1
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Matheson LS, Petkau G, Sáenz-Narciso B, D'Angeli V, McHugh J, Newman R, Munford H, West J, Chakraborty K, Roberts J, Łukasiak S, Díaz-Muñoz MD, Bell SE, Dimeloe S, Turner M. Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4 + T cell. Sci Rep 2022; 12:19657. [PMID: 36385275 PMCID: PMC9669047 DOI: 10.1038/s41598-022-24132-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
The ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.
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Affiliation(s)
- Louise S Matheson
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Georg Petkau
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Beatriz Sáenz-Narciso
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Vanessa D'Angeli
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: IONTAS, The Works, Unity Campus, Cambridge, CB22 3EF, UK
| | - Jessica McHugh
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Nature Reviews Rheumatology, The Campus, 4 Crinan Street, London, N1 9XW, UK
| | - Rebecca Newman
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Immunology Research Unit, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Haydn Munford
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James West
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Krishnendu Chakraborty
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Bioanalysis, Immunogenicity and Biomarkers (BIB), IVIVT, GSK, Stevenage, SG1 2NY, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Sebastian Łukasiak
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Manuel D Díaz-Muñoz
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, BP3028, 31024, Toulouse, France
| | - Sarah E Bell
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Sarah Dimeloe
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Martin Turner
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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2
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Qiu F, Fu Y, Lu C, Feng Y, Wang Q, Huo Z, Jia X, Chen C, Chen S, Xu A. Small Nuclear Ribonucleoprotein Polypeptide A-Mediated Alternative Polyadenylation of STAT5B during Th1 Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2017; 199:3106-3115. [PMID: 28954886 DOI: 10.4049/jimmunol.1601872] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/22/2017] [Indexed: 11/19/2022]
Abstract
T cells are activated and differentiated into Th cells depending on the rapid and accurate changes in the cell transcriptome. In addition to changes in mRNA expression, the sequences of many transcripts are altered by alternative splicing and alternative polyadenylation (APA). We profiled the APA sites of human CD4+ T cell subsets with high-throughput sequencing and found that Th1 cells harbored more genes with shorter tandem 3' untranslated regions (UTRs) than did naive T cells. We observed that STAT5B, a key regulator of Th1 differentiation, possessed three major APA sites and preferred shorter 3' UTRs in Th1 cells. In addition, small nuclear ribonucleoprotein polypeptide A (SNRPA) was found to bind directly to STAT5B 3' UTR and facilitate its APA switching. We also found that p65 activation triggered by TCR signaling could promote SNRPA transcription and 3' UTR shortening of STAT5B. Thus we propose that the APA switching of STAT5B induced by TCR activation is mediated by SNRPA.
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Affiliation(s)
- Feifei Qiu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Yonggui Fu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Chan Lu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Yuchao Feng
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Qiong Wang
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Zhanfeng Huo
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Xin Jia
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Chengyong Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Shangwu Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and
| | - Anlong Xu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China; and .,School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China
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3
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Techasintana P, Ellis JS, Glascock J, Gubin MM, Ridenhour SE, Magee JD, Hart ML, Yao P, Zhou H, Whitney MS, Franklin CL, Martindale JL, Gorospe M, Davis WJ, Fox PL, Li X, Atasoy U. The RNA-Binding Protein HuR Posttranscriptionally Regulates IL-2 Homeostasis and CD4 + Th2 Differentiation. Immunohorizons 2017; 1:109-123. [PMID: 30035254 PMCID: PMC6052877 DOI: 10.4049/immunohorizons.1700017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Posttranscriptional gene regulation by RNA-binding proteins, such as HuR (elavl1), fine-tune gene expression in T cells, leading to powerful effects on immune responses. HuR can stabilize target mRNAs and/or promote translation by interacting with their 3' untranslated region adenylate and uridylate-rich elements. It was previously demonstrated that HuR facilitates Th2 cytokine expression by mRNA stabilization. However, its effects upon IL-2 homeostasis and CD4+ Th2 differentiation are not as well understood. We found that optimal translation of Il2ra (CD25) required interaction of its mRNA with HuR. Conditional HuR knockout in CD4+ T cells resulted in loss of IL-2 homeostasis and defects in JAK-STAT signaling, Th2 differentiation, and cytokine production. HuR-knockout CD4+ T cells from OVA-immunized mice also failed to proliferate in response to Ag. These results demonstrate that HuR plays a pivotal role in maintaining normal IL-2 homeostasis and initiating CD4+ Th2 differentiation.
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Affiliation(s)
- Patsharaporn Techasintana
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Jason S. Ellis
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Jacqueline Glascock
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Matthew M. Gubin
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Suzanne E. Ridenhour
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Joseph D. Magee
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Marcia L. Hart
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201
| | - Peng Yao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Hao Zhou
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Maryln S. Whitney
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201
| | - Craig L. Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201
| | | | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224
| | - Wade J. Davis
- Department of Biostatistics, University of Missouri, Columbia, MO 65212
| | - Paul L. Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Xiaoxia Li
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ulus Atasoy
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
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4
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RNA stability regulates human T cell leukemia virus type 1 gene expression in chronically-infected CD4 T cells. Virology 2017; 508:7-17. [PMID: 28478312 DOI: 10.1016/j.virol.2017.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 11/22/2022]
Abstract
Regulation of expression of HTLV-1 gene products from integrated proviruses plays an important role in HTLV-1-associated disease pathogenesis. Previous studies have shown that T cell receptor (TCR)- and phorbol ester (PMA) stimulation of chronically infected CD4 T cells increases the expression of integrated HTLV-1 proviruses in latently infected cells, however the mechanism remains unknown. Analysis of HTLV-1 RNA and protein species following PMA treatment of the latently HTLV-1-infected, FS and SP T cell lines demonstrated rapid induction of tax/rex mRNA. This rapid increase in tax/rex mRNA was associated with markedly enhanced tax/rex mRNA stability while the stability of unspliced or singly spliced HTLV-1 RNAs did not increase. Tax/rex mRNA in the HTLV-1 constitutively expressing cell lines exhibited high basal stability even without PMA treatment. Our data support a model whereby T cell activation leads to increased HTLV-1 gene expression at least in part through increased tax/rex mRNA stability.
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5
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Vlasova-St Louis I, Bohjanen PR. Feedback Regulation of Kinase Signaling Pathways by AREs and GREs. Cells 2016; 5:cells5010004. [PMID: 26821046 PMCID: PMC4810089 DOI: 10.3390/cells5010004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/20/2016] [Accepted: 01/20/2016] [Indexed: 12/18/2022] Open
Abstract
In response to environmental signals, kinases phosphorylate numerous proteins, including RNA-binding proteins such as the AU-rich element (ARE) binding proteins, and the GU-rich element (GRE) binding proteins. Posttranslational modifications of these proteins lead to a significant changes in the abundance of target mRNAs, and affect gene expression during cellular activation, proliferation, and stress responses. In this review, we summarize the effect of phosphorylation on the function of ARE-binding proteins ZFP36 and ELAVL1 and the GRE-binding protein CELF1. The networks of target mRNAs that these proteins bind and regulate include transcripts encoding kinases and kinase signaling pathways (KSP) components. Thus, kinase signaling pathways are involved in feedback regulation, whereby kinases regulate RNA-binding proteins that subsequently regulate mRNA stability of ARE- or GRE-containing transcripts that encode components of KSP.
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Affiliation(s)
- Irina Vlasova-St Louis
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, USA.
