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Rosario R, Stewart HL, Choudhury NR, Michlewski G, Charlet‐Berguerand N, Anderson RA. Evidence for a fragile X messenger ribonucleoprotein 1 (FMR1) mRNA gain-of-function toxicity mechanism contributing to the pathogenesis of fragile X-associated premature ovarian insufficiency. FASEB J 2022; 36:e22612. [PMID: 36250920 PMCID: PMC9828574 DOI: 10.1096/fj.202200468rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/22/2022] [Accepted: 10/03/2022] [Indexed: 01/12/2023]
Abstract
Fragile X-associated premature ovarian insufficiency (FXPOI) is among a family of disorders caused by expansion of a CGG trinucleotide repeat sequence located in the 5' untranslated region (UTR) of the fragile X messenger ribonucleoprotein 1 (FMR1) gene on the X chromosome. Women with FXPOI have a depleted ovarian follicle population, resulting in amenorrhea, hypoestrogenism, and loss of fertility before the age of 40. FXPOI is caused by expansions of the CGG sequence to lengths between 55 and 200 repeats, known as a FMRI premutation, however the mechanism by which the premutation drives disease pathogenesis remains unclear. Two main hypotheses exist, which describe an mRNA toxic gain-of-function mechanism or a protein-based mechanism, where repeat-associated non-AUG (RAN) translation results in the production of an abnormal protein, called FMRpolyG. Here, we have developed an in vitro granulosa cell model of the FMR1 premutation by ectopically expressing CGG-repeat RNA and FMRpolyG protein. We show that expanded CGG-repeat RNA accumulated in intranuclear RNA structures, and these aggregates were able to cause significant granulosa cell death independent of FMRpolyG expression. Using an innovative RNA pulldown, mass spectrometry-based approach we have identified proteins that are specifically sequestered by CGG RNA aggregates in granulosa cells in vitro, and thus may be deregulated as consequence of this interaction. Furthermore, we have demonstrated reduced expression of three proteins identified via our RNA pulldown (FUS, PA2G4 and TRA2β) in ovarian follicles in a FMR1 premutation mouse model. Collectively, these data provide evidence for the contribution of an mRNA gain-of-function mechanism to FXPOI disease biology.
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Affiliation(s)
- Roseanne Rosario
- MRC Centre for Reproductive Health, Queen's Medical Research InstituteUniversity of EdinburghEdinburghUK,Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Hazel L. Stewart
- MRC Centre for Reproductive Health, Queen's Medical Research InstituteUniversity of EdinburghEdinburghUK
| | | | - Gracjan Michlewski
- Infection MedicineUniversity of EdinburghEdinburghUK,Zhejiang University‐University of Edinburgh InstituteZhejiang UniversityZhejiangP.R. China,Dioscuri Centre for RNA‐Protein Interactions in Human Health and DiseaseInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Nicholas Charlet‐Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)INSERM U 1258, CNRS UMR 7104, Université of StrasbourgIllkirchFrance
| | - Richard A. Anderson
- MRC Centre for Reproductive Health, Queen's Medical Research InstituteUniversity of EdinburghEdinburghUK
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2
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Vaishali, Dimitrova-Paternoga L, Haubrich K, Sun M, Ephrussi A, Hennig J. Validation and classification of RNA binding proteins identified by mRNA interactome capture. RNA (NEW YORK, N.Y.) 2021; 27:1173-1185. [PMID: 34215685 PMCID: PMC8456996 DOI: 10.1261/rna.078700.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
RNA binding proteins (RBPs) take part in all steps of the RNA life cycle and are often essential for cell viability. Most RBPs have a modular organization and comprise a set of canonical RNA binding domains. However, in recent years a number of high-throughput mRNA interactome studies on yeast, mammalian cell lines, and whole organisms have uncovered a multitude of novel mRNA interacting proteins that lack classical RNA binding domains. Whereas a few have been confirmed to be direct and functionally relevant RNA binders, biochemical and functional validation of RNA binding of most others is lacking. In this study, we used a combination of NMR spectroscopy and biochemical studies to test the RNA binding properties of six putative RBPs. Half of the analyzed proteins showed no interaction, whereas the other half displayed weak chemical shift perturbations upon titration with RNA. One of the candidates we found to interact weakly with RNA in vitro is Drosophila melanogaster end binding protein 1 (EB1), a master regulator of microtubule plus-end dynamics. Further analysis showed that EB1's RNA binding occurs on the same surface as that with which EB1 interacts with microtubules. RNA immunoprecipitation and colocalization experiments suggest that EB1 is a rather nonspecific, opportunistic RNA binder. Our data suggest that care should be taken when embarking on an RNA binding study involving these unconventional, novel RBPs, and we recommend initial and simple in vitro RNA binding experiments.
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Affiliation(s)
- Vaishali
- Developmental Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany
| | - Lyudmila Dimitrova-Paternoga
- Developmental Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
- Structural and Computational Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Kevin Haubrich
- Structural and Computational Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Mai Sun
- Genome Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
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3
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Zhu S, Choudhury NR, Rooney S, Pham NT, Koszela J, Kelly D, Spanos C, Rappsilber J, Auer M, Michlewski G. RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels. Nucleic Acids Res 2021; 49:6456-6473. [PMID: 34107032 PMCID: PMC8216281 DOI: 10.1093/nar/gkab484] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
RNA-protein interactions are central to all gene expression processes and contribute to a variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as 'incurable'. Here, we developed a fluorescent on-bead screening platform, RNA Pull-Down COnfocal NAnoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7's primary target is an mRNA of α-synuclein, which contributes to the aetiology of Parkinson's disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of α-synuclein. This opens up new therapeutic avenues towards treatment of Parkinson's disease as well as provides a novel methodology to search for modulators of RNA-protein interaction.
