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Wei XF, Fan SY, Wang YW, Li S, Long SY, Gan CY, Li J, Sun YX, Guo L, Wang PY, Yang X, Wang JL, Cui J, Zhang WL, Huang AL, Hu JL. Identification of STAU1 as a regulator of HBV replication by TurboID-based proximity labeling. iScience 2022; 25:104416. [PMID: 35663023 PMCID: PMC9156947 DOI: 10.1016/j.isci.2022.104416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
The core promoter (CP) of hepatitis B virus (HBV) is critical for HBV replication by controlling the transcription of pregenomic RNA (pgRNA). Host factors regulating the activity of the CP can be identified by different methods. Biotin-based proximity labeling, a powerful method with the capability to capture weak or dynamic interactions, has not yet been used to map proteins interacting with the CP. Here, we established a strategy, based on the newly evolved promiscuous enzyme TurboID, for interrogating host factors regulating the activity of HBV CP. Using this strategy, we identified STAU1 as an important factor involved in the regulation of HBV CP. Mechanistically, STAU1 indirectly binds to CP mediated by TARDBP, and recruits the SAGA transcription coactivator complex to the CP to upregulate its activity. Moreover, STAU1 binds to HBx and enhances the level of HBx by stabilizing it in a ubiquitin-independent manner. HBV core promoter binding factors were interrogated by a proximity labeling method STAU1 enhances HBV transcription and replication STAU1 indirectly binds to core promoter via TARDBP and recruits SAGA complex STAU1 binds to HBx and increases its stability
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Affiliation(s)
- Xia-Fei Wei
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China.,Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Shu-Ying Fan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-Wei Wang
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Shan Li
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shao-Yuan Long
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Chun-Yang Gan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jie Li
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-Xue Sun
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Lin Guo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Pei-Yun Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xue Yang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jin-Lan Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jing Cui
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wen-Lu Zhang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jie-Li Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
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Bonnet-Magnaval F, DesGroseillers L. The Staufen1-dependent cell cycle regulon or how a misregulated RNA-binding protein leads to cancer. Biol Rev Camb Philos Soc 2021; 96:2192-2208. [PMID: 34018319 DOI: 10.1111/brv.12749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
In recent years, an increasing number of reports have linked the RNA-binding protein Staufen1 (STAU1) to the control of cell decision making. In non-transformed cells, STAU1 balances the expression of messenger RNA (mRNA) regulons that regulate differentiation and well-ordered cell division. Misregulation of STAU1 expression and/or functions changes the fragile balance in the expression of pro- and anti-proliferative and apoptotic genes and favours a novel equilibrium that supports cell proliferation and cancer development. The misregulation of STAU1 functions causes multiple coordinated modest effects in the post-transcriptional regulation of many RNA targets that code for cell cycle regulators, leading to dramatic consequences at the cellular level. The new tumorigenic equilibrium in STAU1-mediated gene regulation observed in cancer cells can be further altered by a slight increase in STAU1 expression that favours expression of pro-apoptotic genes and cell death. The STAU1-dependent cell cycle regulon is a good model to study how abnormal expression of an RNA-binding protein promotes cell growth and provides an advantageous selection of malignant cells in the first step of cancer development.