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6
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Ross EA, Smallie T, Ding Q, O'Neil JD, Cunliffe HE, Tang T, Rosner DR, Klevernic I, Morrice NA, Monaco C, Cunningham AF, Buckley CD, Saklatvala J, Dean JL, Clark AR. Dominant Suppression of Inflammation via Targeted Mutation of the mRNA Destabilizing Protein Tristetraprolin. THE JOURNAL OF IMMUNOLOGY 2015; 195:265-76. [PMID: 26002976 PMCID: PMC4472942 DOI: 10.4049/jimmunol.1402826] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/27/2015] [Indexed: 02/07/2023]
Abstract
In myeloid cells, the mRNA-destabilizing protein tristetraprolin (TTP) is induced and extensively phosphorylated in response to LPS. To investigate the role of two specific phosphorylations, at serines 52 and 178, we created a mouse strain in which those residues were replaced by nonphosphorylatable alanine residues. The mutant form of TTP was constitutively degraded by the proteasome and therefore expressed at low levels, yet it functioned as a potent mRNA destabilizing factor and inhibitor of the expression of many inflammatory mediators. Mice expressing only the mutant form of TTP were healthy and fertile, and their systemic inflammatory responses to LPS were strongly attenuated. Adaptive immune responses and protection against infection by Salmonella typhimurium were spared. A single allele encoding the mutant form of TTP was sufficient for enhanced mRNA degradation and underexpression of inflammatory mediators. Therefore, the equilibrium between unphosphorylated and phosphorylated TTP is a critical determinant of the inflammatory response, and manipulation of this equilibrium may be a means of treating inflammatory pathologies.
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Affiliation(s)
- Ewan A Ross
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Tim Smallie
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Qize Ding
- Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - John D O'Neil
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Helen E Cunliffe
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Tina Tang
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Dalya R Rosner
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Iva Klevernic
- Unit of Signal Transduction, Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, University Hospital, 4000 Liege, Belgium
| | - Nicholas A Morrice
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; and
| | - Claudia Monaco
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Adam F Cunningham
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Christopher D Buckley
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jeremy Saklatvala
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Jonathan L Dean
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Andrew R Clark
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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7
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Vlasova-St Louis I, Bohjanen PR. Post-transcriptional regulation of cytokine signaling by AU-rich and GU-rich elements. J Interferon Cytokine Res 2015; 34:233-41. [PMID: 24697201 DOI: 10.1089/jir.2013.0108] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cytokines are necessary for cell communication to enable responses to external stimuli that are imperative for the survival and maintenance of homeostasis. Dysfunction of the cytokine network has detrimental effects on intra- and extracellular environments. Thus, it is critical that the expression of cytokines and the signals transmitted by cytokines to target cells are tightly regulated at numerous levels, including transcriptional and post-transcriptional levels. Here, we briefly summarize the role of AU-rich elements (AREs) in the regulation of cytokine gene expression at the post-transcriptional level and describe a role for GU-rich elements (GREs) in coordinating the regulation of cytokine signaling. GREs function as post-transcriptional regulators of proteins that control cellular activation, growth, and apoptosis. GREs and AREs work in concert to coordinate cytokine signal transduction pathways. The precise regulation of cytokine signaling is particularly important, because its dysregulation can lead to human diseases.
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8
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Beisang D, Reilly C, Bohjanen PR. Alternative polyadenylation regulates CELF1/CUGBP1 target transcripts following T cell activation. Gene 2014; 550:93-100. [PMID: 25123787 PMCID: PMC4162518 DOI: 10.1016/j.gene.2014.08.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/22/2014] [Accepted: 08/10/2014] [Indexed: 01/19/2023]
Abstract
Alternative polyadenylation (APA) is an evolutionarily conserved mechanism for regulating gene expression. Transcript 3' end shortening through changes in polyadenylation site usage occurs following T cell activation, but the consequences of APA on gene expression are poorly understood. We previously showed that GU-rich elements (GREs) found in the 3' untranslated regions of select transcripts mediate rapid mRNA decay by recruiting the protein CELF1/CUGBP1. Using a global RNA sequencing approach, we found that a network of CELF1 target transcripts involved in cell division underwent preferential 3' end shortening via APA following T cell activation, resulting in decreased inclusion of CELF1 binding sites and increased transcript expression. We present a model whereby CELF1 regulates APA site selection following T cell activation through reversible binding to nearby GRE sequences. These findings provide insight into the role of APA in controlling cellular proliferation during biological processes such as development, oncogenesis and T cell activation.
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Affiliation(s)
- Daniel Beisang
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA.
| | - Cavan Reilly
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA.
| | - Paul R Bohjanen
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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9
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Gubin MM, Techasintana P, Magee JD, Dahm GM, Calaluce R, Martindale JL, Whitney MS, Franklin CL, Besch-Williford C, Hollingsworth JW, Abdelmohsen K, Gorospe M, Atasoy U. Conditional knockout of the RNA-binding protein HuR in CD4⁺ T cells reveals a gene dosage effect on cytokine production. Mol Med 2014; 20:93-108. [PMID: 24477678 DOI: 10.2119/molmed.2013.00127] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/23/2014] [Indexed: 12/18/2022] Open
Abstract
The posttranscriptional mechanisms by which RNA binding proteins (RBPs) regulate T-cell differentiation and cytokine production in vivo remain unclear. The RBP HuR binds to labile mRNAs, usually leading to increases in mRNA stability and/or translation. Previous work demonstrated that HuR binds to the mRNAs encoding the Th2 transcription factor trans-acting T-cell-specific transcription factor (GATA-3) and Th2 cytokines interleukin (IL)-4 and IL-13, thereby regulating their expression. By using a novel conditional HuR knockout (KO) mouse in which HuR is deleted in activated T cells, we show that Th2-polarized cells from heterozygous HuR conditional (OX40-Cre HuR(fl/+)) KO mice had decreased steady-state levels of Gata3, Il4 and Il13 mRNAs with little changes at the protein level. Surprisingly, Th2-polarized cells from homozygous HuR conditional (OX40-Cre HuR(fl/fl)) KO mice showed increased Il2, Il4 and Il13 mRNA and protein via different mechanisms. Specifically, Il4 was transcriptionally upregulated in HuR KO T cells, whereas Il2 and Il13 mRNA stabilities increased. Additionally, when using the standard ovalbumin model of allergic airway inflammation, HuR conditional KO mice mounted a robust inflammatory response similar to mice with wild-type HuR levels. These results reveal a complex differential posttranscriptional regulation of cytokines by HuR in which gene dosage plays an important role. These findings may have significant implications in allergies and asthma, as well as autoimmune diseases and infection.
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Affiliation(s)
- Matthew M Gubin
- University of Missouri, Columbia, Missouri, United States of America
| | | | - Joseph D Magee
- University of Missouri, Columbia, Missouri, United States of America
| | - Garrett M Dahm
- University of Missouri, Columbia, Missouri, United States of America
| | - Robert Calaluce
- University of Missouri, Columbia, Missouri, United States of America
| | - Jennifer L Martindale
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Maryln S Whitney
- University of Missouri, Columbia, Missouri, United States of America
| | - Craig L Franklin
- University of Missouri, Columbia, Missouri, United States of America
| | | | - John W Hollingsworth
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Kotb Abdelmohsen
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Myriam Gorospe
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Ulus Atasoy
- University of Missouri, Columbia, Missouri, United States of America
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10
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Yuan J, Muljo SA. Exploring the RNA world in hematopoietic cells through the lens of RNA-binding proteins. Immunol Rev 2013; 253:290-303. [PMID: 23550653 DOI: 10.1111/imr.12048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The discovery of microRNAs has renewed interest in posttranscriptional modes of regulation, fueling an emerging view of a rich RNA world within our cells that deserves further exploration. Much work has gone into elucidating genetic regulatory networks that orchestrate gene expression programs and direct cell fate decisions in the hematopoietic system. However, the focus has been to elucidate signaling pathways and transcriptional programs. To bring us one step closer to reverse engineering the molecular logic of cellular differentiation, it will be necessary to map posttranscriptional circuits as well and integrate them in the context of existing network models. In this regard, RNA-binding proteins (RBPs) may rival transcription factors as important regulators of cell fates and represent a tractable opportunity to connect the RNA world to the proteome. ChIP-seq has greatly facilitated genome-wide localization of DNA-binding proteins, helping us to understand genomic regulation at a systems level. Similarly, technological advances such as CLIP-seq allow transcriptome-wide mapping of RBP binding sites, aiding us to unravel posttranscriptional networks. Here, we review RBP-mediated posttranscriptional regulation, paying special attention to findings relevant to the immune system. As a prime example, we highlight the RBP Lin28B, which acts as a heterochronic switch between fetal and adult lymphopoiesis.
