1
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Triebel S, Lamkiewicz K, Ontiveros N, Sweeney B, Stadler PF, Petrov AI, Niepmann M, Marz M. Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus. Sci Rep 2024; 14:15145. [PMID: 38956134 PMCID: PMC11219754 DOI: 10.1038/s41598-024-62897-0] [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: 12/19/2023] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large 'cloud' of RNA genomes (quasispecies) which-by trial and error-comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.
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Affiliation(s)
- Sandra Triebel
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Nancy Ontiveros
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Blake Sweeney
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Peter F Stadler
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, 04107, Leipzig, Germany
- German Center for Integrative Biodiversity Research (iDiv), 04103, Leipzig, Germany
| | | | - Michael Niepmann
- Institute for Biochemistry, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany.
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Leibniz Institute on Aging-Fritz Lipmann Institute, 07745, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv), 04103, Leipzig, Germany.
- Michael Stifel Center Jena, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
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2
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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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3
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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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4
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Li Y, Li C, Liu M, Liu S, Liu F, Wang L. The RNA-binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling. Development 2023; 150:dev201890. [PMID: 37874038 PMCID: PMC10652045 DOI: 10.1242/dev.201890] [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: 04/17/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
In vertebrates, the earliest hematopoietic stem and progenitor cells (HSPCs) are derived from a subset of specialized endothelial cells, hemogenic endothelial cells, in the aorta-gonad-mesonephros region through endothelial-to-hematopoietic transition. HSPC generation is efficiently and accurately regulated by a variety of factors and signals; however, the precise control of these signals remains incompletely understood. Post-transcriptional regulation is crucial for gene expression, as the transcripts are usually bound by RNA-binding proteins (RBPs) to regulate RNA metabolism. Here, we report that the RBP protein Csde1-mediated translational control is essential for HSPC generation during zebrafish early development. Genetic mutants and morphants demonstrated that depletion of csde1 impaired HSPC production in zebrafish embryos. Mechanistically, Csde1 regulates HSPC generation through modulating Wnt/β-catenin signaling activity. We demonstrate that Csde1 binds to ctnnb1 mRNAs (encoding β-catenin, an effector of Wnt signaling) and regulates translation but not stability of ctnnb1 mRNA, which further enhances β-catenin protein level and Wnt signal transduction activities. Together, we identify Csde1 as an important post-transcriptional regulator and provide new insights into how Wnt/β-catenin signaling is precisely regulated at the post-transcriptional level.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Can Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Mengyao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shicheng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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5
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Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J. Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res 2023; 51:1895-1913. [PMID: 36688322 PMCID: PMC9976900 DOI: 10.1093/nar/gkac1277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical ππ-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). All interactions are validated by mutational analyses and the high-resolution structures presented here will guide further studies to understand how both proteins act together in cellular processes.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Philip Ullmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco Payr
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen S Hub
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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6
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Andreev DE, Niepmann M, Shatsky IN. Elusive Trans-Acting Factors Which Operate with Type I (Poliovirus-like) IRES Elements. Int J Mol Sci 2022; 23:ijms232415497. [PMID: 36555135 PMCID: PMC9778869 DOI: 10.3390/ijms232415497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
The phenomenon of internal initiation of translation was discovered in 1988 on poliovirus mRNA. The prototypic cis-acting element in the 5' untranslated region (5'UTR) of poliovirus mRNA, which is able to direct initiation at an internal start codon without the involvement of a cap structure, has been called an IRES (Internal Ribosome Entry Site or Segment). Despite its early discovery, poliovirus and other related IRES elements of type I are poorly characterized, and it is not yet clear which host proteins (a.k.a. IRES trans-acting factors, ITAFs) are required for their full activity in vivo. Here we discuss recent and old results devoted to type I IRESes and provide evidence that Poly(rC) binding protein 2 (PCBP2), Glycyl-tRNA synthetase (GARS), and Cold Shock Domain Containing E1 (CSDE1, also known as UNR) are major regulators of type I IRES activity.
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Affiliation(s)
- Dmitry E. Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Ivan N. Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence:
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7
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Smith GA, Padmanabhan A, Lau BH, Pampana A, Li L, Lee CY, Pelonero A, Nishino T, Sadagopan N, Xia VQ, Jain R, Natarajan P, Wu RS, Black BL, Srivastava D, Shokat KM, Chorba JS. Cold shock domain-containing protein E1 is a posttranscriptional regulator of the LDL receptor. Sci Transl Med 2022; 14:eabj8670. [PMID: 36103516 PMCID: PMC10174261 DOI: 10.1126/scitranslmed.abj8670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The low-density lipoprotein receptor (LDLR) controls cellular delivery of cholesterol and clears LDL from the bloodstream, protecting against atherosclerotic heart disease, the leading cause of death in the United States. We therefore sought to identify regulators of the LDLR beyond the targets of current therapies and known causes of familial hypercholesterolemia. We found that cold shock domain-containing protein E1 (CSDE1) enhanced hepatic LDLR messenger RNA (mRNA) decay via its 3' untranslated region and regulated atherogenic lipoproteins in vivo. Using parallel phenotypic genome-wide CRISPR interference screens in a tissue culture model, we identified 40 specific regulators of the LDLR that were not previously identified by observational human genetic studies. Among these, we demonstrated that, in HepG2 cells, CSDE1 regulated the LDLR at least as strongly as statins and proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors. In addition, we showed that hepatic gene silencing of Csde1 treated diet-induced dyslipidemia in mice to a similar degree as Pcsk9 silencing. These results suggest the therapeutic potential of targeting CSDE1 to manipulate the posttranscriptional regulation of the LDLR mRNA for the prevention of cardiovascular disease. Our approach of modeling a clinically relevant phenotype in a forward genetic screen, followed by mechanistic pharmacologic dissection and in vivo validation, may serve as a generalizable template for the identification of therapeutic targets in other human disease states.
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Affiliation(s)
- Geoffrey A Smith
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arun Padmanabhan
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Bryan H Lau
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Akhil Pampana
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Li Li
- Department of Medicine and Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clara Y Lee
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Angelo Pelonero
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Tomohiro Nishino
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Nandhini Sadagopan
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Vivian Q Xia
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Cardiology, Zuckerberg San Francisco General Hospital, San Francisco, CA 94110, USA
| | - Rajan Jain
- Department of Medicine and Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Cell and Developmental Biology, Institute of Regenerative Medicine, and Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Roland S Wu
- Division of Cardiology, UCSF Health, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.,Departments of Pediatrics and Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John S Chorba
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Cardiology, Zuckerberg San Francisco General Hospital, San Francisco, CA 94110, USA
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8
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Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
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9
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A de novo truncating variant in CSDE1 in an adult-onset neuropsychiatric phenotype without intellectual disability. Eur J Med Genet 2022; 65:104423. [PMID: 35026469 DOI: 10.1016/j.ejmg.2022.104423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/23/2021] [Accepted: 01/08/2022] [Indexed: 01/04/2023]
Abstract
Variants in CSDE1, a gene encoding a constrained RNA-binding protein, have recently been associated with a spectrum of neurodevelopmental conditions encompassing autism, seizures and ocular abnormalities. According to previously reported individuals, pathogenic variants in CSDE1 are typically associated with developmental delay and intellectual disability. Here, we report one individual with normal neurodevelopment and adult-onset neuropsychiatric features (i.e., acute psychosis) due to the novel de novo truncating variant c.2272C > T, p.(Gln758*) in CSDE1 (NM_001242891.1). Neuropsychological assessment confirmed deficits regarding verbal fluency, semantic memory, executive function and processing speed. Overall, our findings expand the phenotypic spectrum of CSDE1-related disorder towards the mild end.
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10
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Grzybowska EA, Wakula M. Protein Binding to Cis-Motifs in mRNAs Coding Sequence Is Common and Regulates Transcript Stability and the Rate of Translation. Cells 2021; 10:2910. [PMID: 34831133 PMCID: PMC8616275 DOI: 10.3390/cells10112910] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
Protein binding to the non-coding regions of mRNAs is relatively well characterized and its functionality has been described in many examples. New results obtained by high-throughput methods indicate that binding to the coding sequence (CDS) by RNA-binding proteins is also quite common, but the functions thereof are more obscure. As described in this review, CDS binding has a role in the regulation of mRNA stability, but it has also a more intriguing role in the regulation of translational efficiency. Global approaches, which suggest the significance of CDS binding along with specific examples of CDS-binding RBPs and their modes of action, are outlined here, pointing to the existence of a relatively less-known regulatory network controlling mRNA stability and translation on yet another level.
