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Ferreon JC, Kongchan N, Tsoi PS, Choi KJ, Kenrick S, Neilson J, Ferreon ACM. Multivalent Protein-Nucleic Acid Interactions Probed by Composition-Gradient Multiangle Light Scattering. ACS OMEGA 2024; 9:41003-41010. [PMID: 39371993 PMCID: PMC11447847 DOI: 10.1021/acsomega.4c06358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 10/08/2024]
Abstract
Many RNA-binding proteins, such as TDP-43 or CELF1, interact multivalently with nucleic acid repetitive elements. The molecular stoichiometry of protein to nucleic acid is often difficult to assess, particularly by standard electrophoretic mobility shift assays (EMSAs). Here, we investigate the use of composition-gradient multiangle light scattering (CG-MALS) for quantifying binding affinity and stoichiometry for two RNA-binding proteins with their nucleic acid partners of varied sequence and length: TDP43's N-terminal RNA recognition motifs with both TG/GU-repeat ssDNA and ssRNA, respectively, and CELF1's two N-terminal RNA recognition motifs with (TG/UGUU/GU) repeats and an experimentally defined cognate GU-rich element (GRE). Our CG-MALS data derived from each of these interactions is consistent with expected ranges of binding affinity and stoichiometry for proteins binding to shorter nucleic acid repeats. Furthermore, we conclude that CG-MALS can be an excellent method for obtaining quantitative estimates even for high (>2) protein-nucleic acid stoichiometric ratios.
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Affiliation(s)
- Josephine C. Ferreon
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Natee Kongchan
- Department
of Integrative Physiology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Phoebe S. Tsoi
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kyoung-Jae Choi
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Sophia Kenrick
- Wyatt
Technology, LLC, Santa Barbara, California 93111, United States
| | - Joel Neilson
- Department
of Integrative Physiology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Allan Chris M. Ferreon
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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2
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Qin WJ, Shi JJ, Chen RY, Li CY, Liu YJ, Lu JF, Yang GJ, Cao JF, Chen J. Curriculum vitae of CUG binding protein 1 (CELF1) in homeostasis and diseases: a systematic review. Cell Mol Biol Lett 2024; 29:32. [PMID: 38443798 PMCID: PMC10916161 DOI: 10.1186/s11658-024-00556-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
RNA-binding proteins (RBPs) are kinds of proteins with either singular or multiple RNA-binding domains (RBDs), and they can assembly into ribonucleic acid-protein complexes, which mediate transportation, editing, splicing, stabilization, translational efficiency, or epigenetic modifications of their binding RNA partners, and thereby modulate various physiological and pathological processes. CUG-BP, Elav-like family 1 (CELF1) is a member of the CELF family of RBPs with high affinity to the GU-rich elements in mRNA, and thus exerting control over critical processes including mRNA splicing, translation, and decay. Mounting studies support that CELF1 is correlated with occurrence, genesis and development and represents a potential therapeutical target for these malignant diseases. Herein, we present the structure and function of CELF1, outline its role and regulatory mechanisms in varieties of homeostasis and diseases, summarize the identified CELF1 regulators and their structure-activity relationships, and prospect the current challenges and their solutions during studies on CELF1 functions and corresponding drug discovery, which will facilitate the establishment of a targeted regulatory network for CELF1 in diseases and advance CELF1 as a potential drug target for disease therapy.
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Affiliation(s)
- Wan-Jia Qin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jin-Jin Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Ru-Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jia-Feng Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Soueid DM, Garner AL. Adaptation of RiPCA for the Live-Cell Detection of mRNA-Protein Interactions. Biochemistry 2023; 62:3323-3336. [PMID: 37963240 PMCID: PMC11466511 DOI: 10.1021/acs.biochem.3c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
RNA-binding proteins (RBPs) act as essential regulators of cell fate decisions, through their ability to bind and regulate the activity of cellular RNAs. For protein-coding mRNAs, RBPs control the localization, stability, degradation, and ultimately translation of mRNAs to impact gene expression. Disruption of the vast network of mRNA-protein interactions has been implicated in many human diseases, and accordingly, targeting these interactions has surfaced as a new frontier in RNA-targeted drug discovery. To catalyze this new field, methods are needed to enable the detection and subsequent screening of mRNA-RBP interactions, particularly in live cells. Using our laboratory's RNA-interaction with Protein-mediated Complementation Assay (RiPCA) technology, herein we describe its application to mRNA-protein interactions and present a guide for the development of future RiPCA assays for structurally diverse classes of mRNA-protein interactions.