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Affiliation(s)
- Joan Yuan
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
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11
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A stress-activated, p38 mitogen-activated protein kinase-ATF/CREB pathway regulates posttranscriptional, sequence-dependent decay of target RNAs. Mol Cell Biol 2013; 33:3026-35. [PMID: 23732911 DOI: 10.1128/mcb.00349-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Broadly conserved, mitogen-activated/stress-activated protein kinases (MAPK/SAPK) of the p38 family regulate multiple cellular processes. They transduce signals via dimeric, basic leucine zipper (bZIP) transcription factors of the ATF/CREB family (such as Atf2, Fos, and Jun) to regulate the transcription of target genes. We report additional mechanisms for gene regulation by such pathways exerted through RNA stability controls. The Spc1 (Sty1/Phh1) kinase-regulated Atf1-Pcr1 (Mts1-Mts2) heterodimer of the fission yeast Schizosaccharomyces pombe controls the stress-induced, posttranscriptional stability and decay of sets of target RNAs. Whole transcriptome RNA sequencing data revealed that decay is associated nonrandomly with transcripts that contain an M26 sequence motif. Moreover, the ablation of an M26 sequence motif in a target mRNA is sufficient to block its stress-induced loss. Conversely, engineered M26 motifs can render a stable mRNA into one that is targeted for decay. This stress-activated RNA decay (SARD) provides a mechanism for reducing the expression of target genes without shutting off transcription itself. Thus, a single p38-ATF/CREB signal transduction pathway can coordinately induce (promote transcription and RNA stability) and repress (promote RNA decay) transcript levels for distinct sets of genes, as is required for developmental decisions in response to stress and other stimuli.
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12
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Simone LE, Keene JD. Mechanisms coordinating ELAV/Hu mRNA regulons. Curr Opin Genet Dev 2013; 23:35-43. [PMID: 23312841 PMCID: PMC3617084 DOI: 10.1016/j.gde.2012.12.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/05/2012] [Accepted: 12/12/2012] [Indexed: 12/25/2022]
Abstract
The 5' and 3' untranslated regions (UTRs) of messenger RNAs (mRNAs) function as platforms that can determine the fate of each mRNA individually and in aggregate. Multiple mRNAs that encode proteins that are functionally related often interact with RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) that coordinate their expression in time and space as RNA regulons within the ribonucleoprotein (RNP) infrastructure we term the ribonome. Recent ribonomic methods have emerged that can determine which mRNAs are bound and regulated by RBPs and ncRNAs, some of which act in combination to determine global outcomes. ELAV/Hu proteins bind to AU-rich elements (ARE) in mRNAs and regulate their stability from splicing to translation, and the ubiquitous HuR protein has been implicated in cancerous cell growth. Recent work is focused on mechanistic models of how ELAV/Hu proteins increase mRNA stability and translation by repressing microRNAs (miRs) and the RNA induced silencing complex (RISC) via ARE-based ribonucleosomes that may affect global functions of mRNA regulons.
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Affiliation(s)
- Laura E. Simone
- Department of Molecular Genetics & Microbiology Duke University Medical Center Durham, NC 27710
| | - Jack D. Keene
- Department of Molecular Genetics & Microbiology Duke University Medical Center Durham, NC 27710
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Venigalla RKC, Turner M. RNA-binding proteins as a point of convergence of the PI3K and p38 MAPK pathways. Front Immunol 2012; 3:398. [PMID: 23272005 PMCID: PMC3530045 DOI: 10.3389/fimmu.2012.00398] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 12/10/2012] [Indexed: 12/26/2022] Open
Abstract
Understanding the mechanisms by which signal transduction pathways mediate changes in RNA abundance requires the examination of the fate of RNA from its transcription to its degradation. Evidence suggests that RNA abundance is partly regulated by post-transcriptional mechanisms affecting RNA decay and this in turn is modulated by some of the same signaling pathways that control transcription. Furthermore, the translation of mRNA is a key regulatory step that is influenced by signal transduction. These processes are regulated, in part, by RNA-binding proteins (RBPs) which bind to sequence-specific RNA elements. The function of RBPs is controlled and co-ordinated by phosphorylation. Based on the current literature we hypothesize that RBPs may be a point of convergence for the activity of different kinases such as phosphoinositide-3-kinase and mitogen-activated protein kinase which regulate RBP localization and function.
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Affiliation(s)
- Ram K C Venigalla
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute Babraham, UK
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Mou Z, You J, Xiao Q, Wei Y, Yuan J, Liu Y, Brewer G, Ma WJ. HuR posttranscriptionally regulates early growth response-1 (Egr-1) expression at the early stage of T cell activation. FEBS Lett 2012; 586:4319-25. [PMID: 23127556 DOI: 10.1016/j.febslet.2012.10.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 09/26/2012] [Accepted: 10/23/2012] [Indexed: 01/03/2023]
Abstract
T cell activation depends on appropriate and precise regulation of gene expression. Here we find that rapidly translocated RNA-binding protein HuR, forms messenger ribonucleoprotein (mRNP) complexes with transiently expressed mRNAs encoding early-response transcription factors, including c-Fos, c-Jun, and Egr-1. Knockdown and overexpression assays demonstrated that proper posttranscriptional control of Egr-1 expression requires HuR-mediated translation control. Further analysis showed that the Egr-1 3'UTR, which contains AU-rich elements (AREs) and interacts directly with HuR, suppresses reporter gene expression and mediates posttranscriptional regulation of Egr-1 by HuR. These findings underscore an essential role for HuR in regulating early events during T cell activation.
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Affiliation(s)
- Zongchun Mou
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) & Shanghai Jiao Tong University School of Medicine (SJTUSM), 225 South Chongqing Road, Shanghai 200025, China
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15
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Bergen AW, Mallick A, Nishita D, Wei X, Michel M, Wacholder A, David SP, Swan GE, Reid MW, Simons A, Andrews JA. Chronic psychosocial stressors and salivary biomarkers in emerging adults. Psychoneuroendocrinology 2012; 37:1158-70. [PMID: 22172638 PMCID: PMC3774595 DOI: 10.1016/j.psyneuen.2011.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 01/08/2023]
Abstract
We investigated whole saliva as a source of biomarkers to distinguish individuals who have, and who have not, been chronically exposed to severe and threatening life difficulties. We evaluated RNA and DNA metrics, expression of 37 candidate genes, and cortisol release in response to the Trier Social Stress Test, as well as clinical characteristics, from 48 individuals stratified on chronic exposure to psychosocial stressors within the last year as measured by the Life Events and Difficulties Schedule. Candidate genes were selected based on their differential gene expression ratio in circulating monocytes from a published genome-wide analysis of adults experiencing different levels of exposure to a chronic stressor. In univariate analyses, we observed significantly decreased RNA integrity (RIN) score (P = 0.04), and reduced expression of glucocorticoid receptor-regulated genes (Ps < 0.05) in whole saliva RNA from individuals exposed to chronic stressors, as compared to those with no exposure. In those exposed, we observed significantly decreased BMI (P < 0.001), increased ever-smoking and increased lifetime alcohol abuse or dependence (P ≤ 0.03), and a reduction of cortisol release. In post hoc multivariate analyses including clinical and biospecimen-derived variables, we consistently observed significantly decreased expression of IL8 (Ps<0.05) in individuals exposed, with no significant association to RIN score. Alcohol use disorders, tobacco use, a reduced acute stress response and decreased salivary IL8 gene expression characterize emerging adults chronically exposed to severe and threatening psychosocial stressors.