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Affiliation(s)
- Florence Bonnet-Magnaval
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Luc DesGroseillers
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC, H3T 1J4, Canada
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3
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Hassine S, Bonnet-Magnaval F, Benoit Bouvrette LP, Doran B, Ghram M, Bouthillette M, Lecuyer E, DesGroseillers L. Staufen1 localizes to the mitotic spindle and controls the localization of RNA populations to the spindle. J Cell Sci 2020; 133:jcs247155. [PMID: 32576666 DOI: 10.1242/jcs.247155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022] Open
Abstract
Staufen1 (STAU1) is an RNA-binding protein involved in the post-transcriptional regulation of mRNAs. We report that a large fraction of STAU1 localizes to the mitotic spindle in colorectal cancer HCT116 cells and in non-transformed hTERT-RPE1 cells. Spindle-associated STAU1 partly co-localizes with ribosomes and active sites of translation. We mapped the molecular determinant required for STAU1-spindle association within the first 88 N-terminal amino acids, a domain that is not required for RNA binding. Interestingly, transcriptomic analysis of purified mitotic spindles revealed that 1054 mRNAs and the precursor ribosomal RNA (pre-rRNA), as well as the long non-coding RNAs and small nucleolar RNAs involved in ribonucleoprotein assembly and processing, are enriched on spindles compared with cell extracts. STAU1 knockout causes displacement of the pre-rRNA and of 154 mRNAs coding for proteins involved in actin cytoskeleton organization and cell growth, highlighting a role for STAU1 in mRNA trafficking to spindle. These data demonstrate that STAU1 controls the localization of subpopulations of RNAs during mitosis and suggests a novel role of STAU1 in pre-rRNA maintenance during mitosis, ribogenesis and/or nucleoli reassembly.
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Affiliation(s)
- Sami Hassine
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Florence Bonnet-Magnaval
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Louis Philip Benoit Bouvrette
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Bellastrid Doran
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Mathieu Bouthillette
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Eric Lecuyer
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Luc DesGroseillers
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
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Visentin S, Cannone G, Doutch J, Harris G, Gleghorn ML, Clifton L, Smith BO, Spagnolo L. A multipronged approach to understanding the form and function of hStaufen protein. RNA (NEW YORK, N.Y.) 2020; 26:265-277. [PMID: 31852734 PMCID: PMC7025507 DOI: 10.1261/rna.072595.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/09/2019] [Indexed: 05/09/2023]
Abstract
Staufen is a dsRNA-binding protein involved in many aspects of RNA regulation, such as mRNA transport, Staufen-mediated mRNA decay and the regulation of mRNA translation. It is a modular protein characterized by the presence of conserved consensus amino acid sequences that fold into double-stranded RNA binding domains (RBDs) as well as degenerated RBDs that are instead involved in protein-protein interactions. The variety of biological processes in which Staufen participates in the cell suggests that this protein associates with many diverse RNA targets, some of which have been identified experimentally. Staufen binding mediates the recruitment of effectors via protein-protein and protein-RNA interactions. The structural determinants of a number of these interactions, as well as the structure of full-length Staufen, remain unknown. Here, we present the first solution structure models for full-length hStaufen155, showing that its domains are arranged as beads-on-a-string connected by flexible linkers. In analogy with other nucleic acid-binding proteins, this could underpin Stau1 functional plasticity.
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Affiliation(s)
- Silvia Visentin
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, United Kingdom
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council (STFC), Rutherford Appleton Laboratory, Didcot OX11 OQX, United Kingdom
| | - Giuseppe Cannone
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - James Doutch
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council (STFC), Rutherford Appleton Laboratory, Didcot OX11 OQX, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Michael L Gleghorn
- School of Chemistry and Materials Science, College of Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Luke Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council (STFC), Rutherford Appleton Laboratory, Didcot OX11 OQX, United Kingdom
| | - Brian O Smith
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Laura Spagnolo
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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5
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Staufen1 inhibits MyoD translation to actively maintain muscle stem cell quiescence. Proc Natl Acad Sci U S A 2017; 114:E8996-E9005. [PMID: 29073096 DOI: 10.1073/pnas.1708725114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Tissue regeneration depends on the timely activation of adult stem cells. In skeletal muscle, the adult stem cells maintain a quiescent state and proliferate upon injury. We show that muscle stem cells (MuSCs) use direct translational repression to maintain the quiescent state. High-resolution single-molecule and single-cell analyses demonstrate that quiescent MuSCs express high levels of Myogenic Differentiation 1 (MyoD) transcript in vivo, whereas MyoD protein is absent. RNA pulldowns and costainings show that MyoD mRNA interacts with Staufen1, a potent regulator of mRNA localization, translation, and stability. Staufen1 prevents MyoD translation through its interaction with the MyoD 3'-UTR. MuSCs from Staufen1 heterozygous (Staufen1+/-) mice have increased MyoD protein expression, exit quiescence, and begin proliferating. Conversely, blocking MyoD translation maintains the quiescent phenotype. Collectively, our data show that MuSCs express MyoD mRNA and actively repress its translation to remain quiescent yet primed for activation.