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Affiliation(s)
- Dalia M. Soueid
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amanda L. Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Tan Y, Sun X, Xu Y, Tang B, Xu S, Lu D, Ye Y, Luo X, Diao X, Li F, Wang T, Chen J, Xu Q, Wu X. Small molecule targeting CELF1 RNA-binding activity to control HSC activation and liver fibrosis. Nucleic Acids Res 2022; 50:2440-2451. [PMID: 35234905 PMCID: PMC8934652 DOI: 10.1093/nar/gkac139] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/21/2022] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
CUGBP Elav-like family member 1 (CELF1), an RNA-binding protein (RBP), plays important roles in the pathogenesis of diseases such as myotonic dystrophy, liver fibrosis and cancers. However, targeting CELF1 is still a challenge, as RBPs are considered largely undruggable. Here, we discovered that compound 27 disrupted CELF1-RNA binding via structure-based virtual screening and biochemical assays. Compound 27 binds directly to CELF1 and competes with RNA for binding to CELF1. Compound 27 promotes IFN-γ secretion and suppresses TGF-β1-induced hepatic stellate cell (HSC) activation by inhibiting CELF1-mediated IFN-γ mRNA decay. In vivo, compound 27 attenuates CCl4-induced murine liver fibrosis. Furthermore, the structure-activity relationship analysis was performed and compound 841, a derivative of compound 27, was identified as a selective CELF1 inhibitor. In conclusion, targeting CELF1 RNA-binding activity with small molecules was achieved, which provides a novel strategy for treating liver fibrosis and other CELF1-mediated diseases.
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Affiliation(s)
- Yang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xueqing Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yizhu Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bingjie Tang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shuaiqi Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Dong Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yan Ye
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xu Diao
- Department of Pharmacology, Jiangsu Simovay Pharmaceutical Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Fulong Li
- Department of Pharmaceutical Chemistry, Jiangsu Simovay Pharmaceutical Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Tianyi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jiayu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing210023, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xingxin Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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5
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The Roles of Insulin-Like Growth Factor 2 mRNA-Binding Protein 2 in Cancer and Cancer Stem Cells. Stem Cells Int 2018; 2018:4217259. [PMID: 29736175 PMCID: PMC5874980 DOI: 10.1155/2018/4217259] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/12/2017] [Accepted: 01/04/2018] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins (RBPs) mediate the localization, stability, and translation of the target transcripts and fine-tune the physiological functions of the proteins encoded. The insulin-like growth factor (IGF) 2 mRNA-binding protein (IGF2BP, IMP) family comprises three RBPs, IGF2BP1, IGF2BP2, and IGF2BP3, capable of associating with IGF2 and other transcripts and mediating their processing. IGF2BP2 represents the least understood member of this family of RBPs; however, it has been reported to participate in a wide range of physiological processes, such as embryonic development, neuronal differentiation, and metabolism. Its dysregulation is associated with insulin resistance, diabetes, and carcinogenesis and may potentially be a powerful biomarker and candidate target for relevant diseases. This review summarizes the structural features, regulation, and functions of IGF2BP2 and their association with cancer and cancer stem cells.