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Affiliation(s)
- Andrew W. Bergen
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States,Corresponding author at: Center for Health Sciences, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, United States. Tel.: +1 650 859 4618; fax: +1 650 859 5099. (A.W. Bergen)
| | - Aditi Mallick
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States,Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Denise Nishita
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States
| | - Xin Wei
- Center for Education and Human Services, SRI International, Menlo Park, CA 94025, United States
| | - Martha Michel
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States
| | - Aaron Wacholder
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States
| | - Sean P. David
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States,Family & Community Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Gary E. Swan
- Center for Health Sciences, SRI International, Menlo Park, CA 94025, United States
| | - Mark W. Reid
- Oregon Research Institute, Eugene, OR 97403, United States,Department of Psychology, University of Oregon, Eugene, OR 97403, United States
| | - Anne Simons
- Department of Psychology, University of Notre Dame, Notre Dame, IN 46556, United States
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Beisang D, Bohjanen PR. Perspectives on the ARE as it turns 25 years old. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:719-31. [PMID: 22733578 DOI: 10.1002/wrna.1125] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The AU-rich element (ARE) was discovered in 1986 as a conserved mRNA sequence found in the 3' untranslated region of the TNF-α transcript and other transcripts encoding cytokines and inflammatory mediators. Shortly thereafter, the ARE was shown to function as a regulator of mRNA degradation, and AREs were later shown to regulate other posttranscriptional mechanisms such as translation and mRNA localization. AREs coordinately regulate networks of chemokine, cytokine, and growth regulatory transcripts involved in cellular activation, proliferation, and inflammation. ARE-mediated regulation is carried out by a host of ARE-binding proteins, whose activity is regulated in a cell type and activation-dependent manner. The last 25 years of ARE research has offered insight into the mechanisms and regulation of ARE-mediated mRNA decay, and has provided a road map for the discovery of additional mRNA regulatory motifs. The future of ARE research will transition from a discovery phase to a phase focused on translating basic biological findings into novel therapeutic targets. Our understanding of ARE-mediated gene regulation and posttranscriptional control has implications for many fields of study including developmental biology, neuroscience, immunobiology, and cancer biology.
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Affiliation(s)
- Daniel Beisang
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA
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Al-Haj L, Khabar KSA. Cloning of cytokine 3' untranslated regions and posttranscriptional assessment using cell-based GFP assay. Methods Mol Biol 2012; 820:91-104. [PMID: 22131027 DOI: 10.1007/978-1-61779-439-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Cytokine biosynthesis is tightly regulated by a number of processes, including gene expression control. Posttranscriptional control of cytokine gene expression offers a fine-tuning mechanism that contributes not only to transient biosynthesis of cytokines, but also helps in rapid and early initiation of the cytokine response. Deregulation of cytokine biosynthesis has been associated with a number of disease conditions, including autoimmune diseases, cancer, and others. Thus, there is a need for accurate measurement of posttranscriptional gene expression events in cytokine research. The method described here is a cell-based GFP assay that quantitatively measures posttranscriptional effects. This method is used for assessing the effects of modulators and conditions that lead to changes in posttranscriptional gene expression during cytokine production or for assessment of cytokine action on posttranscriptional events of gene expression.
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Affiliation(s)
- Latifa Al-Haj
- Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Abstract
Discoveries made over the past 20 years highlight the importance of mRNA decay as a means of modulating gene expression and thereby protein production. Up until recently, studies largely focused on identifying cis-acting sequences that serve as mRNA stability or instability elements, the proteins that bind these elements, how the process of translation influences mRNA decay and the ribonucleases that catalyse decay. Now, current studies have begun to elucidate how the decay process is regulated. This Review examines our current understanding of how mammalian cell mRNA decay is controlled by different signalling pathways and lays out a framework for future research.
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Abstract
A wide variety of cytokines are necessary for cell-cell communication in multicellular organisms, and cytokine dysregulation has detrimental effects, leading to disease states. Thus, it is a necessity that the expression of cytokines is tightly controlled. Regulation of cytokine gene expression takes place at different levels, including transcriptional and posttranscriptional levels. Ultimately, the steady-state levels of cytokine transcripts are determined by the equilibrium of transcription and degradation of this mRNA. Degradation rates of cytokine mRNAs can be measured in cells by blocking transcription with actinomycin D, harvesting RNA after different time points, and evaluating mRNA levels over time by northern blot. Cis-acting elements that mediate the rapid decay of numerous cytokine transcripts, including AU-rich elements (AREs), are found in the 3' untranslated region (UTR) of these transcripts. Putative regulatory cis-elements can be cloned into the 3' UTR of a reporter transcript in order to assess their function in regulating mRNA decay. Cis-elements, such as AREs, regulate cytokine mRNA decay by binding to trans-acting proteins, such as tristetraprolin or HuR. These RNA-binding proteins can be visualized using electromobility shift assays or UV crosslinking assays based on their binding to radioactively labeled RNA sequences. RNA-binding proteins that regulate cytokine mRNA decay can be purified using an RNA affinity method, using their target RNA sequence as the bait. In this chapter, we review the methods for measuring cytokine mRNA decay and methods for characterizing the cis-acting elements and trans-acting factors that regulate cytokine mRNA decay.
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20
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Beisang D, Rattenbacher B, Vlasova-St Louis IA, Bohjanen PR. Regulation of CUG-binding protein 1 (CUGBP1) binding to target transcripts upon T cell activation. J Biol Chem 2011; 287:950-60. [PMID: 22117072 DOI: 10.1074/jbc.m111.291658] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The RNA-binding protein, CUG-binding protein 1 (CUGBP1), regulates gene expression at the levels of alternative splicing, mRNA degradation, and translation. We used RNA immunoprecipitation followed by microarray analysis to identify the cytoplasmic mRNA targets of CUGBP1 in resting and activated primary human T cells and found that CUGBP1 targets were highly enriched for the presence of GU-rich elements (GREs) in their 3'-untranslated regions. The number of CUGBP1 target transcripts decreased dramatically following T cell activation as a result of activation-dependent phosphorylation of CUGBP1 and decreased ability of CUGBP1 to bind to GRE-containing RNA. A large percentage of CUGBP1 target transcripts exhibited rapid and transient up-regulation, and a smaller percentage exhibited transient down-regulation following T cell activation. Many of the transiently up-regulated CUGBP1 target transcripts encode important regulatory proteins necessary for transition from a quiescent state to a state of cellular activation and proliferation. Overall, our results show that CUGBP1 binding to certain GRE-containing target transcripts decreased following T cell activation through activation-dependent phosphorylation of CUGBP1.
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Affiliation(s)
- Daniel Beisang
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
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21
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Stellato C, Gubin MM, Magee JD, Fang X, Fan J, Tartar DM, Chen J, Dahm GM, Calaluce R, Mori F, Jackson GA, Casolaro V, Franklin CL, Atasoy U. Coordinate regulation of GATA-3 and Th2 cytokine gene expression by the RNA-binding protein HuR. THE JOURNAL OF IMMUNOLOGY 2011; 187:441-9. [PMID: 21613615 DOI: 10.4049/jimmunol.1001881] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The posttranscriptional mechanisms whereby RNA-binding proteins (RBPs) regulate T cell differentiation remain unclear. RBPs can coordinately regulate the expression of functionally related genes via binding to shared regulatory sequences, such as the adenylate-uridylate-rich elements (AREs) present in the 3' untranslated region (UTR) of mRNA. The RBP HuR posttranscriptionally regulates IL-4, IL-13, and other Th2 cell-restricted transcripts. We hypothesized that the ARE-bearing GATA-3 gene, a critical regulator of Th2 polarization, is under HuR control as part of its coordinate posttranscriptional regulation of the Th2 program. We report that in parallel with stimulus-induced increase in GATA-3 mRNA and protein levels, GATA-3 mRNA half-life is increased after restimulation in the human T cell line Jurkat, in human memory and Th2 cells, and in murine Th2-skewed cells. We demonstrate by immunoprecipitation of ribonucleoprotein complexes that HuR associates with the GATA-3 endogenous transcript in human T cells and found, using biotin pulldown assay, that HuR specifically interacts with its 3'UTR. Using both loss-of-function and gain-of-function approaches in vitro and in animal models, we show that HuR is a critical mediator of stimulus-induced increase in GATA-3 mRNA and protein expression and that it positively influences GATA-3 mRNA turnover, in parallel with selective promotion of Th2 cytokine overexpression. These results suggest that HuR-driven posttranscriptional control plays a significant role in T cell development and effector function in both murine and human systems. A better understanding of HuR-mediated control of Th2 polarization may have utility in altering allergic airway inflammation in human asthmatic patients.
