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Gleghorn ML, Maquat LE. 'Black sheep' that don't leave the double-stranded RNA-binding domain fold. Trends Biochem Sci 2014; 39:328-40. [PMID: 24954387 DOI: 10.1016/j.tibs.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/19/2014] [Accepted: 05/19/2014] [Indexed: 12/28/2022]
Abstract
The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.
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Affiliation(s)
- Michael L Gleghorn
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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52
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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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Flury V, Restuccia U, Bachi A, Mühlemann O. Characterization of phosphorylation- and RNA-dependent UPF1 interactors by quantitative proteomics. J Proteome Res 2014; 13:3038-53. [PMID: 24762188 DOI: 10.1021/pr5002143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human up-frameshift 1 (UPF1) is an ATP-dependent RNA helicase and phosphoprotein implicated in several biological processes but is best known for its key function in nonsense-mediated mRNA decay (NMD). Here we employed a combination of stable isotope labeling of amino acids in cell culture experiments to determine by quantitative proteomics UPF1 interactors. We used this approach to distinguish between RNA-mediated and protein-mediated UPF1 interactors and to determine proteins that preferentially bind the hypo- or the hyper-phosphorylated form of UPF1. Confirming and expanding previous studies, we identified the eukaryotic initiation factor 3 (eIF3) as a prominent protein-mediated interactor of UPF1. However, unlike previously reported, eIF3 binds to UPF1 independently of UPF1's phosphorylation state. Furthermore, our data revealed many nucleus-associated RNA-binding proteins that preferentially associate with hyper-phosphorylated UPF1 in an RNase-sensitive manner, suggesting that UPF1 gets recruited to mRNA and becomes phosphorylated before being exported to the cytoplasm as part of the mRNP.
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Affiliation(s)
- Valentin Flury
- Department of Chemistry and Biochemistry, University of Bern , Freiestr. 3, Bern 3012, Switzerland
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54
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Kim MY, Park J, Lee JJ, Ha DH, Kim J, Kim CG, Hwang J, Kim CG. Staufen1-mediated mRNA decay induces Requiem mRNA decay through binding of Staufen1 to the Requiem 3'UTR. Nucleic Acids Res 2014; 42:6999-7011. [PMID: 24799437 PMCID: PMC4066795 DOI: 10.1093/nar/gku388] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Requiem (REQ/DPF2) was originally identified as an apoptosis-inducing protein in mouse myeloid cells and belongs to the novel Krüppel-type zinc finger d4-protein family of proteins, which includes neuro-d4 (DPF1) and cer-d4 (DPF3). Interestingly, when a portion of the REQ messenger ribonucleic acid (mRNA) 3′ untranslated region (3′UTR), referred to as G8, was overexpressed in K562 cells, β-globin expression was induced, suggesting that the 3′UTR of REQ mRNA plays a physiological role. Here, we present evidence that the REQ mRNA 3′UTR, along with its trans-acting factor, Staufen1 (STAU1), is able to reduce the level of REQ mRNA via STAU1-mediated mRNA decay (SMD). By screening a complementary deoxyribonucleic acid (cDNA) expression library with an RNA–ligand binding assay, we identified STAU1 as an interactor of the REQ mRNA 3′UTR. Specifically, we provide evidence that STAU1 binds to putative 30-nucleotide stem–loop-structured RNA sequences within the G8 region, which we term the protein binding site core; this binding triggers the degradation of REQ mRNA and thus regulates translation. Furthermore, we demonstrate that siRNA-mediated silencing of either STAU1 or UPF1 increases the abundance of cellular REQ mRNA and, consequently, the REQ protein, indicating that REQ mRNA is a target of SMD.