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Affiliation(s)
- Ewa A. Grzybowska
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland;
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11
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MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome. Noncoding RNA 2021; 7:ncrna7040061. [PMID: 34698276 PMCID: PMC8544657 DOI: 10.3390/ncrna7040061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Complete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroSalmon GitHub repository provides all results. RNAHybrid and sRNAtoolbox tools predicted the MREs. UTRscan and the Teiresias algorithm predicted other 3′UTR cis-acting motifs, both known vertebrate motifs and putative novel motifs. MicroSalmon provides search programs to retrieve all FL-transcripts targeted by a miRNA (median number 1487), all miRNAs targeting an FL-transcript (median number 27), and other cis-acting motifs. As thousands of FL-transcripts may be targets of each miRNA, additional experimental strategies are necessary to reduce the likely true and relevant targets to a number that may be functionally validated. Low-complexity motifs known to affect mRNA decay in vertebrates were over-represented. Many of these were enriched in the terminal end, while purine- or pyrimidine-rich motifs with unknown functions were enriched immediately downstream of the stop codon. Furthermore, several novel complex motifs were over-represented, indicating conservation and putative function. In conclusion, MicroSalmon is an extensive and useful, searchable resource for study of Atlantic salmon transcript regulation by miRNAs and cis-acting 3′UTR motifs.
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12
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Gangfuß A, Lochmüller H, Töpf A, O'Heir E, Horvath R, Kölbel H, Schweiger B, Schara-Schmidt U, Roos A. A de novo CSDE1 variant causing neurodevelopmental delay, intellectual disability, neurologic and psychiatric symptoms in a child of consanguineous parents. Am J Med Genet A 2021; 188:283-291. [PMID: 34519148 DOI: 10.1002/ajmg.a.62494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/02/2021] [Accepted: 08/21/2021] [Indexed: 01/02/2023]
Abstract
CSDE1 encodes the cytoplasmic cold shock domain-containing protein E1 (CSDE1), which is highly conserved across species and functions as an RNA-binding protein involved in translationally coupled mRNA turnover. CSDE1 displays a bidirectional role: promoting and repressing the translation of RNAs but also increasing and decreasing the abundance of RNAs. Preclinical studies highlighted an involvement of CSDE1 in different forms of cancer. Moreover, CSDE1 is highly expressed in human embryonic stem cells and plays a role in neuronal migration and differentiation. A genome-wide association study suggested CSDE1 as a potential autism-spectrum disorder risk gene. A multicenter next generation sequencing approach unraveled likely causative heterozygous variants in CSDE1 in 18 patients, identifying a new autism spectrum disorder-related syndrome consisting of autism, intellectual disability, and neurodevelopmental delay. Since then, no further patients with CSDE1 variants have been reported in the literature. Here, we report a 9.5-year-old girl from a consanguineous family of Turkish origin suffering from profound delayed speech and motor development, moderate intellectual disability, neurologic and psychiatric symptoms as well as hypoplasia of corpus callosum and mildly reduced brain volume on brain magnetic resonance imaging associated with a recurrent de novo mutation in CSDE1 (c.367C > T; p.R123*) expanding the phenotypical spectrum associated with pathogenic CSDE1 variants.
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Affiliation(s)
- Andrea Gangfuß
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, University of Ottawa, Ottawa, Canada.,Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.,Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, New-castle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Heike Kölbel
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Bernd Schweiger
- Department of Radiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Andreas Roos
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
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13
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Kakumani PK, Guitart T, Houle F, Harvey LM, Goyer B, Germain L, Gebauer F, Simard MJ. CSDE1 attenuates microRNA-mediated silencing of PMEPA1 in melanoma. Oncogene 2021; 40:3231-3244. [PMID: 33833398 DOI: 10.1038/s41388-021-01767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
MicroRNAs and RNA-binding proteins (RBPs) primarily target the 3' UTR of mRNAs to control their translation and stability. However, their co-regulatory effects on specific mRNAs in physiology and disease are yet to be fully explored. CSDE1 is an RBP that promotes metastasis in melanoma and mechanisms underlying its oncogenic activities need to be completely defined. Here we report that CSDE1 interacts with specific miRNA-induced silencing complexes (miRISC) in melanoma. We find an association of CSDE1 with AGO2, the essential component of miRISC, which is facilitated by target mRNAs and depends on the first cold shock domain of CSDE1. Both CSDE1 and AGO2 bind to 3' UTR of PMEPA1. CSDE1 counters AGO2 binding, leading to an increase of PMEPA1 expression. We also identify a miRNA, miR-129-5p, that represses PMEPA1 expression in melanoma. Collectively, our results show that PMEPA1 promotes tumorigenic traits and that CSDE1 along with miR-129-5p/AGO2 miRISC act antagonistically to fine-tune PMEPA1 expression toward the progression of melanoma.
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Affiliation(s)
- Pavan Kumar Kakumani
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada.
- Université Laval Cancer Research Centre, Québec, QC, Canada.
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francois Houle
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada
- Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Louis-Mathieu Harvey
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada
- Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Benjamin Goyer
- Centre de recherche du CHU de Québec-Université Laval (Axe Médecine Régénératrice) and Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, QC, Canada
- Département de chirurgie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Lucie Germain
- Centre de recherche du CHU de Québec-Université Laval (Axe Médecine Régénératrice) and Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, QC, Canada
- Département de chirurgie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martin J Simard
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada.
- Université Laval Cancer Research Centre, Québec, QC, Canada.
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14
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Regulation of Fetal Genes by Transitions among RNA-Binding Proteins during Liver Development. Int J Mol Sci 2020; 21:ijms21239319. [PMID: 33297405 PMCID: PMC7731027 DOI: 10.3390/ijms21239319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
Transcripts of alpha-fetoprotein (Afp), H19, and insulin-like growth factor 2 (Igf2) genes are highly expressed in mouse fetal liver, but decrease drastically during maturation. While transcriptional regulation of these genes has been well studied, the post-transcriptional regulation of their developmental decrease is poorly understood. Here, we show that shortening of poly(A) tails and subsequent RNA decay are largely responsible for the postnatal decrease of Afp, H19, and Igf2 transcripts in mouse liver. IGF2 mRNA binding protein 1 (IMP1), which regulates stability and translation efficiency of target mRNAs, binds to these fetal liver transcripts. When IMP1 is exogenously expressed in mouse adult liver, fetal liver transcripts show higher expression and possess longer poly(A) tails, suggesting that IMP1 stabilizes them. IMP1 declines concomitantly with fetal liver transcripts as liver matures. Instead, RNA-binding proteins (RBPs) that promote RNA decay, such as cold shock domain containing protein E1 (CSDE1), K-homology domain splicing regulatory protein (KSRP), and CUG-BP1 and ETR3-like factors 1 (CELF1), bind to 3' regions of fetal liver transcripts. These data suggest that transitions among RBPs associated with fetal liver transcripts shift regulation from stabilization to decay, leading to a postnatal decrease in those fetal transcripts.
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15
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Ford LK, Fioriti L. Coiled-Coil Motifs of RNA-Binding Proteins: Dynamicity in RNA Regulation. Front Cell Dev Biol 2020; 8:607947. [PMID: 33330512 PMCID: PMC7710910 DOI: 10.3389/fcell.2020.607947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023] Open
Abstract
Neuronal granules are biomolecular condensates that concentrate high quantities of RNAs and RNA-related proteins within neurons. These dense packets of information are trafficked from the soma to distal sites rich in polysomes, where local protein synthesis can occur. Movement of neuronal granules to distal sites, and local protein synthesis, play a critical role in synaptic plasticity. The formation of neuronal granules is intriguing; these granules lack a membrane and instead phase separate due to protein and RNA interactions. Low complexity motifs and RNA binding domains are highly prevalent in these proteins. Here, we introduce the role that coiled-coil motifs play in neuronal granule proteins, and investigate the structure-function relationship of coiled-coil proteins in RNA regulation. Interestingly, low complexity domains and coiled-coil motifs are highly dynamic, allowing for increased functional response to environmental influences. Finally, biomolecular condensates have been suggested to drive the formation of toxic, neurodegenerative proteins such as TDP-43 and tau. Here, we review the conversion of coiled-coil motifs to amyloid structures, and speculate a role that neuronal granules play in coiled-coil to amyloid conversions of neurodegenerative proteins.