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Affiliation(s)
- Cristiana Stellato
- Division of Allergy and Clinical Immunology, The Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
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22
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Vlasova-St Louis I, Bohjanen PR. Coordinate regulation of mRNA decay networks by GU-rich elements and CELF1. Curr Opin Genet Dev 2011; 21:444-51. [PMID: 21497082 DOI: 10.1016/j.gde.2011.03.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 03/21/2011] [Indexed: 01/03/2023]
Abstract
The GU-rich element (GRE) was identified as a conserved sequence enriched in the 3' UTR of human transcripts that exhibited rapid mRNA turnover. In mammalian cells, binding to GREs by the protein CELF1 coordinates mRNA decay of networks of transcripts involved in cell growth, migration, and apoptosis. Depending on the context, GREs and CELF1 also regulate pre-mRNA splicing and translation. GREs are highly conserved throughout evolution and play important roles in the development of organisms ranging from worms to man. In humans, abnormal GRE-mediated regulation contributes to disease states and cancer. Thus, GREs and CELF proteins serve critical functions in gene expression regulation and define an important evolutionarily conserved posttranscriptional regulatory network.
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Affiliation(s)
- Irina Vlasova-St Louis
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA
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Antiretroviral therapy down-regulates innate antiviral response genes in patients with AIDS in sub-saharan Africa. J Acquir Immune Defic Syndr 2011; 55:428-38. [PMID: 20838227 DOI: 10.1097/qai.0b013e3181ef4963] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE HIV pathogenesis is characterized by destructive imbalances between virus-mediated immune damage, antiviral immune responses, and immune activation. We characterized the effects of successful antiretroviral therapy (ART) to identify the breadth and patterns of HIV-associated gene expression. METHODS In a prospective observational, longitudinal cohort study of 10 ART-naive Ugandans with AIDS (median 30 CD4/μL), we measured mRNA gene profiles in peripheral blood using Affymetrix U133_Plus2.0 microarrays at 0, 2, 4, 8, and 24 weeks after ART initiation. RESULTS We identified 160 mRNA transcripts that were consistently down-regulated and 48 that were up-regulated after ART at each point over 24 weeks based on linear regression modeling (adjusted P < 0.05), Of these 208 transcripts, approximately half represent heretofore unrecognized ART-responsive genes and one-third have no known function. The down-regulated genes with known function encoded mediators of innate antiviral responses, including antiviral restriction factors, pattern recognition receptors, and interferon response proteins, and mediators of immune activation, cellular proliferation, and apoptosis. CONCLUSIONS By using ART to block the viral stimulus, we identified transcripts involved in innate antiviral immunity, including antiviral restriction factors and pattern recognition receptors, that were not previously known to be induced by HIV infection.
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Khabar KSA. Post-transcriptional control during chronic inflammation and cancer: a focus on AU-rich elements. Cell Mol Life Sci 2010; 67:2937-55. [PMID: 20495997 PMCID: PMC2921490 DOI: 10.1007/s00018-010-0383-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 04/01/2010] [Accepted: 04/21/2010] [Indexed: 12/21/2022]
Abstract
A considerable number of genes that code for AU-rich mRNAs including cytokines, growth factors, transcriptional factors, and certain receptors are involved in both chronic inflammation and cancer. Overexpression of these genes is affected by aberrations or by prolonged activation of several signaling pathways. AU-rich elements (ARE) are important cis-acting short sequences in the 3'UTR that mediate recognition of an array of RNA-binding proteins and affect mRNA stability and translation. This review addresses the cellular and molecular mechanisms that are common between inflammation and cancer and that also govern ARE-mediated post-transcriptional control. The first part examines the role of the ARE-genes in inflammation and cancer and sequence characteristics of AU-rich elements. The second part addresses the common signaling pathways in inflammation and cancer that regulate the ARE-mediated pathways and how their deregulations affect ARE-gene regulation and disease outcome.
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Affiliation(s)
- Khalid S A Khabar
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia.
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25
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Keene JD. Minireview: global regulation and dynamics of ribonucleic Acid. Endocrinology 2010; 151:1391-7. [PMID: 20332203 PMCID: PMC2850242 DOI: 10.1210/en.2009-1250] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 12/29/2009] [Indexed: 01/09/2023]
Abstract
Gene expression starts with transcription and is followed by multiple posttranscriptional processes that carry out the splicing, capping, polyadenylation, and export of each mRNA. Interest in posttranscriptional regulation has increased recently with explosive discoveries of large numbers of noncoding RNAs such as microRNAs, yet posttranscriptional processes depend largely on the functions of RNA-binding proteins as well. Glucocorticoid nuclear receptors are classical examples of environmentally reactive activators and repressors of transcription, but there has also been a significant increase in studies of the role of posttranscriptional regulation in endocrine responses, including insulin and insulin receptors, and parathyroid hormone as well as other hormonal responses, at the levels of RNA stability and translation. On the global level, the transcriptome is defined as the total RNA complement of the genome, and thereby, represents the accumulated levels of all expressed RNAs, because they are each being produced and eventually degraded in either the nucleus or the cytoplasm. In addition to RNA turnover, the many underlying posttranscriptional layers noted above that follow from the transcriptome function within a dynamic ribonucleoprotein (RNP) environment of global RNA-protein and RNA-RNA interactions. With the exception of the spliceosome and the ribosome, thousands of heterodispersed RNP complexes wherein RNAs are dynamically processed, trafficked, and exchanged are heterogeneous in size and composition, thus providing significant challenges to their investigation. Among the diverse RNPs that show dynamic features in the cytoplasm are processing bodies and stress granules as well as a large number of smaller heterogeneous RNPs distributed throughout the cell. Although the localization of functionally related RNAs within these RNPs are responsive to developmental and environmental signals, recent studies have begun to elucidate the global RNA components of RNPs that are dynamically coordinated in response to these signals. Among the factors that have been found to affect coordinated RNA regulation are developmental signals and treatments with small molecule drugs, hormones, and toxins, but this field is just beginning to understand the role of RNA dynamics in these responses.
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Affiliation(s)
- Jack D Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Ernst J, Ghanem L, Bar-Joseph Z, McNamara M, Brown J, Steinman RA. IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. PLoS One 2009; 4:e7469. [PMID: 19829692 PMCID: PMC2758590 DOI: 10.1371/journal.pone.0007469] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2009] [Accepted: 05/07/2009] [Indexed: 01/08/2023] Open
Abstract
The growth factor interleukin-3 (IL-3) promotes the survival and growth of multipotent hematopoietic progenitors and stimulates myelopoiesis. It has also been reported to oppose terminal granulopoiesis and to support leukemic cell growth through autocrine or paracrine mechanisms. The degree to which IL-3 acts at the posttranscriptional level is largely unknown. We have conducted global mRNA decay profiling and bioinformatic analyses in 32Dcl3 myeloblasts indicating that IL-3 caused immediate early stabilization of hundreds of transcripts in pathways relevant to myeloblast function. Stabilized transcripts were enriched for AU-Response elements (AREs), and an ARE-containing domain from the interleukin-6 (IL-6) 3′-UTR rendered a heterologous gene responsive to IL-3-mediated transcript stabilization. Many IL-3-stabilized transcripts had been associated with leukemic transformation. Deregulated Abl kinase shared with IL-3 the ability to delay turnover of transcripts involved in proliferation or differentiation blockade, relying, in part, on signaling through the Mek/Erk pathway. These findings support a model of IL-3 action through mRNA stability control and suggest that aberrant stabilization of an mRNA network linked to IL-3 contributes to leukemic cell growth.
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Affiliation(s)
- Jason Ernst
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
| | - Louis Ghanem
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ziv Bar-Joseph
- Department of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Michael McNamara
- Regional Oncology Department, The Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Jason Brown
- Oncology staff, Meadeville Medical Center, Meadevill, Pennsylvania, United States of America
| | - Richard A. Steinman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Fan D, Bitterman PB, Larsson O. Regulatory element identification in subsets of transcripts: comparison and integration of current computational methods. RNA (NEW YORK, N.Y.) 2009; 15:1469-82. [PMID: 19553345 PMCID: PMC2714745 DOI: 10.1261/rna.1617009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/20/2009] [Indexed: 05/20/2023]
Abstract
Regulatory elements in mRNA play an often pivotal role in post-transcriptional regulation of gene expression. However, a systematic approach to efficiently identify putative regulatory elements from sets of post-transcriptionally coregulated genes is lacking, hampering studies of coregulation mechanisms. Although there are several analytical methods that can be used to detect conserved mRNA regulatory elements in a set of transcripts, there has been no systematic study of how well any of these methods perform individually or as a group. We therefore compared how well three algorithms, each based on a different principle (enumeration, optimization, or structure/sequence profiles), can identify elements in unaligned untranslated sequence regions. Two algorithms were originally designed to detect transcription factor binding sites, Weeder and BioProspector; and one was designed to detect RNA elements conserved in structure, RNAProfile. Three types of elements were examined: (1) elements conserved in both primary sequence and secondary structure; (2) elements conserved only in primary sequence; and (3) microRNA targets. Our results indicate that all methods can uniquely identify certain known RNA elements, and therefore, integrating the output from all algorithms leads to the most complete identification of elements. We therefore developed an approach to integrate results and guide selection of candidate elements from several algorithms presented as a web service (https://dbw.msi.umn.edu:8443/recit). These findings together with the approach for integration can be used to identify candidate elements from genome-wide post-transcriptional profiling data sets.
