Microarrays containing 7,075 sequence-verified human cDNAs were screened with mRNA from human epidermal keratinocytes treated with 200 mu M agent for 2 h. A large number of differentially expressed genes were identified, with many similarities observed between agents. Many genes not previously associated with SM and L injury were also identified, including a large percentage of unknown function. A comparison of the differential expression profiles revealed that L had the broadest and most robustly altered expression. Apoptotic transcripts were clearly evident in L but not in SM, suggesting a late stage in L injury.
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López-Urrutia E, Valdés J, Bonilla-Moreno R, Martínez-Salazar M, Martínez-Garcia M, Berumen J, Villegas-Sepúlveda N. A few nucleotide polymorphisms are sufficient to recruit nuclear factors differentially to the intron 1 of HPV-16 intratypic variants. Virus Res 2012; 166:43-53. [DOI: 10.1016/j.virusres.2012.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 01/24/2023]
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Abstract
Interference with stress granule (SG) accumulation is gaining increased appreciation as a common strategy used by diverse viruses to facilitate their replication and to cope with translational arrest. Here, we examined the impact of infection by herpes simplex virus 2 (HSV-2) on SG accumulation by monitoring the localization of the SG components T cell internal antigen 1 (TIA-1), Ras-GTPase-activating SH3-domain-binding protein (G3BP), and poly(A)-binding protein (PABP). Our results indicate that SGs do not accumulate in HSV-2-infected cells and that HSV-2 can interfere with arsenite-induced SG accumulation early after infection. Surprisingly, SG accumulation was inhibited despite increased phosphorylation of eukaryotic translation initiation factor 2α (eIF2α), implying that HSV-2 encodes previously unrecognized activities designed to maintain translation initiation downstream of eIF2α. SG accumulation was not inhibited in HSV-2-infected cells treated with pateamine A, an inducer that works independently of eIF2α phosphorylation. The SGs that accumulated following pateamine A treatment of infected cells contained G3BP and PABP but were largely devoid of TIA-1. We also identified novel nuclear structures containing TIA-1 that form late in infection. These structures contain the RNA binding protein 68-kDa Src-associated in mitosis (Sam68) and were noticeably absent in infected cells treated with inhibitors of viral DNA replication, suggesting that they arise as a result of late events in the virus replicative cycle.
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