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Affiliation(s)
- Lenzie K Ford
- Department of Neuroscience, Zuckerman Institute, Columbia University, New York, NY, United States
| | - Luana Fioriti
- Laboratory of Molecular Mechanisms of Polyglutamine Disorders, Department of Neuroscience, Dulbecco Telethon Institute, Istituto di Ricerche Farmacologiche Mario Negri (IRCCS), Milan, Italy
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16
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17
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Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Mooijman D, Benes V, Savitski MM, Gebauer F, Hennig J. Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep 2020; 32:107930. [PMID: 32697992 PMCID: PMC7383231 DOI: 10.1016/j.celrep.2020.107930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lara Jayne Sweetapple
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Laura Villacorta
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dylan Mooijman
- Developmental Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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18
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Takahashi A, Suzuki T, Soeda S, Takaoka S, Kobori S, Yamaguchi T, Mohamed HMA, Yanagiya A, Abe T, Shigeta M, Furuta Y, Kuba K, Yamamoto T. The CCR4-NOT complex maintains liver homeostasis through mRNA deadenylation. Life Sci Alliance 2020; 3:3/5/e201900494. [PMID: 32238456 PMCID: PMC7119370 DOI: 10.26508/lsa.201900494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 12/12/2022] Open
Abstract
The biological significance of deadenylation in global gene expression is not fully understood. Here, we show that the CCR4-NOT deadenylase complex maintains expression of mRNAs, such as those encoding transcription factors, cell cycle regulators, DNA damage response-related proteins, and metabolic enzymes, at appropriate levels in the liver. Liver-specific disruption of Cnot1, encoding a scaffold subunit of the CCR4-NOT complex, leads to increased levels of mRNAs for transcription factors, cell cycle regulators, and DNA damage response-related proteins because of reduced deadenylation and stabilization of these mRNAs. CNOT1 suppression also results in an increase of immature, unspliced mRNAs (pre-mRNAs) for apoptosis-related and inflammation-related genes and promotes RNA polymerase II loading on their promoter regions. In contrast, mRNAs encoding metabolic enzymes become less abundant, concomitant with decreased levels of these pre-mRNAs. Lethal hepatitis develops concomitantly with abnormal mRNA expression. Mechanistically, the CCR4-NOT complex targets and destabilizes mRNAs mainly through its association with Argonaute 2 (AGO2) and butyrate response factor 1 (BRF1) in the liver. Therefore, the CCR4-NOT complex contributes to liver homeostasis by modulating the liver transcriptome through mRNA deadenylation.
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Affiliation(s)
- Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
| | - Shou Soeda
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shohei Takaoka
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | | | - Akiko Yanagiya
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mayo Shigeta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yasuhide Furuta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan .,Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
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19
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Kakumani PK, Harvey LM, Houle F, Guitart T, Gebauer F, Simard MJ. CSDE1 controls gene expression through the miRNA-mediated decay machinery. Life Sci Alliance 2020; 3:e201900632. [PMID: 32161113 PMCID: PMC7067469 DOI: 10.26508/lsa.201900632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022] Open
Abstract
In animals, miRNAs are the most prevalent small non-coding RNA molecules controlling posttranscriptional gene regulation. The Argonaute proteins (AGO) mediate miRNA-guided gene silencing by recruiting multiple factors involved in translational repression, deadenylation, and decapping. Here, we report that CSDE1, an RNA-binding protein linked to stem cell maintenance and metastasis in cancer, interacts with AGO2 within miRNA-induced silencing complex and mediates gene silencing through its N-terminal domains. We show that CSDE1 interacts with LSM14A, a constituent of P-body assembly and further associates to the DCP1-DCP2 decapping complex, suggesting that CSDE1 could promote the decay of miRNA-induced silencing complex-targeted mRNAs. Together, our findings uncover a hitherto unknown mechanism used by CSDE1 in the control of gene expression mediated by the miRNA pathway.
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Affiliation(s)
- Pavan Kumar Kakumani
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
| | - Louis-Mathieu Harvey
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
| | - François Houle
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin J Simard
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
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20
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Guo AX, Cui JJ, Wang LY, Yin JY. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun Signal 2020; 18:14. [PMID: 31987048 PMCID: PMC6986143 DOI: 10.1186/s12964-019-0496-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract CSDE1 (cold shock domain containing E1) plays a key role in translational reprogramming, which determines the fate of a number of RNAs during biological processes. Interestingly, the role of CSDE1 is bidirectional. It not only promotes and represses the translation of RNAs but also increases and decreases the abundance of RNAs. However, the mechanisms underlying this phenomenon are still unknown. In this review, we propose a “protein-RNA connector” model to explain this bidirectional role and depict its three versions: sequential connection, mutual connection and facilitating connection. As described in this molecular model, CSDE1 binds to RNAs and cooperates with other protein regulators. CSDE1 connects with different RNAs and their regulators for different purposes. The triple complex of CSDE1, a regulator and an RNA reprograms translation in different directions for each transcript. Meanwhile, a number of recent studies have found important roles for CSDE1 in human diseases. This model will help us to understand the role of CSDE1 in translational reprogramming and human diseases. Video Abstract
Graphical abstract ![]()
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Affiliation(s)
- Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jia-Jia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, 410078, People's Republic of China. .,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, 410078, People's Republic of China.
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21
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Phillips BT, Williams JG, Atchley DT, Xu X, Li JL, Adams AL, Johnson KL, Hall TMT. Mass spectrometric identification of candidate RNA-binding proteins associated with Transition Nuclear Protein mRNA in the mouse testis. Sci Rep 2019; 9:13618. [PMID: 31541158 PMCID: PMC6754440 DOI: 10.1038/s41598-019-50052-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 11/23/2022] Open
Abstract
Spermatogenesis is a differentiation process that requires dramatic changes to DNA architecture, a process governed in part by Transition Nuclear Proteins 1 and 2 (TNP1 and TNP2). Translation of Tnp1 and Tnp2 mRNAs is temporally disengaged from their transcription. We hypothesized that RNA regulatory proteins associate specifically with Tnp mRNAs to control the delayed timing of their translation. To identify potential regulatory proteins, we isolated endogenous mRNA/protein complexes from testis extract and identified by mass spectrometry proteins that associated with one or both Tnp transcripts. Five proteins showed strong association with Tnp transcripts but had low signal when Actin mRNA was isolated. We visualized the expression patterns in testis sections of the five proteins and found that each of the proteins was detected in germ cells at the appropriate stages to regulate Tnp RNA expression.