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Affiliation(s)
- Danhua Fan
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Vavassori S, Covey LR. Post-transcriptional regulation in lymphocytes: the case of CD154. RNA Biol 2009; 6:259-65. [PMID: 19395873 DOI: 10.4161/rna.6.3.8581] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The control of mRNA decay is emerging as an important control point and a major contributor to gene expression in both immune and non-immune cells. The identification of protein factors and cis-acting elements responsible for transcript degradation has illuminated a comprehensive picture of precisely orchestrated events required to both regulate and establish the decay process. One gene that is highly regulated at the post-transcriptional level is CD40 ligand (CD154 or CD40L). CD154 on CD4(+) T cells is tightly controlled by an interacting network of transcriptional and post-transcriptional processes that result in precise surface levels of protein throughout an extended time course of antigen stimulation. The activation-induced stabilization of the CD154 transcript by a polypyrimidine tract-binding protein (PTB)-complex is a key event that corresponds to the temporal expression of CD154. In this review, we discuss known and potential roles of major mRNA decay pathways in lymphocytes and focus on the unique post-transcriptional mechanisms leading to CD154 expression by activated CD4(+) T cells.
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Affiliation(s)
- Stefano Vavassori
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA.
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Abstract
The ribonome is the total cellular complement of RNAs and their regulatory factors functioning dynamically in time and space within ribonucleoprotein complexes. We theorize that the ribonome is an ancient central co-ordinator that has evolved to communicate on multiple levels to the proteome on the one hand (feed-forward), and the transcriptome and RNA processing machinery on the other (feed-back). Furthermore, the ribonome can potentially communicate to other cells horizontally with implications for biological information transfer and for the evolution of both RNA and DNA operating systems. The post-transcriptional RNA operon theory of co-regulated gene expression accounts for the co-ordinated dynamics of RNA-binding proteins within the cellular ribonome, thus allowing for the recombination and remodelling of the RNPs (ribonucleoproteins) to generate new combinations of functionally related proteins. Thus, post-transcriptional RNA operons form the core of the ribonomic operating system in which both their control and co-ordination govern outcomes. Within the ribonome, RNA-binding proteins control one another's mRNAs to keep the global mRNA environment in balance. We argue that these post-transcriptional ribonomic systems provide an information management and distribution centre for evolutionary expansion of multicellularity in tissues, organs, organisms, and their communities.
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Abstract
CD28 is recognized as the primary costimulatory molecule involved in the activation of naïve T cells. However, the biochemical signaling pathways that are activated by CD28 and how these pathways are integrated with TCR signaling are still not understood. We have recently shown that there are at least two independent activation pathways induced by CD28 costimulation. One is integrated with TCR signaling in the context of the immunological synapse and is mediated through transcriptional enhancement and the second is mediated through the induction of mRNA stability. Here, we review the immunological consequences and biochemical mechanisms associated with CD28 costimulation and discuss the major questions that need to be resolved to understand the molecular mechanisms that transduce CD28 costimulation.
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Vlasova IA, Bohjanen PR. Posttranscriptional regulation of gene networks by GU-rich elements and CELF proteins. RNA Biol 2008; 5:201-7. [PMID: 18971639 DOI: 10.4161/rna.7056] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
GU-rich elements found in pre-mRNA and mRNA transcripts play diverse roles in the control of gene expression by regulating mRNA stability, translation and pre-mRNA processing. Regulatory GU-rich elements are highly conserved throughout evolution, and play major roles in development in diverse species from worms to mammals. The conservation of the GU-rich element allowed it to be identified as a sequence that was enriched in the 3' UTR of human transcripts that exhibited rapid mRNA decay. This element functions, at least in part, as a molecular target for members of the CELF family of RNA-binding proteins, which recruit other components of the cellular posttranscriptional gene regulatory machinery to the transcript. Depending on the context, binding to GU-rich sequences by CELF proteins direct a variety of posttranscriptional regulatory events, including deadenylation, mRNA decay, translation or pre-mRNA processing. Thus, GU-rich elements and CELF proteins serve multiple functions in gene expression regulation and define an important evolutionarily conserved posttranscriptional regulatory network.
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Affiliation(s)
- Irina A Vlasova
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, McGuire Translational Research Facility, Minneapolis, Minnesota 55455, USA
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Abstract
Post-transcriptional regulation of gene expression plays important roles in diverse cellular processes such as development, metabolism and cancer progression. Whereas many classical studies explored the mechanistics and physiological impact on specific mRNA substrates, the recent development of genome-wide analysis tools enables the study of post-transcriptional gene regulation on a global scale. Importantly, these studies revealed distinct programs of RNA regulation, suggesting a complex and versatile post-transcriptional regulatory network. This network is controlled by specific RNA-binding proteins and/or non-coding RNAs, which bind to specific sequence or structural elements in the RNAs and thereby regulate subsets of mRNAs that partly encode functionally related proteins. It will be a future challenge to link the spectra of targets for RNA-binding proteins to post-transcriptional regulatory programs and to reveal its physiological implications.
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Abstract
In this issue of Molecular Cell, Vlasova et al. (2008) identify the GU-rich element (GRE) as a novel, widespread, degradation-promoting sequence through which the RNA-binding protein CUGBP1 elicits mRNA decay.
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Affiliation(s)
- Hyeon Ho Kim
- Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Vlasova IA, Tahoe NM, Fan D, Larsson O, Rattenbacher B, Sternjohn JR, Vasdewani J, Karypis G, Reilly CS, Bitterman PB, Bohjanen PR. Conserved GU-rich elements mediate mRNA decay by binding to CUG-binding protein 1. Mol Cell 2008; 29:263-70. [PMID: 18243120 DOI: 10.1016/j.molcel.2007.11.024] [Citation(s) in RCA: 195] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 10/04/2007] [Accepted: 11/16/2007] [Indexed: 11/19/2022]
Abstract
We used computational algorithms to find conserved sequences in the 3' untranslated region (UTR) of transcripts that exhibited rapid decay in primary human T cells and found that the consensus sequence UGUUUGUUUGU, which we have termed a GU-rich element (GRE), was enriched in short-lived transcripts. Using a tet-off reporter system, we showed that insertion of GRE-containing sequences from c-jun, jun B, or TNF receptor 1B, but not mutated GRE sequences, into the 3'UTR of a beta-globin transcript conferred instability on the otherwise stable beta-globin transcript. CUG-binding protein 1 (CUGBP1) was identified as the major GRE-binding activity in cytoplasmic extracts from primary human T cells based on supershift and immunoprecipitation assays. siRNA-mediated knockdown of CUGBP1 in HeLa cells caused stabilization of GRE-containing transcripts, suggesting that CUGBP1 is a mediator of GRE-dependent mRNA decay. Overall, our results suggest that the GRE mediates coordinated mRNA decay by binding to CUGBP1.