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6
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Nutter CA, Kuyumcu-Martinez MN. Emerging roles of RNA-binding proteins in diabetes and their therapeutic potential in diabetic complications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 29280295 DOI: 10.1002/wrna.1459] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/19/2017] [Accepted: 11/05/2017] [Indexed: 12/11/2022]
Abstract
Diabetes is a debilitating health care problem affecting 422 million people around the world. Diabetic patients suffer from multisystemic complications that can cause mortality and morbidity. Recent advancements in high-throughput next-generation RNA-sequencing and computational algorithms led to the discovery of aberrant posttranscriptional gene regulatory programs in diabetes. However, very little is known about how these regulatory programs are mis-regulated in diabetes. RNA-binding proteins (RBPs) are important regulators of posttranscriptional RNA networks, which are also dysregulated in diabetes. Human genetic studies provide new evidence that polymorphisms and mutations in RBPs are linked to diabetes. Therefore, we will discuss the emerging roles of RBPs in abnormal posttranscriptional gene expression in diabetes. Questions that will be addressed are: Which posttranscriptional mechanisms are disrupted in diabetes? Which RBPs are responsible for such changes under diabetic conditions? How are RBPs altered in diabetes? How does dysregulation of RBPs contribute to diabetes? Can we target RBPs using RNA-based methods to restore gene expression profiles in diabetic patients? Studying the evolving roles of RBPs in diabetes is critical not only for a comprehensive understanding of diabetes pathogenesis but also to design RNA-based therapeutic approaches for diabetic complications. WIREs RNA 2018, 9:e1459. doi: 10.1002/wrna.1459 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing Translation > Translation Regulation.
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Affiliation(s)
- Curtis A Nutter
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas.,Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas
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7
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Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Mol Cell 2017; 66:270-284.e13. [PMID: 28431233 DOI: 10.1016/j.molcel.2017.03.014] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/22/2016] [Accepted: 03/20/2017] [Indexed: 12/19/2022]
Abstract
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.
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Affiliation(s)
- Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Simone Harlander
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Julia-Lisa Daiß
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gerhard Lehmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Schall
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany.
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8
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Xia H, Chen D, Wu Q, Wu G, Zhou Y, Zhang Y, Zhang L. CELF1 preferentially binds to exon-intron boundary and regulates alternative splicing in HeLa cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:911-921. [DOI: 10.1016/j.bbagrm.2017.07.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022]
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9
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Bai Z, Chai XR, Yoon MJ, Kim HJ, LO KA, Zhang ZC, Xu D, Siang DTC, Walet ACE, Xu SH, Chia SY, Chen P, Yang H, Ghosh S, Sun L. Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators. PLoS Biol 2017; 15:e2002176. [PMID: 28763438 PMCID: PMC5538645 DOI: 10.1371/journal.pbio.2002176] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/03/2017] [Indexed: 01/22/2023] Open
Abstract
Enhancing brown fat activity and promoting white fat browning are attractive therapeutic strategies for treating obesity and associated metabolic disorders. To provide a comprehensive picture of the gene regulatory network in these processes, we conducted a series of transcriptome studies by RNA sequencing (RNA-seq) and quantified the mRNA and long noncoding RNA (lncRNA) changes during white fat browning (chronic cold exposure, beta-adrenergic agonist treatment, and intense exercise) and brown fat activation or inactivation (acute cold exposure or thermoneutrality, respectively). mRNA–lncRNA coexpression networks revealed dynamically regulated lncRNAs to be largely embedded in nutrient and energy metabolism pathways. We identified a brown adipose tissue–enriched lncRNA, lncBATE10, that was governed by the cAMP-cAMP response element-binding protein (Creb) axis and required for a full brown fat differentiation and white fat browning program. Mechanistically, lncBATE10 can decoy Celf1 from Pgc1α, thereby protecting Pgc1α mRNA from repression by Celf1. Together, these studies provide a comprehensive data framework to interrogate the transcriptomic changes accompanying energy homeostasis transition in adipose tissue. Fat accumulation is a major health problem in many countries, but unlike white fat—which stores calories—brown fat is packed with mitochondria to burn energy. Therefore, promoting “browning” of white fat and enhancing brown fat activity are seen as promising therapeutic strategies to fight obesity. Long noncoding RNAs (lncRNAs), once largely believed to be functionally irrelevant, are receiving special attention because of the recent realization of their important role in many biological processes. Here, we performed a series of transcriptome analyses, including lncRNAs, during white fat browning and brown fat activation. Based on the mRNA–lncRNA coexpression network, we identified brown adipose tissue–enriched lncRNA 10 (lncBATE10) as a new regulator in brown adipocyte differentiation. Loss of lncBATE10 impaired expression of a brown fat–selective program in brown adipocytes and during browning of white adipocytes. We further showed that lncBATE10 could facilitate browning of white fat and brown fat activation by promoting Pgc1a expression. Taken together, we depicted a comprehensive noncoding transcriptome network during white fat browning and brown fat activation and identified lncBATE10 as a novel regulator in these processes.