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Affiliation(s)
- Bart T Phillips
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Dustin T Atchley
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Xiaojiang Xu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jian-Liang Li
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Andrea L Adams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Katina L Johnson
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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22
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García-Cárdenas JM, Guerrero S, López-Cortés A, Armendáriz-Castillo I, Guevara-Ramírez P, Pérez-Villa A, Yumiceba V, Zambrano AK, Leone PE, Paz-y-Miño C. Post-transcriptional Regulation of Colorectal Cancer: A Focus on RNA-Binding Proteins. Front Mol Biosci 2019; 6:65. [PMID: 31440515 PMCID: PMC6693420 DOI: 10.3389/fmolb.2019.00065] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/23/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a major health problem with an estimated 1. 8 million new cases worldwide. To date, most CRC studies have focused on DNA-related aberrations, leaving post-transcriptional processes under-studied. However, post-transcriptional alterations have been shown to play a significant part in the maintenance of cancer features. RNA binding proteins (RBPs) are uprising as critical regulators of every cancer hallmark, yet little is known regarding the underlying mechanisms and key downstream oncogenic targets. Currently, more than a thousand RBPs have been discovered in humans and only a few have been implicated in the carcinogenic process and even much less in CRC. Identification of cancer-related RBPs is of great interest to better understand CRC biology and potentially unveil new targets for cancer therapy and prognostic biomarkers. In this work, we reviewed all RBPs which have a role in CRC, including their control by microRNAs, xenograft studies and their clinical implications.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - César Paz-y-Miño
- Facultad de Ciencias de la Salud Eugenio Espejo, Centro de Investigación Genética y Genómica, Universidad UTE, Quito, Ecuador
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UNR/ CSDE1 Expression Is Critical to Maintain Invasive Phenotype of Colorectal Cancer through Regulation of c-MYC and Epithelial-to-Mesenchymal Transition. J Clin Med 2019; 8:jcm8040560. [PMID: 31027221 PMCID: PMC6517883 DOI: 10.3390/jcm8040560] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/11/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
CSDE1 (cold shock domain containing E1) gene is located upstream of the N-RAS locus, and codes for an RNA-binding protein named Upstream of N-Ras (UNR). In cancer, CSDE1 has been shown to regulate c-Fos, c-Myc, Pten, Rac1, or Vimentin. UNR/CSDE1 has been studied in breast, melanoma, pancreatic and prostate cancer. Then, the aim of this study is to evaluate the role of CSDE1/UNR in colorectal cancer progression and maintenance of aggressive phenotype. We firstly evaluated UNR/CSDE1 expression in human colon cancer derived cell lines and patient samples. Subsequently, we performed functional experiments by UNR/CSDE1 downregulation. We also evaluated UNR/CSDE1 prognostic relevance in two independent sets of patients. Not only was UNR/CSDE1 expression higher in tumor samples compared to untransformed samples, but also in colonospheres and metastatic origin cell lines than their parental and primary cell lines, respectively. Downregulation of UNR/CSDE1 reduced cell viability and migration throughout a restrain of epithelial-to-mesenchymal transition and increases sensitivity to apoptosis. Interestingly, high UNR/CSDE1 expression was associated with poor prognosis and correlated positively with c-MYC expression in colorectal cancer samples and cell lines. Here, we show for the first time compelling data reporting the oncogenic role of UNR/CSDE1 in human colorectal cancer.
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Suzuki T, Kikuguchi C, Nishijima S, Nagashima T, Takahashi A, Okada M, Yamamoto T. Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes. Development 2019; 146:dev.168146. [PMID: 30733279 PMCID: PMC6398447 DOI: 10.1242/dev.168146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
Liver development involves dramatic gene expression changes mediated by transcriptional and post-transcriptional control. Here, we show that the Cnot deadenylase complex plays a crucial role in liver functional maturation. The Cnot3 gene encodes an essential subunit of the Cnot complex. Mice lacking Cnot3 in liver have reduced body and liver masses, and they display anemia and severe liver damage. Histological analyses indicate that Cnot3-deficient (Cnot3−/−) hepatocytes are irregular in size and morphology, resulting in formation of abnormal sinusoids. We observe hepatocyte death, increased abundance of mitotic and mononucleate hepatocytes, and inflammation. Cnot3−/− livers show increased expression of immune response-related, cell cycle-regulating and immature liver genes, while many genes relevant to liver functions, such as oxidation-reduction, lipid metabolism and mitochondrial function, decrease, indicating impaired liver functional maturation. Highly expressed mRNAs possess elongated poly(A) tails and are stabilized in Cnot3−/− livers, concomitant with an increase of the proteins they encode. In contrast, transcription of liver function-related mRNAs was lower in Cnot3−/− livers. We detect efficient suppression of Cnot3 protein postnatally, demonstrating the crucial contribution of mRNA decay to postnatal liver functional maturation. Summary: Regulation of both mRNA transcription and stability plays a crucial role in postnatal liver development; in particular, Cnot complex-mediated mRNA decay is essential for postnatal liver functional maturation.
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Affiliation(s)
- Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
| | - Chisato Kikuguchi
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
| | - Saori Nishijima
- Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Takeshi Nagashima
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mariko Okada
- Laboratory for Integrated Cellular Systems, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan.,Laboratory for Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadashi Yamamoto
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan .,Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
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Mendoza-Topaz C, Yeow I, Riento K, Nichols BJ. BioID identifies proteins involved in the cell biology of caveolae. PLoS One 2018; 13:e0209856. [PMID: 30589899 PMCID: PMC6307745 DOI: 10.1371/journal.pone.0209856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/12/2018] [Indexed: 01/20/2023] Open
Abstract
The mechanisms controlling the abundance and sub-cellular distribution of caveolae are not well described. A first step towards determining such mechanisms would be identification of relevant proteins that interact with known components of caveolae. Here, we applied proximity biotinylation (BioID) to identify a list of proteins that may interact with the caveolar protein cavin1. Screening of these candidates using siRNA to reduce their expression revealed that one of them, CSDE1, regulates the levels of mRNAs and protein expression for multiple components of caveolae. A second candidate, CD2AP, co-precipitated with cavin1. Caveolar proteins were observed in characteristic and previously un-described linear arrays adjacent to cell-cell junctions in both MDCK cells, and in HeLa cells overexpressing an active form of the small GTPase Rac1. CD2AP was required for the recruitment of caveolar proteins to these linear arrays. We conclude that BioID will be useful in identification of new proteins involved in the cell biology of caveolae, and that interaction between CD2AP and cavin1 may have an important role in regulating the sub-cellular distribution of caveolae.
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Affiliation(s)
| | - I. Yeow
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - K. Riento
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - B. J. Nichols
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail:
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Culjkovic-Kraljacic B, Borden KLB. The Impact of Post-transcriptional Control: Better Living Through RNA Regulons. Front Genet 2018; 9:512. [PMID: 30455716 PMCID: PMC6230556 DOI: 10.3389/fgene.2018.00512] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Traditionally, cancer is viewed as a disease driven by genetic mutations and/or epigenetic and transcriptional dysregulation. While these are undoubtedly important drivers, many recent studies highlight the disconnect between the proteome and the genome or transcriptome. At least in part, this disconnect arises as a result of dysregulated RNA metabolism which underpins the altered proteomic landscape observed. Thus, it is important to understand the basic mechanisms governing post-transcriptional control and how these processes can be co-opted to drive cancer cell phenotypes. In some cases, groups of mRNAs that encode protein involved in specific oncogenic processes can be co-regulated at multiple processing levels in order to turn on entire biochemical pathways. Indeed, the RNA regulon model was postulated as a means to understand how cells coordinately regulate transcripts encoding proteins in the same biochemical pathways. In this review, we describe some of the basic mRNA processes that are dysregulated in cancer and the biological impact this has on the cell. This dysregulation can affect networks of RNAs simultaneously thereby underpinning the oncogenic phenotypes observed.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
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Moore KS, Yagci N, van Alphen F, Meijer AB, ‘t Hoen PAC, von Lindern M. Strap associates with Csde1 and affects expression of select Csde1-bound transcripts. PLoS One 2018; 13:e0201690. [PMID: 30138317 PMCID: PMC6107111 DOI: 10.1371/journal.pone.0201690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 07/22/2018] [Indexed: 02/06/2023] Open
Abstract
Erythropoiesis is regulated at many levels, including control of mRNA translation. Changing environmental conditions, such as hypoxia or the availability of nutrients and growth factors, require a rapid response enacted by the enhanced or repressed translation of existing transcripts. Cold shock domain protein e1 (Csde1/Unr) is an RNA-binding protein required for erythropoiesis and strongly upregulated in erythroblasts relative to other hematopoietic progenitors. The aim of this study is to identify the Csde1-containing protein complexes and investigate their role in post-transcriptional expression control of Csde1-bound transcripts. We show that Serine/Threonine kinase receptor-associated protein (Strap/Unrip), was the protein most strongly associated with Csde1 in erythroblasts. Strap is a WD40 protein involved in signaling and RNA splicing, but its role when associated with Csde1 is unknown. Reduced expression of Strap did not alter the pool of transcripts bound by Csde1. Instead, it altered the mRNA and/or protein expression of several Csde1-bound transcripts that encode for proteins essential for translational regulation during hypoxia, such as Hmbs, eIF4g3 and Pabpc4. Also affected by Strap knockdown were Vim, a Gata-1 target crucial for erythrocyte enucleation, and Elavl1, which stabilizes Gata-1 mRNA. The major cellular processes affected by both Csde1 and Strap were ribosome function and cell cycle control.