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Affiliation(s)
- Irina A Vlasova
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN 55455, USA
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Halees AS, El-Badrawi R, Khabar KSA. ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse. Nucleic Acids Res 2007; 36:D137-40. [PMID: 17984078 PMCID: PMC2238997 DOI: 10.1093/nar/gkm959] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
ARED Organism represents the expansion of the adenylate uridylate (AU)-rich element (ARE)-containing human mRNA database into the transcriptomes of mouse and rat. As a result, we performed quantitative assessment of ARE conservation in human, mouse and rat transcripts. We found that a significant proportion (∼25%) of human genes differ in their ARE patterns from mouse and rat transcripts. ARED-Integrated, another updated and expanded version of ARED, is a compilation of ARED versions 1.0 to 3.0 and updated version 4.0 that is devoted to human mRNAs. Thus, ARED-Integrated and ARED-Organism databases, both publicly available at http://brp.kfshrc.edu.sa/ARED, offer scientists a comprehensive view of AREs in the human transcriptome and the ability to study the comparative genomics of AREs in model organisms. This ultimately will help in inferring the biological consequences of ARE variation in these key animal models as opposed to humans, particularly, in relationships to the role of RNA stability in disease.
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Affiliation(s)
- Anason S Halees
- The Biomolecular Research Program, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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36
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Abstract
Many oncogenes, growth factor, cytokine and cell-cycle genes are regulated post-transcriptionally. The major mechanism is by controlling the rate of mRNA turnover for transcripts bearing destabilizing cis-elements. To date, only a handful of regulatory factors have been identified that appear to control a large pool of target mRNAs, suggesting that a slight perturbation in the control mechanism may generate wide-ranging effects that could contribute to the development of a complex disorder such as cancer. In support of this view, mRNA turnover responds to signalling pathways that are often overactive in cancer, suggesting a post-transcriptional component in addition to the well-recognised transcriptional aspect of oncogenesis. Here the authors review examples of deregulated post-transcriptional control in oncogenesis, discuss post-transcriptionally regulated transcripts of oncologic significance, and consider the key role of signalling pathways in linking both processes and as an enticing therapeutic prospect.
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Affiliation(s)
- Don Benjamin
- Institute for Medical Microbiology, Petersplatz 10, 4001 Basel, Switzerland.
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Hau HH, Walsh RJ, Ogilvie RL, Williams DA, Reilly CS, Bohjanen PR. Tristetraprolin recruits functional mRNA decay complexes to ARE sequences. J Cell Biochem 2007; 100:1477-92. [PMID: 17133347 DOI: 10.1002/jcb.21130] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AU-rich elements (AREs) in the 3' untranslated region (UTR) of numerous mammalian transcripts function as instability elements that promote rapid mRNA degradation. Tristetraprolin (TTP) is an ARE-binding protein that promotes rapid mRNA decay through mechanisms that are poorly understood. A 31 nucleotide ARE sequences from the TNF-alpha 3' UTR promoted TTP-dependent mRNA decay when it was inserted into the 3' UTR of a beta-globin reporter transcript, indicating that this short sequence was sufficient for TTP function. We used a gel shift assay to identify a TTP-containing complex in cytoplasmic extracts from TTP-transfected HeLa cells that bound specifically to short ARE sequences. This TTP-containing complex also contained the 5'-3' exonuclease Xrn1 and the exosome component PM-scl75 because it was super-shifted with anti-Xrn1 or anti-PMscl75 antibodies. RNA affinity purification verified that these proteins associated specifically with ARE sequences in a TTP-dependent manner. Using a competition binding assay, we found that the TTP-containing complex bound with high affinity to short ARE sequences from GM-CSF, IL-3, TNF-alpha, IL-2, and c-fos, but did not bind to a U-rich sequence from c-myc, a 22 nucleotide poly U sequence or a mutated GM-CSF control sequence. High affinity binding by the TTP-containing complex correlated with TTP-dependent deadenylation and decay of capped, polyadenylated transcripts in a cell-free mRNA decay assay, suggesting that the TTP-containing complex was functional. These data support a model whereby TTP functions to enhance mRNA decay by recruiting components of the cellular mRNA decay machinery to the transcript.
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Affiliation(s)
- Heidi H Hau
- Department of Microbiology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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38
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Abstract
Recent findings demonstrate that multiple mRNAs are co-regulated by one or more sequence-specific RNA-binding proteins that orchestrate their splicing, export, stability, localization and translation. These and other observations have given rise to a model in which mRNAs that encode functionally related proteins are coordinately regulated during cell growth and differentiation as post-transcriptional RNA operons or regulons, through a ribonucleoprotein-driven mechanism. Here I describe several recently discovered examples of RNA operons in budding yeast, fruitfly and mammalian cells, and their potential importance in processes such as immune response, oxidative metabolism, stress response, circadian rhythms and disease. I close by considering the evolutionary wiring and rewiring of these combinatorial post-transcriptional gene-expression networks.
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Affiliation(s)
- Jack D Keene
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Box 3020, Durham, North Carolina 27710, USA.
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Identification of a set of KSRP target transcripts upregulated by PI3K-AKT signaling. BMC Mol Biol 2007; 8:28. [PMID: 17437629 PMCID: PMC1858702 DOI: 10.1186/1471-2199-8-28] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 04/16/2007] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND KSRP is a AU-rich element (ARE) binding protein that causes decay of select sets of transcripts in different cell types. We have recently described that phosphatidylinositol 3-kinase/AKT (PI3K-AKT) activation induces stabilization and accumulation of the labile beta-catenin mRNA through an impairment of KSRP function. RESULTS Aim of this study was to identify additional KSRP targets whose stability and steady-state levels are enhanced by PI3K-AKT activation. First, through microarray analyses of the AU-rich transcriptome in pituitary alphaT3-1 cells, we identified 34 ARE-containing transcripts upregulated in cells expressing a constitutively active form of AKT1. In parallel, by an affinity chromatography-based technique followed by microarray analyses, 12 mRNAs target of KSRP, additional to beta-catenin, were identified. Among them, seven mRNAs were upregulated in cells expressing activated AKT1. Both steady-state levels and stability of these new KSRP targets were consistently increased by either KSRP knock-down or PI3K-AKT activation. CONCLUSION Our study identified a set of transcripts that are targets of KSRP and whose expression is increased by PI3K-AKT activation. These mRNAs encode RNA binding proteins, signaling molecules and a replication-independent histone. The increased expression of these gene products upon PI3K-AKT activation could play a role in the cellular events initiated by this signaling pathway.
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Abstract
There have been recent, significant advances about the role of mRNA turnover in controlling gene expression in immune cells. Post‐transcriptional regulation of gene expression contributes to the characteristics of many of the processes underlying the immune response by ensuring early, rapid, and transient action. The emphasis of this review is on current work that deals with the regulation of mRNA decay during innate immunity against microbes and T cell activation as a model of the adaptive response.
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Affiliation(s)
- Khalid S A Khabar
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, P3354, mBC-03, Riyadh 11211, Saudi Arabia.
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Khabar KSA, Young HA. Post-transcriptional control of the interferon system. Biochimie 2007; 89:761-9. [PMID: 17408842 PMCID: PMC1994070 DOI: 10.1016/j.biochi.2007.02.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/16/2007] [Indexed: 01/07/2023]
Abstract
The interferon (IFN) system is a well-controlled network of signaling, transcriptional, and post-transcriptional processes that orchestrate host defense against microbes. The IFN response comprises a multi-array of IFN-stimulated gene products that mediate a variety of biological processes designed to control infection and regulate specific immune responses. In this review, we focus on post-transcriptional mechanisms of gene regulation that occur during the course of IFN induction and during the response of cells to IFN. Post-transcriptional mechanisms involve different levels of regulation such as mRNA stability, alternative splicing, and translation. Such controls offer a fine tuning mechanism for efficient and rapid response and as a negative feedback control in IFN biosynthesis and response.
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Affiliation(s)
- Khalid S A Khabar
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, P3354, MBC-03, Takhasusi Road, Riyadh 11211, Saudi Arabia.