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Affiliation(s)
- Siran Zhu
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Nila Roy Choudhury
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Saul Rooney
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Nhan T Pham
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Joanna Koszela
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - David Kelly
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Christos Spanos
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Juri Rappsilber
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Manfred Auer
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Gracjan Michlewski
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, P.R. China
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4
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Guo F, Xing L. RNA helicase A as co-factor for DNA viruses during replication. Virus Res 2020; 291:198206. [PMID: 33132162 DOI: 10.1016/j.virusres.2020.198206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022]
Abstract
RNA helicase A (RHA) is a ubiquitously expressed DExH-box helicase enzyme that is involved in a wide range of biological processes including transcription, translation, and RNA processing. A number of RNA viruses recruit RHA to the viral RNA to facilitate virus replication. DNA viruses contain a DNA genome and replicate using a DNA-dependent DNA polymerase. RHA has also been reported to associate with some DNA viruses during replication, in which the enzyme acts on the viral RNA or protein products. As shown for Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, RHA has potential to allow the virus to control a switch in cellular gene expression to modulate the antiviral response. While the study of the interaction of RHA with DNA viruses is still at an early stage, preliminary evidence indicates that the underlying molecular mechanisms are diverse. We now review the current status of this emerging field.
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Affiliation(s)
- Fan Guo
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, PR China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, PR China.
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Sajini AA, Choudhury NR, Wagner RE, Bornelöv S, Selmi T, Spanos C, Dietmann S, Rappsilber J, Michlewski G, Frye M. Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat Commun 2019; 10:2550. [PMID: 31186410 PMCID: PMC6560067 DOI: 10.1038/s41467-019-10020-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/09/2019] [Indexed: 12/20/2022] Open
Abstract
The presence and absence of RNA modifications regulates RNA metabolism by modulating the binding of writer, reader, and eraser proteins. For 5-methylcytosine (m5C) however, it is largely unknown how it recruits or repels RNA-binding proteins. Here, we decipher the consequences of m5C deposition into the abundant non-coding vault RNA VTRNA1.1. Methylation of cytosine 69 in VTRNA1.1 occurs frequently in human cells, is exclusively mediated by NSUN2, and determines the processing of VTRNA1.1 into small-vault RNAs (svRNAs). We identify the serine/arginine rich splicing factor 2 (SRSF2) as a novel VTRNA1.1-binding protein that counteracts VTRNA1.1 processing by binding the non-methylated form with higher affinity. Both NSUN2 and SRSF2 orchestrate the production of distinct svRNAs. Finally, we discover a functional role of svRNAs in regulating the epidermal differentiation programme. Thus, our data reveal a direct role for m5C in the processing of VTRNA1.1 that involves SRSF2 and is crucial for efficient cellular differentiation.
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Affiliation(s)
- Abdulrahim A Sajini
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, P.O. Box 71491, Saudi Arabia
| | - Nila Roy Choudhury
- Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Rebecca E Wagner
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Susanne Bornelöv
- Wellcome MRC Cambridge Stem Cell Institute, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Tommaso Selmi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Sabine Dietmann
- Wellcome MRC Cambridge Stem Cell Institute, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK.
- ZJU-UoE Institute, Zhejiang University, 718 East Haizhou Road, Haining, Zhejiang, 314400, P.R. China.
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- German Cancer Research Centre (Deutsches Krebsforschungszentrum, DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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7
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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8
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Downie Ruiz Velasco A, Welten SMJ, Goossens EAC, Quax PHA, Rappsilber J, Michlewski G, Nossent AY. Posttranscriptional Regulation of 14q32 MicroRNAs by the CIRBP and HADHB during Vascular Regeneration after Ischemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 14:329-338. [PMID: 30665182 PMCID: PMC6350214 DOI: 10.1016/j.omtn.2018.11.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022]
Abstract
After induction of ischemia in mice, 14q32 microRNAs are regulated in three distinct temporal patterns. These expression patterns, as well as basal expression levels, are independent of the microRNA genes’ order in the 14q32 locus. This implies that posttranscriptional processing is a major determinant of 14q32 microRNA expression. Therefore, we hypothesized that RNA binding proteins (RBPs) regulate posttranscriptional processing of 14q32, and we aimed to identify these RBPs. To identify proteins responsible for this posttranscriptional regulation, we used RNA pull-down SILAC mass spectrometry (RP-SMS) on selected precursor microRNAs. We observed differential binding of cold-inducible RBP (CIRBP) and hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta (HADHB) to the precursors of late-upregulated miR-329-3p and unaffected miR-495-3p. Immunohistochemical staining confirmed expression of both CIRBP and HADHB in the adductor muscle of mice. Expression of both CIRBP and HADHB was upregulated after hindlimb ischemia in mice. Using RBP immunoprecipitation experiments, we showed specific binding of CIRBP to pre-miR-329 but not to pri-miR-329. Finally, using CRISPR/Cas9, we generated HADHB−/− 3T3 cells, which display reduced expression of miR-329 and miR-495 but not their precursors. These data suggest a novel role for CIRBP and HADHB in posttranscriptional regulation of 14q32 microRNAs.
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Affiliation(s)
- Angela Downie Ruiz Velasco
- Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, Edinburgh, UK; The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Sabine M J Welten
- Department of Surgery, Leiden University Medical, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical, Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, Leiden University Medical, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical, Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical, Leiden, the Netherlands
| | - Juri Rappsilber
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, Edinburgh, UK; The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Zhejiang University - University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, P.R. China.
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical, Leiden, the Netherlands; Ludwig Boltzmann Cluster for Cardiovascular Research, Vienna, Austria.
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