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Affiliation(s)
- Kat S. Moore
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Nurcan Yagci
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floris van Alphen
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
| | - Alexander B. Meijer
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter A. C. ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marieke von Lindern
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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28
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Moore KS, von Lindern M. RNA Binding Proteins and Regulation of mRNA Translation in Erythropoiesis. Front Physiol 2018; 9:910. [PMID: 30087616 PMCID: PMC6066521 DOI: 10.3389/fphys.2018.00910] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Control of gene expression in erythropoiesis has to respond to signals that may emerge from intracellular processes or environmental factors. Control of mRNA translation allows for relatively rapid modulation of protein synthesis from the existing transcriptome. For instance, the protein synthesis rate needs to be reduced when reactive oxygen species or unfolded proteins accumulate in the cells, but also when iron supply is low or when growth factors are lacking in the environment. In addition, regulation of mRNA translation can be important as an additional layer of control on top of gene transcription, in which RNA binding proteins (RBPs) can modify translation of a set of transcripts to the cell’s actual protein requirement. The 5′ and 3′ untranslated regions of mRNA (5′UTR, 3′UTR) contain binding sites for general and sequence specific translation factors. They also contain secondary structures that may hamper scanning of the 5′UTR by translation complexes or may help to recruit translation factors. In addition, the term 5′UTR is not fully correct because many transcripts contain small open reading frames in their 5′UTR that are translated and contribute to regulation of mRNA translation. It is becoming increasingly clear that the transcriptome only partly predicts the proteome. The aim of this review is (i) to summarize how the availability of general translation initiation factors can selectively regulate transcripts because the 5′UTR contains secondary structures or short translated sequences, (ii) to discuss mechanisms that control the length of the mRNA poly(A) tail in relation to mRNA translation, and (iii) to give examples of sequence specific RBPs and their targets. We focused on transcripts and RBPs required for erythropoiesis. Whereas differentiation of erythroblasts to erythrocytes is orchestrated by erythroid transcription factors, the production of erythrocytes needs to respond to the availability of growth factors and nutrients, particularly the availability of iron.
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Affiliation(s)
- Kat S Moore
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
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29
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Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line. Sci Rep 2018; 8:2628. [PMID: 29422612 PMCID: PMC5805679 DOI: 10.1038/s41598-018-20518-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/18/2018] [Indexed: 01/12/2023] Open
Abstract
Expression of the RNA-binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis compared to other hematopoietic lineages. Csde1 expression is impaired in the severe congenital anemia Diamond Blackfan Anemia (DBA), and reduced expression of Csde1 in healthy erythroblasts impaired their proliferation and differentiation. To investigate the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1 in erythroid cells. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. For instance, protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced indicating more efficient translation of Pabpc1 followed by negative feedback on mRNA stability. Overall, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. Clones with complete loss of Csde1, however, could not be generated. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression.
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30
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Kumari K, Pathakota GB, Kumar S, Krishna G. Gene structure and comparative and phylogenetic analyses of Catla catla CYP1A full-length cDNA and its responsiveness to benzo(a)pyrene and copper sulphate at early developmental stages. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:95-108. [PMID: 28822029 DOI: 10.1007/s10695-017-0416-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
In the present study, full-length CYP1A cDNA from Catla catla (Catla) has been identified, and its real-time quantitative reverse transcription PCR (qRT-PCR) expression has been evaluated in different tissues, developmental stages (0, 3, 6, 12 and 24 h and 5, 7 and 9 days post-fertilization) and copper sulphate and benzo(a)pyrene (BaP)-treated 5-day post-fertilization (dpf) larvae (6 to 6.5 mm). Various structural, comparative and phylogenetic analyses of the deduced amino acid sequence revealed that the identified gene of Catla belongs to the CYP1A1 subfamily. Among different tissues of Catla, the highest CYP1A expression was observed in the kidney followed by the liver, muscle, gill, intestine and brain. CYP1A mRNA expression was detected during all the larval developmental stages, including the unfertilized egg with the highest expression on 9 dpf. BaP (3.5 ppb) and copper sulphate (sublethal dose 0.516 ppm) challenge test for 96 h to Catla larvae revealed the highest CYP1A1 expression at 48 h post-challenge. CYP1A1 transcript also showed a concentration-dependent increase in expression following exposure at 1.75 and 3.5 ppb of BaP for 48 h. Its expression profiling indicates that it is functional at early developmental stages. It can also be used to develop a specific biomarker tool for monitoring environmental pollution.
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Affiliation(s)
- Kavita Kumari
- Central Inland Fisheries Research Institute, Barrackpore, 700120, India
- Central Institute of Fisheries Education, Versova, Mumbai, 400061, India
| | | | - Shivendra Kumar
- Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, Samastipur, Bihar, India.
| | - Gopal Krishna
- Central Institute of Fisheries Education, Versova, Mumbai, 400061, India
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31
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Lin Y, Tan KT, Liu J, Kong X, Huang Z, Xu XQ. Global profiling of Rbm24 bound RNAs uncovers a multi-tasking RNA binding protein. Int J Biochem Cell Biol 2017; 94:10-21. [PMID: 29104163 DOI: 10.1016/j.biocel.2017.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/28/2017] [Accepted: 11/02/2017] [Indexed: 11/16/2022]
Abstract
RNA binding proteins serve as critical molecular switches in a multitude of post-transcriptional regulatory processes. In the heart and muscles, the tissue specific RNA binding protein, Rbm24, is known to play important developmental roles via driving different post-transcriptional processes. Nonetheless, the currently identified molecular targets and regulatory pathways seem inadequate to completely explain the observed developmental effects upon Rbm24 knockdown/knockout. Here, by performing RNA Immunoprecipitation and coupling it to microarrays (RIP-Chip), we have generated an atlas of the mRNA binding repertoire of Rbm24. Further functional evaluation of its targets led to the elucidation of novel roles for Rbm24 in post-transcriptional processing, besides its already known roles in regulation of mRNA stability and alternative splicing. Interestingly, Rbm24 is found to cause the destabilization of Chrm2 via binding to an element in the coding region. In addition, Rbm24 is also found to have an uncharacterized role in driving the generation of isoforms with alternative transcriptional start sites. We have, for the first time, demonstrated that Rbm24 is a multi-tasking RNA binding protein capable of regulating its bound targets via a range of mechanisms.
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Affiliation(s)
- Yu Lin
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361000, PR China
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jing Liu
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361000, PR China
| | - Xu Kong
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361000, PR China
| | - Zhengrong Huang
- Department of Cardiology, The First Affiliated Hospital of Xiamen University, Fujian Province, 361000, PR China.
| | - Xiu Qin Xu
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361000, PR China; ShenZhen Research Institute of Xiamen University, PR China.
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32
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A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells. Nat Commun 2017; 8:1456. [PMID: 29129916 PMCID: PMC5682285 DOI: 10.1038/s41467-017-01744-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 10/11/2017] [Indexed: 12/29/2022] Open
Abstract
While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 (cold shock domain containing E1) is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs, as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis. Unlike transcriptional regulation of hESC identity, little is known post-transcriptionally. Here, the authors show that the RNA binding protein CSDE1 regulates core components of hESC identity, neurectoderm commitment and neurogenesis to maintain pluripotency and prevent neural differentiation.
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33
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Mattijssen S, Arimbasseri AG, Iben JR, Gaidamakov S, Lee J, Hafner M, Maraia RJ. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. eLife 2017; 6:e28889. [PMID: 28895529 PMCID: PMC5626478 DOI: 10.7554/elife.28889] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022] Open
Abstract
Messenger RNA function is controlled by the 3' poly(A) tail (PAT) and poly(A)-binding protein (PABP). La-related protein-4 (LARP4) binds poly(A) and PABP. LARP4 mRNA contains a translation-dependent, coding region determinant (CRD) of instability that limits its expression. Although the CRD comprises <10% of LARP4 codons, the mRNA levels vary >20 fold with synonymous CRD substitutions that accommodate tRNA dynamics. Separately, overexpression of the most limiting tRNA increases LARP4 levels and reveals its functional activity, net lengthening of the PATs of heterologous mRNAs with concomitant stabilization, including ribosomal protein (RP) mRNAs. Genetic deletion of cellular LARP4 decreases PAT length and RPmRNA stability. This LARP4 activity requires its PABP-interaction domain and the RNA-binding module which we show is sensitive to poly(A) 3'-termini, consistent with protection from deadenylation. The results indicate that LARP4 is a posttranscriptional regulator of ribosomal protein production in mammalian cells and suggest that this activity can be controlled by tRNA levels.