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Affiliation(s)
- Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences
| | - Jungyun Park
- Graduate School for Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Korea
| | - Jong Joo Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences
| | - Dae Hyun Ha
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences
| | - Jonghwan Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences
| | - Chan Gil Kim
- Department of Biotechnology, Konkuk University, Chungju 380-701, Korea
| | - Jungwook Hwang
- Graduate School for Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Korea
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences
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55
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Heraud-Farlow JE, Sharangdhar T, Li X, Pfeifer P, Tauber S, Orozco D, Hörmann A, Thomas S, Bakosova A, Farlow AR, Edbauer D, Lipshitz HD, Morris QD, Bilban M, Doyle M, Kiebler MA. Staufen2 regulates neuronal target RNAs. Cell Rep 2013; 5:1511-8. [PMID: 24360961 DOI: 10.1016/j.celrep.2013.11.039] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 11/04/2013] [Accepted: 11/21/2013] [Indexed: 11/30/2022] Open
Abstract
RNA-binding proteins play crucial roles in directing RNA translation to neuronal synapses. Staufen2 (Stau2) has been implicated in both dendritic RNA localization and synaptic plasticity in mammalian neurons. Here, we report the identification of functionally relevant Stau2 target mRNAs in neurons. The majority of Stau2-copurifying mRNAs expressed in the hippocampus are present in neuronal processes, further implicating Stau2 in dendritic mRNA regulation. Stau2 targets are enriched for secondary structures similar to those identified in the 3' UTRs of Drosophila Staufen targets. Next, we show that Stau2 regulates steady-state levels of many neuronal RNAs and that its targets are predominantly downregulated in Stau2-deficient neurons. Detailed analysis confirms that Stau2 stabilizes the expression of one synaptic signaling component, the regulator of G protein signaling 4 (Rgs4) mRNA, via its 3' UTR. This study defines the global impact of Stau2 on mRNAs in neurons, revealing a role in stabilization of the levels of synaptic targets.
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Affiliation(s)
- Jacki E Heraud-Farlow
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria; Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Tejaswini Sharangdhar
- Department of Anatomy and Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Xiao Li
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 1E3, Canada
| | - Philipp Pfeifer
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria
| | - Stefanie Tauber
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Denise Orozco
- Adolf Butenandt Institute, Ludwig-Maximilians-University, 80336 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 80336 Munich, Germany
| | - Alexandra Hörmann
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria
| | - Sabine Thomas
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria; Department of Anatomy and Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Anetta Bakosova
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria
| | - Ashley R Farlow
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Dieter Edbauer
- Adolf Butenandt Institute, Ludwig-Maximilians-University, 80336 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 80336 Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 1E3, Canada
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael Doyle
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria.
| | - Michael A Kiebler
- Department of Neuronal Cell Biology, Center for Brain Research, 1090 Vienna, Austria; Department of Anatomy and Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany.
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56
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Staufen1 senses overall transcript secondary structure to regulate translation. Nat Struct Mol Biol 2013; 21:26-35. [PMID: 24336223 PMCID: PMC4605437 DOI: 10.1038/nsmb.2739] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/19/2013] [Indexed: 12/31/2022]
Abstract
Human Staufen1 (Stau1) is a double-stranded RNA (dsRNA)-binding protein implicated in multiple post-transcriptional gene-regulatory processes. Here we combined RNA immunoprecipitation in tandem (RIPiT) with RNase footprinting, formaldehyde cross-linking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1-binding sites transcriptome wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3' untranslated regions (UTRs) or in 'strongly distal' 3' UTRs. Stau1 also interacts with actively translating ribosomes and with mRNA coding sequences (CDSs) and 3' UTRs in proportion to their GC content and propensity to form internal secondary structure. On mRNAs with high CDS GC content, higher Stau1 levels lead to greater ribosome densities, thus suggesting a general role for Stau1 in modulating translation elongation through structured CDS regions. Our results also indicate that Stau1 regulates translation of transcription-regulatory proteins.