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Affiliation(s)
- Zhiqiang Bai
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-ran Chai
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Myeong Jin Yoon
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Hye-Jin Kim
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Kinyui Alice LO
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Zhi-chun Zhang
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Dan Xu
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Diana Teh Chee Siang
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | | | - Shao-hai Xu
- Division of Bioengineering, School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sook-Yoong Chia
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Peng Chen
- Division of Bioengineering, School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Sujoy Ghosh
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- * E-mail: (S.G.); (L.S.)
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
- * E-mail: (S.G.); (L.S.)
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10
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Berhani O, Nachmani D, Yamin R, Schmiedel D, Bar-On Y, Mandelboim O. Vigilin Regulates the Expression of the Stress-Induced Ligand MICB by Interacting with Its 5' Untranslated Region. THE JOURNAL OF IMMUNOLOGY 2017; 198:3662-3670. [PMID: 28356383 DOI: 10.4049/jimmunol.1601589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/28/2017] [Indexed: 01/20/2023]
Abstract
NK cells are part of the innate immune system, and are able to identify and kill hazardous cells. The discrimination between normal and hazardous cells is possible due to an array of inhibitory and activating receptors. NKG2D is one of the prominent activating receptors expressed by all human NK cells. This receptor binds stress-induced ligands, including human MICA, MICB, and UL16-binding proteins 1-6. The interaction between NKG2D and its ligands facilitates the elimination of cells under cellular stress, such as tumor transformation. However, the mechanisms regulating the expression of these ligands are still not well understood. Under normal conditions, the NKG2D ligands were shown to be posttranscriptionally regulated by cellular microRNAs and RNA-binding proteins (RBPs). Thus far, only the 3' untranslated regions (UTRs) of MICA, MICB, and UL16-binding protein 2 were shown to be regulated by RBPs and microRNAs, usually resulting in their downregulation. In this study we investigated whether MICB expression is controlled by RBPs through its 5'UTR. We used an RNA pull-down assay followed by mass spectrometry and identified vigilin, a ubiquitously expressed multifunctional RNA-binding protein. We demonstrated that vigilin binds and negatively regulates MICB expression through its 5'UTR. Additionally, vigilin downregulation in target cells led to a significant increase in NK cell activation against said target cells. Taken together, we have discovered a novel mode of MICB regulation.
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Affiliation(s)
- Orit Berhani
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Daphna Nachmani
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Rachel Yamin
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Dominik Schmiedel
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Yotam Bar-On
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
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11
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Bohjanen PR, Moua ML, Guo L, Taye A, Vlasova-St Louis IA. Altered CELF1 binding to target transcripts in malignant T cells. RNA (NEW YORK, N.Y.) 2015; 21:1757-1769. [PMID: 26249002 PMCID: PMC4574752 DOI: 10.1261/rna.049940.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
The RNA-binding protein, CELF1, binds to a regulatory sequence known as the GU-rich element (GRE) and controls a network of mRNA transcripts that regulate cellular activation, proliferation, and apoptosis. We performed immunoprecipitation using an anti-CELF1 antibody, followed by identification of copurified transcripts using microarrays. We found that CELF1 is bound to a distinct set of target transcripts in the H9 and Jurkat malignant T-cell lines, compared with primary human T cells. CELF1 was not phosphorylated in resting normal T cells, but in malignant T cells, phosphorylation of CELF1 correlated with its inability to bind to GRE-containing mRNAs that served as CELF1 targets in normal T cells. Lack of binding by CELF1 to these mRNAs in malignant T cells correlated with stabilization and increased expression of these transcripts. Several of these GRE-containing transcripts that encode regulators of cell growth were also stabilized and up-regulated in primary tumor cells from patients with T-cell acute lymphoblastic leukemia. Interestingly, transcripts encoding numerous suppressors of cell proliferation that served as targets of CELF1 in malignant T cells, but not normal T cells, exhibited accelerated degradation and reduced expression in malignant compared with normal T cells, consistent with the known function of CELF1 to mediate degradation of bound transcripts. Overall, CELF1 dysfunction in malignant T cells led to the up-regulation of a subset of GRE-containing transcripts that promote cell growth and down-regulation of another subset that suppress cell growth, producing a net effect that would drive a malignant phenotype.