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Affiliation(s)
- Sandy Mattijssen
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | | | - James R Iben
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Sergei Gaidamakov
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Joowon Lee
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Markus Hafner
- National Institute of Arthritis and Musculoskeletal and Skin DiseasesNational Institutes of HealthBethesdaUnited States
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
- Commissioned CorpsUS Public Health ServiceBethesdaUnited Staes
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Chen CYA, Zhang Y, Xiang Y, Han L, Chang JT, Shyu AB. Antagonistic actions of two human Pan3 isoforms on global mRNA turnover. RNA (NEW YORK, N.Y.) 2017; 23:1404-1418. [PMID: 28559491 PMCID: PMC5558910 DOI: 10.1261/rna.061556.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/25/2017] [Indexed: 05/03/2023]
Abstract
Deadenylation is a fundamental process that regulates eukaryotic gene expression. Mammalian deadenylation exhibits biphasic kinetics, with the Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes mediating the first and second phase, respectively; however, the significance of the biphasic nature of deadenylation in mRNA turnover remains unclear. In this study, we discovered that two distinct isoforms of human Pan3 display opposing properties necessary for coordinating the two phases of deadenylation. The shorter isoform (Pan3S) interacts more strongly with PABP than the longer isoform (Pan3L) does. Pan2 deadenylase activity is enhanced by Pan3S but suppressed by Pan3L. Knocking down individual Pan3 isoforms has opposing effects on the global poly(A) tail length profile, P-body formation, and different mRNA decay pathways. Transcriptome-wide analysis of Pan3 knockdown effects on mRNA turnover shows that depleting either Pan3 isoform causes profound and extensive changes in mRNA stability globally. These results reveal a new fundamental step governing mammalian mRNA metabolism. We propose that the first phase of deadenylation, coordinated through the interplay among the two Pan3 isoforms, Pan2, and PABP, represents a cytoplasmic mRNA maturation step important for proper mRNA turnover.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yueqiang Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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35
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When mRNA translation meets decay. Biochem Soc Trans 2017; 45:339-351. [DOI: 10.1042/bst20160243] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 12/19/2016] [Accepted: 01/11/2017] [Indexed: 12/26/2022]
Abstract
Messenger RNA (mRNA) translation and mRNA degradation are important determinants of protein output, and they are interconnected. Previously, it was thought that translation of an mRNA, as a rule, prevents its degradation. mRNA surveillance mechanisms, which degrade mRNAs as a consequence of their translation, were considered to be exceptions to this rule. Recently, however, it has become clear that many mRNAs are degraded co-translationally, and it has emerged that codon choice, by influencing the rate of ribosome elongation, affects the rate of mRNA decay. In this review, we discuss the links between translation and mRNA stability, with an emphasis on emerging data suggesting that codon optimality may regulate mRNA degradation.
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36
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Wurth L, Papasaikas P, Olmeda D, Bley N, Calvo GT, Guerrero S, Cerezo-Wallis D, Martinez-Useros J, García-Fernández M, Hüttelmaier S, Soengas MS, Gebauer F. UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis. Cancer Cell 2016; 30:694-707. [PMID: 27908735 DOI: 10.1016/j.ccell.2016.10.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 06/13/2016] [Accepted: 10/03/2016] [Indexed: 12/11/2022]
Abstract
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.
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Affiliation(s)
- Laurence Wurth
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Panagiotis Papasaikas
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Olmeda
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Nadine Bley
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Guadalupe T Calvo
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Daniela Cerezo-Wallis
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Martinez-Useros
- Translational Oncology Division, Oncohealth Institute - Health Research Institute - University Hospital "Fundacion Jimenez Diaz", 28040 Madrid, Spain
| | - María García-Fernández
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Stefan Hüttelmaier
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Maria S Soengas
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M. Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution. Nucleic Acids Res 2016; 45:938-950. [PMID: 27604873 PMCID: PMC5314787 DOI: 10.1093/nar/gkw792] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/22/2016] [Accepted: 08/28/2016] [Indexed: 12/11/2022] Open
Abstract
Our current knowledge about the mechanisms of miRNA silencing is restricted to few lineages such as vertebrates, arthropods, nematodes and land plants. miRNA-mediated silencing in bilaterian animals is dependent on the proteins of the GW182 family. Here, we dissect the function of GW182 protein in the cnidarian Nematostella, separated by 600 million years from other Metazoa. Using cultured human cells, we show that Nematostella GW182 recruits the CCR4-NOT deadenylation complexes via its tryptophan-containing motifs, thereby inhibiting translation and promoting mRNA decay. Further, similarly to bilaterians, GW182 in Nematostella is recruited to the miRNA repression complex via interaction with Argonaute proteins, and functions downstream to repress mRNA. Thus, our work suggests that this mechanism of miRNA-mediated silencing was already active in the last common ancestor of Cnidaria and Bilateria.
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Affiliation(s)
- Marta Mauri
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Marieluise Kirchner
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Reuven Aharoni
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Camilla Ciolli Mattioli
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - David van den Bruck
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Nadya Gutkovitch
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Matthias Selbach
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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38
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Dashti ZJS, Gamieldien J, Christoffels A. Computational characterization of Iron metabolism in the Tsetse disease vector, Glossina morsitans: IRE stem-loops. BMC Genomics 2016; 17:561. [PMID: 27503259 PMCID: PMC4977773 DOI: 10.1186/s12864-016-2932-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/12/2016] [Indexed: 11/29/2022] Open
Abstract
Background Iron metabolism and regulation is an indispensable part of species survival, most importantly for blood feeding insects. Iron regulatory proteins are central regulators of iron homeostasis, whose binding to iron response element (IRE) stem-loop structures within the UTRs of genes regulate expression at the post-transcriptional level. Despite the extensive literature on the mechanism of iron regulation in human, less attention has been given to insect and more specifically the blood feeding insects, where research has mainly focused on the characterization of ferritin and transferrin. We thus, examined the mechanism of iron homeostasis through a genome-wide computational identification of IREs and other enriched motifs in the UTRs of Glossina morsitans with the view to identify new IRE-regulated genes. Results We identified 150 genes, of which two are known to contain IREs, namely the ferritin heavy chain and the MRCK-alpha. The remainder of the identified genes is considered novel including 20 hypothetical proteins, for which an iron-regulatory mechanism of action was inferred. Forty-three genes were found with IRE-signatures of regulation in two or more insects, while 46 were only found to be IRE-regulated in two species. Notably 39 % of the identified genes exclusively shared IRE-signatures in other Glossina species, which are potentially Glossina-specific adaptive measures in addressing its unique reproductive biology and blood meal-induced iron overload. In line with previous findings, we found no evidence pertaining to an IRE regulation of Transferrin, which highlight the importance of ferritin heavy chain and the other proposed transporters in the tsetse fly. In the context of iron-sequestration, key players of tsetse immune defence against trypanosomes have been introduced namely 14 stress and immune response genes, while 28 cell-envelop, transport, and binding genes were assigned a putative role in iron trafficking. Additionally, we identified and annotated enriched motifs in the UTRs of the putative IRE-regulated genes to derive at a co-regulatory network that maintains iron homeostasis in tsetse flies. Three putative microRNA-binding sites namely Gy-box, Brd-box and K-box motifs were identified among the regulatory motifs, enriched in the UTRs of the putative IRE-regulated genes. Conclusion Beyond our current view of iron metabolism in insects, with ferritin and transferrin as its key players, this study provides a comprehensive catalogue of genes with possible roles in the acquisition; transport and storage of iron hence iron homeostasis in the tsetse fly. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2932-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zahra Jalali Sefid Dashti
- South African Medical Research Council Bioinformatics Unit, The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Street, Bellville, South Africa
| | - Junaid Gamieldien
- South African Medical Research Council Bioinformatics Unit, The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Street, Bellville, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Street, Bellville, South Africa.