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57
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Cho H, Han S, Park OH, Kim YK. SMG1 regulates adipogenesis via targeting of staufen1-mediated mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1276-87. [DOI: 10.1016/j.bbagrm.2013.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 12/21/2022]
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58
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Nonsense-mediated mRNA decay: inter-individual variability and human disease. Neurosci Biobehav Rev 2013; 46 Pt 2:175-86. [PMID: 24239855 DOI: 10.1016/j.neubiorev.2013.10.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 01/09/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a regulatory pathway that functions to degrade transcripts containing premature termination codons (PTCs) and to maintain normal transcriptome homeostasis. Nonsense and frameshift mutations that generate PTCs cause approximately one-third of all known human genetic diseases and thus NMD has a potentially important role in human disease. In genetic disorders in which the affected genes carry PTC-generating mutations, NMD acts as a double-edge sword. While it can benefit the patient by degrading PTC-containing mRNAs that encode detrimental, dominant-negative truncated proteins, it can also make the disease worse when a PTC-containing mRNA is degraded that encodes a mutant but still functional protein. There is evidence that the magnitude of NMD varies between individuals, which, in turn, has been shown to correlate with both clinical presentations and the patients' responses to drugs that promote read-through of PTCs. In this review, we examine the evidence supporting the existence of inter-individual variability in NMD efficiency and discuss the genetic factors that underlie this variability. We propose that inter-individual variability in NMD efficiency is a common phenomenon in human populations and that an individual's NMD efficiency should be taken into consideration when testing, developing, and making therapeutic decisions for diseases caused by genes harboring PTCs.
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59
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CK2-mediated TEL2 phosphorylation augments nonsense-mediated mRNA decay (NMD) by increase of SMG1 stability. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1047-55. [DOI: 10.1016/j.bbagrm.2013.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/13/2013] [Accepted: 06/21/2013] [Indexed: 11/23/2022]
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60
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mRNA-mRNA duplexes that autoelicit Staufen1-mediated mRNA decay. Nat Struct Mol Biol 2013; 20:1214-20. [PMID: 24056942 PMCID: PMC3947523 DOI: 10.1038/nsmb.2664] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/08/2013] [Indexed: 12/28/2022]
Abstract
We report a new mechanism by which human mRNAs crosstalk: an Alu element in the 3'-untranslated region (3' UTR) of one mRNA can base-pair with a partially complementary Alu element in the 3' UTR of a different mRNA thereby creating a Staufen1 (STAU1)-binding site (SBS). STAU1 binding to a 3' UTR SBS was previously shown to trigger STAU1-mediated mRNA decay (SMD) by directly recruiting the ATP-dependent RNA helicase UPF1, which is also a key factor in the mechanistically related nonsense-mediated mRNA decay (NMD) pathway. In the case of a 3' UTR SBS created via mRNA–mRNA base-pairing, we show that SMD targets both mRNAs in the duplex provided that both mRNAs are translated. If only one mRNA is translated, then it alone is targeted for SMD. We demonstrate the importance of mRNA–mRNA-triggered SMD to the processes of cell migration and invasion.
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61
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Raman AV, Pitts MW, Seyedali A, Hashimoto AC, Bellinger FP, Berry MJ. Selenoprotein W expression and regulation in mouse brain and neurons. Brain Behav 2013; 3:562-74. [PMID: 24392277 PMCID: PMC3869984 DOI: 10.1002/brb3.159] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/24/2013] [Accepted: 06/26/2013] [Indexed: 12/03/2022] Open
Abstract
Background Selenoprotein W (Sepw1) is a selenium-containing protein that is abundant in brain and muscle of vertebrate animals. Muscular expression of Sepw1 is reduced by dietary selenium (Se) deficiency in mammals, whereas brain expression is maintained. However, expression of Sepw1 depends on the Se transporter selenoprotein P (Sepp1). Methods We assessed the regional and cellular expression of Sepw1 in the mouse brain and neuronal cultures. Results We found that Sepw1 is widespread in neurons and neuropil of mouse brain and appears in both the soma and processes of neurons in culture. Pyramidal neurons of cortex and hippocampus express high levels of Sepw1. It is also abundant in Purkinje neurons and their dendritic arbors in the cerebellum. Analysis of synaptosome fractions prepared from mice brains indicated that Sepw1 is present at synapses, as were several proteins involved in selenoprotein synthesis. Synaptic expression of Sepw1 expression is reduced in mice lacking Sepp1 compared with control mice, although selenoprotein synthesis factors were similarly expressed in both genotypes. Lastly, Sepw1 mRNA coimmunoprecipitates with Staufen 2 protein in a human neuronal cell line. Conclusions Our results suggest that Sepw1 may be locally synthesized in distal compartments of neurons including synapses.