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Affiliation(s)
- Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Department of Microbiology, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mai Lee Moua
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Liang Guo
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ammanuel Taye
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Irina A Vlasova-St Louis
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
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12
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Bauermeister D, Claußen M, Pieler T. A novel role for Celf1 in vegetal RNA localization during Xenopus oogenesis. Dev Biol 2015; 405:214-24. [PMID: 26164657 DOI: 10.1016/j.ydbio.2015.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 06/22/2015] [Accepted: 07/07/2015] [Indexed: 12/23/2022]
Abstract
The localization of certain mRNAs to the vegetal cortex of Xenopus oocytes is of crucial importance for germ cell development and early embryonic patterning. Vegetal RNA localization is mediated by cis-acting RNA localization elements (LE). Several proteins assemble on the RNA LE and direct transport to the vegetal cortex. Although a number of localization RNP components have been identified, their full composition is unknown. In an RNA affinity purification approach, using the dead end 1 (dnd1) RNA LE, we identified Xenopus Celf1 as a novel component of vegetal localization RNP complexes. Celf1 is part of an RNP complex together with known vegetal localization factors and shows specific interactions with LEs from several but not all vegetally localizing RNAs. Immunostaining experiments reveal co-localization of Celf1 with vegetally localizing RNA and with known localization factors. Inhibition of Celf1 protein binding by localization element mutagenesis as well as Celf1 overexpression interfere with vegetal RNA localization. These results argue for a role of Celf1 in vegetal RNA localization during Xenopus oogenesis.
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Affiliation(s)
- Diana Bauermeister
- Department of Developmental Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany.
| | - Maike Claußen
- Department of Developmental Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany.
| | - Tomas Pieler
- Department of Developmental Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany.
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13
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Nachmani D, Gutschner T, Reches A, Diederichs S, Mandelboim O. RNA-binding proteins regulate the expression of the immune activating ligand MICB. Nat Commun 2014; 5:4186. [PMID: 24924487 DOI: 10.1038/ncomms5186] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/22/2014] [Indexed: 12/28/2022] Open
Abstract
The recognition of stress-induced ligands by the activating receptor NKG2D expressed on cytotoxic lymphocytes is crucial for the prevention and containment of various diseases and is also one of the best-studied examples of how danger is sensed by the immune system. Still, however, the mechanisms leading to the expression of the NKG2D ligands are far from being completely understood. Here, we use an unbiased and systematic RNA pull-down approach combined with mass spectrometry to identify six RNA-binding proteins (RBPs) that bind and regulate the expression of MICB, one of the major stress-induced ligands of NKG2D. We further demonstrate that at least two of the identified RBPs function during genotoxic stress. Our data provide insights into stress recognition and hopefully open new therapeutic venues.