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Kamenska A, Simpson C, Vindry C, Broomhead H, Bénard M, Ernoult-Lange M, Lee BP, Harries LW, Weil D, Standart N. The DDX6-4E-T interaction mediates translational repression and P-body assembly. Nucleic Acids Res 2016; 44:6318-34. [PMID: 27342281 PMCID: PMC5291280 DOI: 10.1093/nar/gkw565] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
Abstract
4E-Transporter binds eIF4E via its consensus sequence YXXXXLΦ, shared with eIF4G, and is a nucleocytoplasmic shuttling protein found enriched in P-(rocessing) bodies. 4E-T inhibits general protein synthesis by reducing available eIF4E levels. Recently, we showed that 4E-T bound to mRNA however represses its translation in an eIF4E-independent manner, and contributes to silencing of mRNAs targeted by miRNAs. Here, we address further the mechanism of translational repression by 4E-T by first identifying and delineating the interacting sites of its major partners by mass spectrometry and western blotting, including DDX6, UNR, unrip, PAT1B, LSM14A and CNOT4. Furthermore, we document novel binding between 4E-T partners including UNR-CNOT4 and unrip-LSM14A, altogether suggesting 4E-T nucleates a complex network of RNA-binding protein interactions. In functional assays, we demonstrate that joint deletion of two short conserved motifs that bind UNR and DDX6 relieves repression of 4E-T-bound mRNA, in part reliant on the 4E-T-DDX6-CNOT1 axis. We also show that the DDX6-4E-T interaction mediates miRNA-dependent translational repression and de novo P-body assembly, implying that translational repression and formation of new P-bodies are coupled processes. Altogether these findings considerably extend our understanding of the role of 4E-T in gene regulation, important in development and neurogenesis.
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Affiliation(s)
- Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Clare Simpson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Caroline Vindry
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Marianne Bénard
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Michèle Ernoult-Lange
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Benjamin P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Dominique Weil
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
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40
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Abstract
RNA granules are dynamic cellular structures essential for proper gene expression and homeostasis. The two principal types of cytoplasmic RNA granules are stress granules, which contain stalled translation initiation complexes, and processing bodies (P bodies), which concentrate factors involved in mRNA degradation. RNA granules are associated with gene silencing of transcripts; thus, viruses repress RNA granule functions to favor replication. This article discusses the breadth of viral interactions with cytoplasmic RNA granules, focusing on mechanisms that modulate the functions of RNA granules and that typically promote viral replication. Currently, mechanisms for virus manipulation of RNA granules can be loosely grouped into three nonexclusive categories: (a) cleavage of key RNA granule factors, (b) regulation of PKR activation, and (c) co-opting of RNA granule factors for new roles in viral replication. Viral modulation of RNA granules supports productive infection by inhibiting their gene-silencing functions and counteracting their role in linking stress sensing with innate immune activation.
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Affiliation(s)
- Wei-Chih Tsai
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030;
| | - Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030;
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41
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Kleene KC. Position-dependent interactions of Y-box protein 2 (YBX2) with mRNA enable mRNA storage in round spermatids by repressing mRNA translation and blocking translation-dependent mRNA decay. Mol Reprod Dev 2016; 83:190-207. [PMID: 26773323 DOI: 10.1002/mrd.22616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/08/2016] [Indexed: 12/18/2022]
Abstract
Many mRNAs encoding proteins needed for the construction of the specialized organelles of spermatozoa are stored as translationally repressed, free messenger ribonucleoproteins in round spermatids, to be actively translated in elongating and elongated spermatids. The factors that repress translation in round spermatids, however, have been elusive. Two lines of evidence implicate the highly abundant and well-known translational repressor, Y-box protein 2 (YBX2), as a critical factor: First, protamine 1 (Prm1) and sperm-mitochondria cysteine-rich protein (Smcp) mRNAs are prematurely recruited onto polysomes in Ybx2-knockout mouse round spermatids. Second, mutations in 3' untranslated region (3'UTR) cis-elements that abrogate YBX2 binding activate translation of Prm1 and Smcp mRNAs in round spermatids of transgenic mice. The abundance of YBX2 and its affinity for variable sequences, however, raise questions of how YBX2 targets specific mRNAs for repression. Mutations to the Prm1 and Smcp mRNAs in transgenic mice reveal that strong repression in round spermatids requires YBX2 binding sites located near the 3' ends of their 3'UTRs as locating the same sites in upstream positions produce negligible repression. This location-dependence implies that the assembly of repressive complexes is nucleated by adjacent cis-elements that enable cooperative interactions of YBX2 with co-factors. The available data suggest that, in vertebrates, YBX2 has the important role of coordinating the storage of translationally repressed mRNAs in round spermatids by inhibiting translational activity and the degradation of transcripts via translation-dependent deadenylation. These insights should facilitiate future experiments designed to unravel how YBX2 targets mRNAs for repression in round spermatids and how mutations in the YBX2 gene cause infertility in humans. Mol. Reprod. Dev. 83: 190-207, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kenneth C Kleene
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts
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42
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Stimulation of translation by human Unr requires cold shock domains 2 and 4, and correlates with poly(A) binding protein interaction. Sci Rep 2016; 6:22461. [PMID: 26936655 PMCID: PMC4776140 DOI: 10.1038/srep22461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/11/2016] [Indexed: 11/09/2022] Open
Abstract
The RNA binding protein Unr, which contains five cold shock domains, has several specific roles in post-transcriptional control of gene expression. It can act as an activator or inhibitor of translation initiation, promote mRNA turnover, or stabilise mRNA. Its role depends on the mRNA and other proteins to which it binds, which includes cytoplasmic poly(A) binding protein 1 (PABP1). Since PABP1 binds to all polyadenylated mRNAs, and is involved in translation initiation by interaction with eukaryotic translation initiation factor 4G (eIF4G), we investigated whether Unr has a general role in translational control. We found that Unr strongly stimulates translation in vitro, and mutation of cold shock domains 2 or 4 inhibited its translation activity. The ability of Unr and its mutants to stimulate translation correlated with its ability to bind RNA, and to interact with PABP1. We found that Unr stimulated the binding of PABP1 to mRNA, and that Unr was required for the stable interaction of PABP1 and eIF4G in cells. siRNA-mediated knockdown of Unr reduced the overall level of cellular translation in cells, as well as that of cap-dependent and IRES-dependent reporters. These data describe a novel role for Unr in regulating cellular gene expression.
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43
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Identification of Proteins Bound to Dengue Viral RNA In Vivo Reveals New Host Proteins Important for Virus Replication. mBio 2016; 7:e01865-15. [PMID: 26733069 PMCID: PMC4725007 DOI: 10.1128/mbio.01865-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Due to the limited coding capacity of the viral genome and the complexity of the viral life cycle, host cell proteins play essential roles throughout the course of viral infection. Host RNA-binding proteins mediate various aspects of virus replication through their physical interactions with viral RNA. Here we describe a technique designed to identify such interactions in the context of infected cells using UV cross-linking followed by antisense-mediated affinity purification and mass spectrometry. Using this approach, we identified interactions, several of them novel, between host proteins and dengue viral RNA in infected Huh7 cells. Most of these interactions were subsequently validated using RNA immunoprecipitation. Using small interfering RNA (siRNA)-mediated gene silencing, we showed that more than half of these host proteins are likely involved in regulating virus replication, demonstrating the utility of this method in identifying biologically relevant interactions that may not be identified using traditional in vitro approaches. Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Viral RNA molecules physically interact with cellular RNA-binding proteins (RBPs) throughout the course of infection; the identification of such interactions will lead to the elucidation of the molecular mechanisms of virus replication. Until now, the identification of host proteins bound to dengue viral RNA has been accomplished using in vitro strategies. Here, we used a method for the specific purification of dengue viral ribonucleoprotein (RNP) complexes from infected cells and subsequently identified the associated proteins by mass spectrometry. We then validated a functional role for the majority of these proteins in mediating efficient virus replication. This approach has broad relevance to virology and RNA biology, as it could theoretically be used to purify any viral RNP complex of interest.