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Bondy-Chorney E, Crawford Parks TE, Ravel-Chapuis A, Jasmin BJ, Côté J. Staufen1s role as a splicing factor and a disease modifier in Myotonic Dystrophy Type I. Rare Dis 2016; 4:e1225644. [PMID: 27695661 PMCID: PMC5027583 DOI: 10.1080/21675511.2016.1225644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/23/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022] Open
Abstract
In a recent issue of PLOS Genetics, we reported that the double-stranded RNA-binding protein, Staufen1, functions as a disease modifier in the neuromuscular disorder Myotonic Dystrophy Type I (DM1). In this work, we demonstrated that Staufen1 regulates the alternative splicing of exon 11 of the human Insulin Receptor, a highly studied missplicing event in DM1, through Alu elements located in an intronic region. Furthermore, we found that Staufen1 overexpression regulates numerous alternative splicing events, potentially resulting in both positive and negative effects in DM1. Here, we discuss our major findings and speculate on the details of the mechanisms by which Staufen1 could regulate alternative splicing, in both normal and DM1 conditions. Finally, we highlight the importance of disease modifiers, such as Staufen1, in the DM1 pathology in order to understand the complex disease phenotype and for future development of new therapeutic strategies.
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Affiliation(s)
- Emma Bondy-Chorney
- Department of Cellular and Molecular Medicine, University of Ottawa, Center for Neuromuscular Disease , Ottawa, Ontario, Canada
| | - Tara E Crawford Parks
- Department of Cellular and Molecular Medicine, University of Ottawa, Center for Neuromuscular Disease , Ottawa, Ontario, Canada
| | - Aymeric Ravel-Chapuis
- Department of Cellular and Molecular Medicine, University of Ottawa, Center for Neuromuscular Disease , Ottawa, Ontario, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, University of Ottawa, Center for Neuromuscular Disease , Ottawa, Ontario, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, University of Ottawa, Center for Neuromuscular Disease , Ottawa, Ontario, Canada
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Dixit U, Pandey AK, Mishra P, Sengupta A, Pandey VN. Staufen1 promotes HCV replication by inhibiting protein kinase R and transporting viral RNA to the site of translation and replication in the cells. Nucleic Acids Res 2016; 44:5271-87. [PMID: 27106056 PMCID: PMC4914112 DOI: 10.1093/nar/gkw312] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/14/2016] [Indexed: 01/23/2023] Open
Abstract
Persistent hepatitis C virus (HCV) infection leads to chronic hepatitis C (CHC), which often progresses to liver cirrhosis (LC) and hepatocellular carcinoma (HCC). The molecular mechanisms that establish CHC and cause its subsequent development into LC and HCC are poorly understood. We have identified a cytoplasmic double-stranded RNA binding protein, Stau1, which is crucial for HCV replication. In this study, Stau1 specifically interacted with the variable-stem-loop region in the 3′ NTR and domain IIId of the HCV-IRES in the 5′ NTR, and promoted HCV replication and translation. Stau1 coimmunoprecipitates HCV NS5B and a cell factor, protein kinase R (PKR), which is critical for interferon-induced cellular antiviral and antiproliferative responses. Like Stau1, PKR displayed binding specificity to domain IIId of HCV-IRES. Stau1 binds to PKR and strongly inhibits PKR-autophosphorylation. We demonstrated that the transport of HCV RNA on the polysomes is Stau1-dependent, being mainly localized in the monosome fractions when Stau1 is downregulated and exclusively localized in the polysomes when Stau1 is overexpressed. Our findings suggest that HCV may appropriate Stau1 to its advantage to prevent PKR-mediated inhibition of eIF2α, which is required for the synthesis of HCV proteins for translocation of viral RNA genome to the polysomes for efficient translation and replication.