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Affiliation(s)
- Arjun V Raman
- Cell and Molecular Biology Department John A. Burns School of Medicine, University of Hawai'i at Manoa Honolulu, Hawaii
| | - Matthew W Pitts
- Cell and Molecular Biology Department John A. Burns School of Medicine, University of Hawai'i at Manoa Honolulu, Hawaii
| | - Ali Seyedali
- Cell and Molecular Biology Department John A. Burns School of Medicine, University of Hawai'i at Manoa Honolulu, Hawaii
| | - Ann C Hashimoto
- Cell and Molecular Biology Department John A. Burns School of Medicine, University of Hawai'i at Manoa Honolulu, Hawaii
| | - Frederick P Bellinger
- Cell and Molecular Biology Department John A. Burns School of Medicine, University of Hawai'i at Manoa Honolulu, Hawaii
| | - Marla J Berry
- Cell and Molecular Biology Department John A. Burns School of Medicine, University of Hawai'i at Manoa Honolulu, Hawaii
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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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63
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Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD. Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. Nucleic Acids Res 2013; 41:9438-60. [PMID: 23945942 PMCID: PMC3814352 DOI: 10.1093/nar/gkt702] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite studies that have investigated the interactions of double-stranded RNA-binding proteins like Staufen with RNA in vitro, how they achieve target specificity in vivo remains uncertain. We performed RNA co-immunoprecipitations followed by microarray analysis to identify Staufen-associated mRNAs in early Drosophila embryos. Analysis of the localization and functions of these transcripts revealed a number of potentially novel roles for Staufen. Using computational methods, we identified two sequence features that distinguish Staufen’s target transcripts from non-targets. First, these Drosophila transcripts, as well as those human transcripts bound by human Staufen1 and 2, have 3′ untranslated regions (UTRs) that are 3–4-fold longer than unbound transcripts. Second, the 3′UTRs of Staufen-bound transcripts are highly enriched for three types of secondary structures. These structures map with high precision to previously identified Staufen-binding regions in Drosophila bicoid and human ARF1 3′UTRs. Our results provide the first systematic genome-wide analysis showing how a double-stranded RNA-binding protein achieves target specificity.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8, Department of Cell & Systems Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6, Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario, Canada M5S 3E1
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64
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Elbarbary RA, Li W, Tian B, Maquat LE. STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown. Genes Dev 2013; 27:1495-510. [PMID: 23824540 PMCID: PMC3713430 DOI: 10.1101/gad.220962.113] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 05/29/2013] [Indexed: 11/24/2022]
Abstract
For a number of human genes that encode transcripts containing inverted repeat Alu elements (IRAlus) within their 3' untranslated region (UTR), product mRNA is efficiently exported to the cytoplasm when the IRAlus, which mediate nuclear retention, are removed by alternative polyadenylation. Here we report a new mechanism that promotes gene expression by targeting mRNAs that maintain their 3' UTR IRAlus: Binding of the dsRNA-binding protein Staufen1 (STAU1) to 3' UTR IRAlus inhibits nuclear retention so as to augment the nuclear export of 3' UTR IRAlus-containing mRNAs (IRAlus mRNAs). Moreover, we found that 3' UTR IRAlus-bound STAU1 enhances 3' UTR IRAlus mRNA translation by precluding protein kinase R (PKR) binding, which obviates PKR activation, eukaryotic translation initiation factor 2α (eIF2α) phosphorylation, and repression of global cell translation. Thus, STAU1 binding to 3' UTR IRAlus functions along with 3' UTR IRAlus-mediated nuclear retention to suppress the shutdown of cellular translation triggered by PKR binding to endogenous cytoplasmic dsRNAs. We also show that a changing STAU1/PKR ratio contributes to myogenesis via effects on the 3' UTR IRAlus of mRNA encoding the microRNA-binding protein LIN28.