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Abstract
Unr (upstream of N-ras) is a eukaryotic RNA-binding protein that has a number of roles in the post-transcriptional regulation of gene expression. Originally identified as an activator of internal initiation of picornavirus translation, it has since been shown to act as an activator and inhibitor of cellular translation and as a positive and negative regulator of mRNA stability, regulating cellular processes such as mitosis and apoptosis. The different post-transcriptional functions of Unr depend on the identity of its mRNA and protein partners and can vary with cell type and changing cellular conditions. Recent high-throughput analyses of RNA–protein interactions indicate that Unr binds to a large subset of cellular mRNAs, suggesting that Unr may play a wider role in translational responses to cellular signals than previously thought.
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45
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Lloyd RE. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses. Virology 2015; 479-480:457-74. [PMID: 25818028 PMCID: PMC4426963 DOI: 10.1016/j.virol.2015.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/12/2015] [Accepted: 03/03/2015] [Indexed: 01/18/2023]
Abstract
Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.
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Affiliation(s)
- Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States.
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46
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Lenarcic EM, Ziehr BJ, Moorman NJ. An unbiased proteomics approach to identify human cytomegalovirus RNA-associated proteins. Virology 2015; 481:13-23. [PMID: 25765003 DOI: 10.1016/j.virol.2015.02.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/18/2014] [Accepted: 02/06/2015] [Indexed: 12/13/2022]
Abstract
Post-transcriptional events regulate herpesvirus gene expression, yet few herpesvirus RNA-binding proteins have been identified. We used an unbiased approach coupling oligo(dT) affinity capture with proteomics to identify viral RNA-associated proteins during infection. Using this approach, we identified and confirmed changes in the abundance or activity of two host RNA-associated proteins, DHX9 and DDX3, in cells infected with human cytomegalovirus (HCMV). We also identified and confirmed previously unreported activities for the HCMV US22 and pp71 proteins as RNA-associated viral proteins and confirmed that a known viral RNA-binding protein, pTRS1, associates with RNA in infected cells. Further, we found that HCMV pp71 co-sedimented with polysomes, associated with host and viral RNAs, and stimulated the overall rate of protein synthesis. These results demonstrate that oligo(dT) affinity capture coupled with proteomics provides a rapid and straightforward means to identify RNA-associated viral proteins during infection that may participate in the post-transcriptional control of gene expression.
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Affiliation(s)
- Erik M Lenarcic
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Benjamin J Ziehr
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Nathaniel J Moorman
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States.
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47
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Morelos RM, Ramírez JL, García-Gasca A, Ibarra AM. Expression of the myostatin gene in the adductor muscle of the Pacific lion-paw scallop Nodipecten subnodosus in association with growth and environmental conditions. ACTA ACUST UNITED AC 2015; 323:239-55. [PMID: 25731876 DOI: 10.1002/jez.1914] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 11/07/2014] [Accepted: 12/27/2014] [Indexed: 12/25/2022]
Abstract
The cDNA sequence of the myostatin gene in the Pacific lion-paw Nodipecten subnodosus (Ns-mstn) was characterized, and the temporal expression during grow-out was analyzed for the first time in a scallop. Ns-mstn encodes a 459-amino-acid protein in which two propeptide proteolytic sites were identified, the previously recognized (RSKR) and a second one at position 266-269 aa (RRKR). The alternative furin cleavage site could be related with post-translational processing, or it could be a tissue-specific mechanism for signaling activity. The Ns-mstn transcript was located by in situ hybridization in sarcomeres and around the nucleus of muscle fibers. The temporal expression analysis by qPCR in the adductor muscle showed that Ns-mstn expression was significantly different (P < 0.05) between months during the grow-out period, increasing largely during the summer months when both biomass and muscle weight did not increase or even decreased; muscle fiber size and number were found to decrease significantly. Exogenous and endogenous factors such as high temperature and low food availability, as well as gametogenesis and reproduction, can be associated with the growth pattern and Ns-mstn expression changes. Our results indicate that MSTN is involved in adductor muscle growth regulation in N. subnodosus as it occurs in vertebrate skeletal muscle although Ns-mstn expression in non-muscle organs/tissues suggests additional functions.
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Affiliation(s)
- Rosa M Morelos
- Aquaculture Genetics and Breeding Laboratory, Centro de Investigaciones Biológicas del Noroeste S.C., La Paz, Mexico
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48
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di Masi A, Leboffe L, De Marinis E, Pagano F, Cicconi L, Rochette-Egly C, Lo-Coco F, Ascenzi P, Nervi C. Retinoic acid receptors: from molecular mechanisms to cancer therapy. Mol Aspects Med 2015; 41:1-115. [PMID: 25543955 DOI: 10.1016/j.mam.2014.12.003] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 02/07/2023]
Abstract
Retinoic acid (RA), the major bioactive metabolite of retinol or vitamin A, induces a spectrum of pleiotropic effects in cell growth and differentiation that are relevant for embryonic development and adult physiology. The RA activity is mediated primarily by members of the retinoic acid receptor (RAR) subfamily, namely RARα, RARβ and RARγ, which belong to the nuclear receptor (NR) superfamily of transcription factors. RARs form heterodimers with members of the retinoid X receptor (RXR) subfamily and act as ligand-regulated transcription factors through binding specific RA response elements (RAREs) located in target genes promoters. RARs also have non-genomic effects and activate kinase signaling pathways, which fine-tune the transcription of the RA target genes. The disruption of RA signaling pathways is thought to underlie the etiology of a number of hematological and non-hematological malignancies, including leukemias, skin cancer, head/neck cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer, renal cell carcinoma, pancreatic cancer, liver cancer, glioblastoma and neuroblastoma. Of note, RA and its derivatives (retinoids) are employed as potential chemotherapeutic or chemopreventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. In humans, retinoids reverse premalignant epithelial lesions, induce the differentiation of myeloid normal and leukemic cells, and prevent lung, liver, and breast cancer. Here, we provide an overview of the biochemical and molecular mechanisms that regulate the RA and retinoid signaling pathways. Moreover, mechanisms through which deregulation of RA signaling pathways ultimately impact on cancer are examined. Finally, the therapeutic effects of retinoids are reported.
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Affiliation(s)
- Alessandra di Masi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Loris Leboffe
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Elisabetta De Marinis
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Francesca Pagano
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Laura Cicconi
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS UMR 7104 - Inserm U 964, University of Strasbourg, 1 rue Laurent Fries, BP10142, Illkirch Cedex F-67404, France.
| | - Francesco Lo-Coco
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy.
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, Roma I-00146, Italy.
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100.
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Ciuzan O, Hancock J, Pamfil D, Wilson I, Ladomery M. The evolutionarily conserved multifunctional glycine-rich RNA-binding proteins play key roles in development and stress adaptation. PHYSIOLOGIA PLANTARUM 2015; 153:1-11. [PMID: 25243592 DOI: 10.1111/ppl.12286] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/11/2014] [Accepted: 08/20/2014] [Indexed: 05/24/2023]
Abstract
The class IV glycine-rich RNA-binding proteins are a distinct subgroup within the heterogenous superfamily of glycine-rich proteins (GRPs). They are distinguished by the presence of an RNA-binding domain in the N-terminus; generally in the form of an RNA-recognition motif (RRM) or a cold-shock domain (CSD). These are followed by a C-terminal glycine-rich domain. Growing evidence suggests that these proteins play key roles in the adaptation of organisms to biotic and abiotic stresses including those resulting from pathogenesis, alterations in the osmotic, saline and oxidative environment and changes in temperature. Similar vertebrate proteins are also cold-induced and involved in, e.g. hibernation, suggesting evolutionarily conserved functions. The class IV RNA-binding GRPs are likely to operate as key molecular components of hormonally regulated development and to work by regulating gene expression at multiple levels by modifying alternative splicing, mRNA export, mRNA translation and mRNA degradation.
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Affiliation(s)
- Oana Ciuzan
- University of Agricultural Science and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, 400372, Romania; Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, D-33615, Germany
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Eliseeva IA, Lyabin DN, Ovchinnikov LP. Poly(A)-binding proteins: structure, domain organization, and activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1377-91. [PMID: 24490729 DOI: 10.1134/s0006297913130014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA interactions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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