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Affiliation(s)
- Updesh Dixit
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, Rutgers, the State University of New Jersey, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Ashutosh K Pandey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, Rutgers, the State University of New Jersey, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Priya Mishra
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, Rutgers, the State University of New Jersey, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Amitabha Sengupta
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, Rutgers, the State University of New Jersey, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Virendra N Pandey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, Rutgers, the State University of New Jersey, 185 South Orange Avenue, Newark, NJ 07103, USA
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Boulay K, Ghram M, Viranaicken W, Trépanier V, Mollet S, Fréchina C, DesGroseillers L. Cell cycle-dependent regulation of the RNA-binding protein Staufen1. Nucleic Acids Res 2014; 42:7867-83. [PMID: 24906885 PMCID: PMC4081104 DOI: 10.1093/nar/gku506] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Staufen1 (Stau1) is a ribonucleic acid (RNA)-binding protein involved in the post-transcriptional regulation of gene expression. Recent studies indicate that Stau1-bound messenger RNAs (mRNAs) mainly code for proteins involved in transcription and cell cycle control. Consistently, we report here that Stau1 abundance fluctuates through the cell cycle in HCT116 and U2OS cells: it is high from the S phase to the onset of mitosis and rapidly decreases as cells transit through mitosis. Stau1 down-regulation is mediated by the ubiquitin-proteasome system and the E3 ubiquitin ligase anaphase promoting complex/cyclosome (APC/C). Stau1 interacts with the APC/C co-activators Cdh1 and Cdc20 via its first 88 N-terminal amino acids. The importance of controlling Stau155 levels is underscored by the observation that its overexpression affects mitosis entry and impairs proliferation of transformed cells. Microarray analyses identified 275 Stau155-bound mRNAs in prometaphase cells, an early mitotic step that just precedes Stau1 degradation. Interestingly, several of these mRNAs are more abundant in Stau155-containing complexes in cells arrested in prometaphase than in asynchronous cells. Our results point out for the first time to the possibility that Stau1 participates in a mechanism of post-transcriptional regulation of gene expression that is linked to cell cycle progression in cancer cells.
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Affiliation(s)
- Karine Boulay
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Mehdi Ghram
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Wildriss Viranaicken
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Véronique Trépanier
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Stéphanie Mollet
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Céline Fréchina
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Luc DesGroseillers
- Département de Biochimie, Faculté de médecine, Université de Montréal, 2900 Edouard Montpetit, Montréal, QC, H3T 1J4, Canada
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Abstract
The human genome encodes several thousand long non-protein coding transcripts>200 nucleotides in length, a subset of which were shown to play important roles in regulation of gene expression. We recently identified TINCR, a lncRNA required for induction of key differentiation genes in epidermal tissue, including genes mutated in human skin diseases characterized by disrupted epidermal barrier formation. High-throughput analyses of TINCR RNA- and protein-interactomes revealed TINCR interaction with differentiation mRNAs as well as the Staufen1 protein. TINCR, together with Staufen1, seems to stabilize a subset of mRNAs required for epidermal differentiation. Here, we discuss the emerging roles of Staufen1 and TINCR in the regulation of mammalian cell differentiation mediated by interaction with target mRNAs. We consider a role for TINCR as an epithelial-specific guide for targeting the Staufen1 protein to specific mRNAs, reflecting the increasing complexity of gene regulatory processes in mammalian cells and tissue.