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Affiliation(s)
- Reyad A. Elbarbary
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Wencheng Li
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey–New Jersey Medical School, Newark, New Jersey 07101, USA
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey–New Jersey Medical School, Newark, New Jersey 07101, USA
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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65
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The intertwining of transposable elements and non-coding RNAs. Int J Mol Sci 2013; 14:13307-28. [PMID: 23803660 PMCID: PMC3742188 DOI: 10.3390/ijms140713307] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/05/2013] [Accepted: 06/05/2013] [Indexed: 12/15/2022] Open
Abstract
Growing evidence shows a close association of transposable elements (TE) with non-coding RNAs (ncRNA), and a significant number of small ncRNAs originate from TEs. Further, ncRNAs linked with TE sequences participate in a wide-range of regulatory functions. Alu elements in particular are critical players in gene regulation and molecular pathways. Alu sequences embedded in both long non-coding RNAs (lncRNA) and mRNAs form the basis of targeted mRNA decay via short imperfect base-pairing. Imperfect pairing is prominent in most ncRNA/target RNA interactions and found throughout all biological kingdoms. The piRNA-Piwi complex is multifunctional, but plays a major role in protection against invasion by transposons. This is an RNA-based genetic immune system similar to the one found in prokaryotes, the CRISPR system. Thousands of long intergenic non-coding RNAs (lincRNAs) are associated with endogenous retrovirus LTR transposable elements in human cells. These TEs can provide regulatory signals for lincRNA genes. A surprisingly large number of long circular ncRNAs have been discovered in human fibroblasts. These serve as "sponges" for miRNAs. Alu sequences, encoded in introns that flank exons are proposed to participate in RNA circularization via Alu/Alu base-pairing. Diseases are increasingly found to have a TE/ncRNA etiology. A single point mutation in a SINE/Alu sequence in a human long non-coding RNA leads to brainstem atrophy and death. On the other hand, genomic clusters of repeat sequences as well as lncRNAs function in epigenetic regulation. Some clusters are unstable, which can lead to formation of diseases such as facioscapulohumeral muscular dystrophy. The future may hold more surprises regarding diseases associated with ncRNAs andTEs.
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Park E, Maquat LE. Staufen-mediated mRNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:423-35. [PMID: 23681777 DOI: 10.1002/wrna.1168] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/28/2013] [Accepted: 03/28/2013] [Indexed: 12/26/2022]
Abstract
Staufen1 (STAU1)-mediated mRNA decay (SMD) is an mRNA degradation process in mammalian cells that is mediated by the binding of STAU1 to a STAU1-binding site (SBS) within the 3'-untranslated region (3'-UTR) of target mRNAs. During SMD, STAU1, a double-stranded (ds) RNA-binding protein, recognizes dsRNA structures formed either by intramolecular base pairing of 3'-UTR sequences or by intermolecular base pairing of 3'-UTR sequences with a long-noncoding RNA (lncRNA) via partially complementary Alu elements. Recently, STAU2, a paralog of STAU1, has also been reported to mediate SMD. Both STAU1 and STAU2 interact directly with the ATP-dependent RNA helicase UPF1, a key SMD factor, enhancing its helicase activity to promote effective SMD. Moreover, STAU1 and STAU2 form homodimeric and heterodimeric interactions via domain-swapping. Because both SMD and the mechanistically related nonsense-mediated mRNA decay (NMD) employ UPF1; SMD and NMD are competitive pathways. Competition contributes to cellular differentiation processes, such as myogenesis and adipogenesis, placing SMD at the heart of various physiologically important mechanisms.
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Affiliation(s)
- Eonyoung Park
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Center for RNA Biology, University of Rochester, Rochester, NY, USA
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Abstract
Staufen1-mediated mRNA decay (SMD) degrades mRNAs that harbor a Staufen1-binding site (SBS) in their 3' untranslated regions (UTRs). Human SBSs can form by intermolecular base-pairing between a 3' UTR Alu element and an Alu element within a long noncoding RNA (lncRNA) called a ½-sbsRNA. Since Alu elements are confined to primates, it was unclear how SMD occurs in rodents. Here we identify mouse mRNA 3' UTRs and lncRNAs that contain a B1, B2, B4, or identifier (ID) element. We show that SMD occurs in mouse cells via mRNA-lncRNA base-pairing of partially complementary elements and that mouse ½-sbsRNA (m½-sbsRNA)-triggered SMD regulates C2C12 cell myogenesis. Our findings define new roles for lncRNAs as well as B and ID short interspersed elements (SINEs) in mice that undoubtedly influence many developmental and homeostatic pathways.
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Affiliation(s)
- Jiashi Wang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
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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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