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Affiliation(s)
- Daphna Nachmani
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, 91120 Jerusalem, Israel
| | - Tony Gutschner
- Helmholtz-University-Group "Molecular RNA Biology & Cancer", German Cancer Research Center DKFZ and Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Adi Reches
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, 91120 Jerusalem, Israel
| | - Sven Diederichs
- Helmholtz-University-Group "Molecular RNA Biology & Cancer", German Cancer Research Center DKFZ and Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, 91120 Jerusalem, Israel
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14
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Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
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Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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15
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Edwards JM, Long J, de Moor CH, Emsley J, Searle MS. Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1. Nucleic Acids Res 2013; 41:7153-66. [PMID: 23748565 PMCID: PMC3737555 DOI: 10.1093/nar/gkt470] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The CUG-BP, Elav-like family (CELF) of RNA-binding proteins control gene expression at a number of different levels by regulating pre-mRNA splicing, deadenylation and mRNA stability. We present structural insights into the binding selectivity of CELF member 1 (CELF1) for GU-rich mRNA target sequences of the general form 5'-UGUNxUGUNyUGU and identify a high affinity interaction (Kd ∼ 100 nM for x = 2 and y = 4) with simultaneous binding of all three RNA recognition motifs within a single 15-nt binding element. RNA substrates spin-labelled at either the 3' or 5' terminus result in differential nuclear magnetic resonance paramagnetic relaxation enhancement effects, which are consistent with a non-sequential 2-1-3 arrangement of the three RNA recognition motifs on UGU sites in a 5' to 3' orientation along the RNA target. We further demonstrate that CELF1 binds to dispersed single-stranded UGU sites at the base of an RNA hairpin providing a structural rationale for recognition of CUG expansion repeats and splice site junctions in the regulation of alternative splicing.
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Affiliation(s)
- John M Edwards
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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16
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Vlasova-St Louis I, Dickson AM, Bohjanen PR, Wilusz CJ. CELFish ways to modulate mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:695-707. [PMID: 23328451 DOI: 10.1016/j.bbagrm.2013.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/03/2013] [Accepted: 01/05/2013] [Indexed: 12/14/2022]
Abstract
The CELF family of RNA-binding proteins regulates many steps of mRNA metabolism. Although their best characterized function is in pre-mRNA splice site choice, CELF family members are also powerful modulators of mRNA decay. In this review we focus on the different modes of regulation that CELF proteins employ to mediate mRNA decay by binding to GU-rich elements. After starting with an overview of the importance of CELF proteins during development and disease pathogenesis, we then review the mRNA networks and cellular pathways these proteins regulate and the mechanisms by which they influence mRNA decay. Finally, we discuss how CELF protein activity is modulated during development and in response to cellular signals. We conclude by highlighting the priorities for new experiments in this field. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Jones K, Timchenko L, Timchenko NA. The role of CUGBP1 in age-dependent changes of liver functions. Ageing Res Rev 2012; 11:442-9. [PMID: 22446383 DOI: 10.1016/j.arr.2012.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 12/14/2022]
Abstract
Aging liver is characterized by alterations of liver biology and by a reduction of many functions which are important for the maintenance of body homeostasis. The main dysfunctions include appearance of enlarged hepatocytes, impaired liver regeneration after partial hepatectomy (PH), development of hepatic steatosis, reduction of secretion of proteins and alterations in the hepatic sinusoid. RNA binding proteins are involved in the regulation of gene expression in all tissues including regulation of biological processes in the liver. This review is focused on the role of a conserved, multi-functional RNA-binding protein, CUGBP1, in the development of aging phenotype in the liver. CUGBP1 has been identified as a protein which binds to RNA CUG repeats expanded in Myotonic Dystrophy type 1 (DM1). CUGBP1 is highly expressed in the liver and regulates translation of proteins which are critical for maintenance of liver functions. In livers of young mice, CUGBP1 forms complexes with eukaryotic translation initiation factor eIF2 and supports translation of C/EBPβ and HDAC1 proteins, which are involved in liver growth, differentiation and liver cancer. Aging changes several signaling pathways which lead to the elevation of the CUGBP1-eIF2α complex and to an increase of translation of C/EBPβ and HDAC1. These proteins form multi-protein complexes with additional transcription factors and with chromatin remodeling proteins causing epigenetic alterations of gene expression in livers of old mice. It appears that CUGBP1-mediated translational elevation of HDAC1 is one of the key events in the epigenetic changes in livers of old mice, leading to the development of age-associated dysfunctions of the liver. This review will also discuss a possible role of CUGBP1 in liver dysfunction in patients affected with DM1.
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Mackereth CD, Sattler M. Dynamics in multi-domain protein recognition of RNA. Curr Opin Struct Biol 2012; 22:287-96. [DOI: 10.1016/j.sbi.2012.03.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/25/2012] [Indexed: 12/28/2022]
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