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Affiliation(s)
- Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology; University of Regensburg; Regensburg, Germany
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10
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Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay. Nat Struct Mol Biol 2013; 20:515-24. [PMID: 23524536 PMCID: PMC4096160 DOI: 10.1038/nsmb.2528] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/05/2013] [Indexed: 11/23/2022]
Abstract
Staufen (STAU)1-mediated mRNA decay (SMD) degrades mammalian-cell mRNAs that bind the double-stranded (ds)RNA-binding protein STAU1 in their 3′-untranslated region. We report a new motif, which typifies STAU homologs from all vertebrate classes, that is responsible for human (h)STAU1 homodimerization. Our crystal structure and mutagenesis analyses reveal that this motif, now named the Staufen-swapping motif (SSM), and dsRNA-binding domain 5 (‘RBD’5) mediate protein dimerization: the two SSM α-helices of one molecule interact primarily through a hydrophobic patch with the two ‘RBD’5 α-helices of a second molecule. ‘RBD’5 adopts the canonical α-β-β-β-α fold of a functional RBD, but it lacks residues and features needed to bind duplex RNA. In cells, SSM-mediated hSTAU1 dimerization increases the efficiency of SMD by augmenting hSTAU1 binding to the ATP-dependent RNA helicase hUPF1. Dimerization regulates keratinocyte-mediated wound-healing and, undoubtedly, many other cellular processes.
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Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity. Proc Natl Acad Sci U S A 2012; 110:405-12. [PMID: 23263869 DOI: 10.1073/pnas.1213508110] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staufen (STAU)1-mediated mRNA decay (SMD) is a posttranscriptional regulatory mechanism in mammals that degrades mRNAs harboring a STAU1-binding site (SBS) in their 3'-untranslated regions (3' UTRs). We show that SMD involves not only STAU1 but also its paralog STAU2. STAU2, like STAU1, is a double-stranded RNA-binding protein that interacts directly with the ATP-dependent RNA helicase up-frameshift 1 (UPF1) to reduce the half-life of SMD targets that form an SBS by either intramolecular or intermolecular base-pairing. Compared with STAU1, STAU2 binds ~10-fold more UPF1 and ~two- to fivefold more of those SBS-containing mRNAs that were tested, and it comparably promotes UPF1 helicase activity, which is critical for SMD. STAU1- or STAU2-mediated augmentation of UPF1 helicase activity is not accompanied by enhanced ATP hydrolysis but does depend on ATP binding and a basal level of UPF1 ATPase activity. Studies of STAU2 demonstrate it changes the conformation of RNA-bound UPF1. These findings, and evidence for STAU1-STAU1, STAU2-STAU2, and STAU1-STAU2 formation in vitro and in cells, are consistent with results from tethering assays: the decrease in mRNA abundance brought about by tethering siRNA-resistant STAU2 or STAU1 to an mRNA 3' UTR is inhibited by downregulating the abundance of cellular STAU2, STAU1, or UPF1. It follows that the efficiency of SMD in different cell types reflects the cumulative abundance of STAU1 and STAU2. We propose that STAU paralogs contribute to SMD by "greasing the wheels" of RNA-bound UPF1 so as to enhance its unwinding capacity per molecule of ATP hydrolyzed.
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12
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Cassar PA, Stanford WL. Integrating post-transcriptional regulation into the embryonic stem cell gene regulatory network. J Cell Physiol 2012; 227:439-49. [PMID: 21503874 DOI: 10.1002/jcp.22787] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Stem cell behavior is orchestrated as a multilayered, concert of gene regulatory mechanisms collectively referred to as the gene regulatory network (GRN). Via cooperative mechanisms, transcriptional, epigenetic, and post-transcriptional regulators activate and repress gene expression to finely regulate stem cell self-renewal and commitment. Due to their tractability, embryonic stem cells (ESCs) serve as the model stem cell to dissect the complexities of the GRN, and discern its relation to stem cell fate. By way of high-throughput genomic analysis, targets of individual gene regulators have been established in ESCs. The compilation of these discrete networks has revealed convergent, multi-dimensional gene regulatory mechanisms involving transcription factors, epigenetic modifiers, non-coding RNA (ncRNA), and RNA-binding proteins. Here we highlight the seminal genomic studies that have shaped our understanding of the ESC GRN and describe alternate post-transcriptional gene regulatory mechanisms that require in depth analyses to draft networks that fully model ESC behavior.