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Moraes KC, Wilusz CJ, Wilusz J. CUG-BP and 3'UTR sequences influence PARN-mediated deadenylation in mammalian cell extracts. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000400024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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43
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Al-Zoghaibi F, Ashour T, Al-Ahmadi W, Abulleef H, Demirkaya O, Khabar KSA. Bioinformatics and experimental derivation of an efficient hybrid 3' untranslated region and use in expression active linear DNA with minimum poly(A) region. Gene 2006; 391:130-9. [PMID: 17258873 DOI: 10.1016/j.gene.2006.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2006] [Revised: 12/11/2006] [Accepted: 12/15/2006] [Indexed: 11/25/2022]
Abstract
Untranslated regions at the 3' end of the messenger RNA (3' UTR) contain regulatory elements that affect mRNA stability and translation and subsequently the protein levels. In this report, we performed bioinformatics analysis on housekeeping genes with putative stable mRNAs in comparison with Class II AU-rich elements (ARE)-containing mRNAs, a group of mRNAs known to represent many labile transcripts. We have found that ARE-mRNAs are less abundant and had longer 3' UTR than stable housekeeping mRNAs. As a result of the analysis, we evaluated the use of a 3' UTR derived from the abundant elongation factor 1 alpha 1 (EEF1A1) mRNA, in expression vectors. Due to the excellent consequence of the modified 3' UTR, we were able to produce expression active linear DNA generated by cloning-free PCR. We have also applied this approach to study the in vivo minimum requirement of poly(A) signal context that allows efficient protein synthesis. The efficient 3' UTR may find use in enhanced recombinant protein production and also provide a simplified tool for generation of expression active linear DNA.
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Affiliation(s)
- Fahad Al-Zoghaibi
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Semplicini A, Lenzini L, Sartori M, Papparella I, Calò LA, Pagnin E, Strapazzon G, Benna C, Costa R, Avogaro A, Ceolotto G, Pessina AC. Reduced expression of regulator of G-protein signaling 2 (RGS2) in hypertensive patients increases calcium mobilization and ERK1/2 phosphorylation induced by angiotensin II. J Hypertens 2006; 24:1115-24. [PMID: 16685212 DOI: 10.1097/01.hjh.0000226202.80689.8f] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
CONTEXT RGS2 (regulators of G-protein signaling) is a negative regulator of Galphaq protein signaling, which mediates the action of several vasoconstrictors. RGS2-deficient mouse line exhibits a hypertensive phenotype and a prolonged response to vasoconstrictors. OBJECTIVE To compare RGS2 expression in peripheral blood mononuclear cells (PBMs) and cultured fibroblasts from normotensive subjects and hypertensive patients. METHODS PBMs were isolated from 100 controls and 150 essential hypertensives. Additionally, fibroblasts were isolated from skin biopsy of 11 normotensives and 12 hypertensives and cultured up to the third passage. Quantitative mRNA and protein RGS2 expression were performed by real-time quantitative reverse transcriptase-polymerase chain reaction and by immunoblotting, respectively. Free Ca measurement was performed in monolayers of 24-h serum-deprived cells, using FURA-2 AM. Phosphorylation of the extracellular signal-regulated kinases ERK1/2 was measured by immunoblotting. Polymorphism (C1114G) in the 3' untranslated region of the RGS2 gene was investigated by direct sequencing and real-time polymerase chain reaction (PCR). RESULTS RGS2 mRNA expression was significantly lower in PBM and in fibroblasts from hypertensives, in comparison to normotensives. C1114G polymorphism was associated with RGS2 expression, with the lowest values in GG hypertensives. The 1114G allele frequency was increased in hypertensives compared with normotensives. Angiotensin II-stimulated intracellular Ca increase and ERK1/2 phosphorylation were higher in fibroblasts from hypertensive patients compared with control subjects, and in those with the G allele, independently of the blood pressure status. The angiotensin II-stimulated Ca mobilization and ERK1/2 phosphorylation were negatively correlated with RGS2 mRNA expression. CONCLUSION Low expression of RGS2 contributes to increased G-protein-coupled signaling in hypertensive patients. The allele G is associated with low RGS2 expression and blood pressure increase in humans.
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Affiliation(s)
- Andrea Semplicini
- Department of Clinical and Experimental Medicine, University of Padova, Italy.
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Sanchez-Lockhart M, Miller J. Engagement of CD28 outside of the immunological synapse results in up-regulation of IL-2 mRNA stability but not IL-2 transcription. THE JOURNAL OF IMMUNOLOGY 2006; 176:4778-84. [PMID: 16585571 DOI: 10.4049/jimmunol.176.8.4778] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During T cell activation by APC, CD28 is colocalized with TCR in the central supramolecular activation cluster (cSMAC) region of the immunological synapse. CD28 signaling through PI3K results in the recruitment of protein kinase C (PKC)theta to the cSMAC, activation of NF-kappaB, and induction of IL-2 transcription. These results suggest that localized engagement of CD28 within the cSMAC may be required for CD28 activation and/or signal integration with TCR signals. To test this model we have examined the mechanism of CD28-mediated induction of IL-2 secretion when CD28 is engaged outside of the immunological synapse. CD4 T cells were stimulated with Ag presented by B7-negative APC and CD28 costimulation was provided in trans by anti-CD28-coated beads or by class II-negative, B7-positive cells. We show that induction of IL-2 secretion under these conditions did not require expression of PKCtheta and did not induce NF-kappaB activation or IL-2 transcription. In contrast, CD28 costimulation in trans did induce IL-2 mRNA stability, accounting for the up-regulation of IL-2 secretion. These data indicate that the ability of CD28 to up-regulate IL-2 transcription requires colocalization of TCR and CD28 at the plasma membrane, possibly within the cSMAC of the immunological synapse. In contrast, the ability of CD28 to promote IL-2 mRNA stability can be transduced from a distal site from the TCR, suggesting that signal integration occurs downstream from the plasma membrane. These data support the potential role of trans costimulation in tumor and allograft rejection, but limit the potential functional impact that trans costimulation may have on T cell activation.
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Affiliation(s)
- Mariano Sanchez-Lockhart
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences and the Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
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Abstract
A comprehensive search that utilized a large set of mRNA data from human genome databases and additionally, expressed sequence tag (EST) database characterized this latest update of AU-rich elements (AREs) containing mRNA database (ARED). A large number of ARE-mRNA, as much as 4000, were recovered and include many of ARE alternative forms. This number represents as much as 5–8% of the human genes depending on the entire number of genes. The new ARED does not contain only larger and diverse number of ARE-mRNAs but additional functionality and enhanced search capabilities are given in the database website . These include class and cluster of AREs, source mRNAs, EST evidence, buildup information, retrieval of lists of genes, and integration with current and new NCBI data, such as Entrez ID and Unigene. Gene Ontology analysis shows there are significant differences in functional diversity of ARED when compared with the overall genome. Many of ARE-genes mediate regulatory processes, reactions to outside stimuli, RNA metabolism, and developmental processes particularly those of early and transient responses. The wide interest in mRNA turnover and importance of AREs in health and disease signify the compilation of ARE-genes.
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Affiliation(s)
| | - Bryan R. G. Williams
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic FoundationCleveland, OH 44195, USA
| | - Khalid S. A. Khabar
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research CenterRiyadh 11211, Saudi Arabia
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic FoundationCleveland, OH 44195, USA
- To whom correspondence should be addressed. Tel: +1 966 1 442 7876, Fax: +1 966 1 442 7858;
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Khabar KSA, Bakheet T, Williams BRG. AU-rich transient response transcripts in the human genome: expressed sequence tag clustering and gene discovery approach. Genomics 2005; 85:165-75. [PMID: 15676275 DOI: 10.1016/j.ygeno.2004.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Accepted: 10/08/2004] [Indexed: 12/13/2022]
Abstract
Transient response genes regulate critical biological responses that include cell proliferation, signal transduction events, and responses to exogenous agents such as inflammatory stimuli, microbes, and radiation. An important feature that ensures a timely response is the short half-life of the messenger RNA (mRNA), which is thought to be predominantly mediated by adenylate uridylate-rich sequence elements (AREs) in the 3' untranslated region (3' UTR). The repertoire and extent of transient response genes in the human genome are not known. We used a computational approach to delineate those genes that code for transient ARE mRNAs. We utilized a 3' UTR-specific ARE motif to retrieve and cluster 3'-end ESTs using a refined extraction protocol. With the availability of the entire human genome, we were able to utilize ARE EST clusters for further mining and computational prediction of ARE genes. The described approaches led to the finding of more than 1500 ARE genes in the human genome. In particular, "hidden" ARE mRNAs and alternative forms due to 3'UTR completeness, variant polyadenylation, and splicing were uncovered.
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Affiliation(s)
- Khalid S A Khabar
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, MBC-03-67, Riyadh 11211, Saudi Arabia.
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