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Affiliation(s)
- Paul A Cassar
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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Fang X, Yoon JG, Li L, Tsai YS, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B. Landscape of the SOX2 protein-protein interactome. Proteomics 2011; 11:921-34. [PMID: 21280222 DOI: 10.1002/pmic.201000419] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 11/19/2010] [Accepted: 12/05/2010] [Indexed: 01/21/2023]
Abstract
SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells that appears to re-activate in several human cancers including glioblastoma multiforme. Using immunoprecipitation (IP)/MS/MS, we identified 144 proteins that are putative SOX2 interacting proteins. Of note, SOX2 was found to interact with several heterogeneous nuclear ribonucleoprotein family proteins, including HNRNPA2B1, HNRNPA3, HNRNPC, HNRNPK, HNRNPL, HNRNPM, HNRNPR, HNRNPU, as well as other ribonucleoproteins, DNA repair proteins and helicases. Gene ontology (GO) analysis revealed that the SOX2 interactome was enriched for GO terms GO:0030529 ribonucleoprotein complex and GO:0004386 helicase activity. These findings indicate that SOX2 associates with the heterogeneous nuclear ribonucleoprotein complex, suggesting a possible role for SOX2 in post-transcriptional regulation in addition to its function as a transcription factor.
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Affiliation(s)
- Xuefeng Fang
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA, USA
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Hartwig S, Ho J, Pandey P, Macisaac K, Taglienti M, Xiang M, Alterovitz G, Ramoni M, Fraenkel E, Kreidberg JA. Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development. Development 2010; 137:1189-203. [PMID: 20215353 DOI: 10.1242/dev.045732] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Wilms' tumor suppressor 1 (WT1) gene encodes a DNA- and RNA-binding protein that plays an essential role in nephron progenitor differentiation during renal development. To identify WT1 target genes that might regulate nephron progenitor differentiation in vivo, we performed chromatin immunoprecipitation (ChIP) coupled to mouse promoter microarray (ChIP-chip) using chromatin prepared from embryonic mouse kidney tissue. We identified 1663 genes bound by WT1, 86% of which contain a previously identified, conserved, high-affinity WT1 binding site. To investigate functional interactions between WT1 and candidate target genes in nephron progenitors, we used a novel, modified WT1 morpholino loss-of-function model in embryonic mouse kidney explants to knock down WT1 expression in nephron progenitors ex vivo. Low doses of WT1 morpholino resulted in reduced WT1 target gene expression specifically in nephron progenitors, whereas high doses of WT1 morpholino arrested kidney explant development and were associated with increased nephron progenitor cell apoptosis, reminiscent of the phenotype observed in Wt1(-/-) embryos. Collectively, our results provide a comprehensive description of endogenous WT1 target genes in nephron progenitor cells in vivo, as well as insights into the transcriptional signaling networks controlled by WT1 that might direct nephron progenitor fate during renal development.
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Affiliation(s)
- Sunny Hartwig
- Department of Medicine, Children's Hospital Boston; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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Gene expression networks: competing mRNA decay pathways in mammalian cells. Biochem Soc Trans 2010; 37:1287-92. [PMID: 19909264 DOI: 10.1042/bst0371287] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nonsense-mediated mRNA decay and Staufen1-mediated mRNA decay are mechanistically related pathways that serve distinct purposes. In the present article, we give an overview of each pathway. We describe how a factor that is common to both pathways results in their competition. We also explain how competition between the two pathways contributes to the differentiation of C2C12 myoblasts to multinucleated myotubes.
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