1
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Sharma S, Kajjo S, Harra Z, Hasaj B, Delisle V, Ray D, Gutierrez RL, Carrier I, Kleinman C, Morris Q, Hughes TR, McInnes R, Fabian MR. Uncovering a mammalian neural-specific poly(A) binding protein with unique properties. Genes Dev 2023; 37:760-777. [PMID: 37704377 PMCID: PMC10546976 DOI: 10.1101/gad.350597.123] [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: 03/03/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
The mRNA 3' poly(A) tail plays a critical role in regulating both mRNA translation and turnover. It is bound by the cytoplasmic poly(A) binding protein (PABPC), an evolutionarily conserved protein that can interact with translation factors and mRNA decay machineries to regulate gene expression. Mammalian PABPC1, the prototypical PABPC, is expressed in most tissues and interacts with eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation in specific contexts. In this study, we uncovered a new mammalian PABPC, which we named neural PABP (neuPABP), as it is predominantly expressed in the brain. neuPABP maintains a unique architecture as compared with other PABPCs, containing only two RNA recognition motifs (RRMs) and maintaining a unique N-terminal domain of unknown function. neuPABP expression is activated in neurons as they mature during synaptogenesis, where neuPABP localizes to the soma and postsynaptic densities. neuPABP interacts with the noncoding RNA BC1, as well as mRNAs coding for ribosomal and mitochondrial proteins. However, in contrast to PABPC1, neuPABP does not associate with actively translating mRNAs in the brain. In keeping with this, we show that neuPABP has evolved such that it does not bind eIF4G and as a result fails to support protein synthesis in vitro. Taken together, these results indicate that mammals have expanded their PABPC repertoire in the brain and propose that neuPABP may support the translational repression of select mRNAs.
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Affiliation(s)
- Sahil Sharma
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Sam Kajjo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Zineb Harra
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Benedeta Hasaj
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Victoria Delisle
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Rodrigo L Gutierrez
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Isabelle Carrier
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Claudia Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Quaid Morris
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Roderick McInnes
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada;
- Department of Biochemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Oncology, McGill University, Montreal, Quebec H3A 0G4, Canada
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2
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Muslimov IA, Berardi V, Stephenson S, Ginzler EM, Hanly JG, Tiedge H. Autoimmune RNA dysregulation and seizures: therapeutic prospects in neuropsychiatric lupus. Life Sci Alliance 2022; 5:5/12/e202201496. [PMID: 36229064 PMCID: PMC9559755 DOI: 10.26508/lsa.202201496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Lupus autoimmunity frequently presents with neuropsychiatric manifestations, but underlying etiology remains poorly understood. Human brain cytoplasmic 200 RNA (BC200 RNA) is a translational regulator in neuronal synapto-dendritic domains. Here, we show that a BC200 guanosine-adenosine dendritic transport motif is recognized by autoantibodies from a subset of neuropsychiatric lupus patients. These autoantibodies impact BC200 functionality by quasi irreversibly displacing two RNA transport factors from the guanosine-adenosine transport motif. Such anti-BC autoantibodies, which can gain access to brains of neuropsychiatric lupus patients, give rise to clinical manifestations including seizures. To establish causality, naive mice with a permeabilized blood-brain barrier were injected with anti-BC autoantibodies from lupus patients with seizures. Animals so injected developed seizure susceptibility with high mortality. Seizure activity was entirely precluded when animals were injected with lupus anti-BC autoantibodies together with BC200 decoy autoantigen. Seizures are a common clinical manifestation in neuropsychiatric lupus, and our work identifies anti-BC autoantibody activity as a mechanistic cause. The results demonstrate potential utility of BC200 decoys for autoantibody-specific therapeutic interventions in neuropsychiatric lupus.
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Affiliation(s)
- Ilham A Muslimov
- Department of Physiology and Pharmacology, The Robert F Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Correspondence: ;
| | - Valerio Berardi
- Department of Physiology and Pharmacology, The Robert F Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Stacy Stephenson
- Division of Comparative Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Ellen M Ginzler
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - John G Hanly
- Division of Rheumatology, Department of Medicine, Department of Pathology, Queen Elizabeth II Health Sciences Center and Dalhousie University, Halifax, Canada
| | - Henri Tiedge
- Department of Physiology and Pharmacology, The Robert F Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Department of Neurology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Correspondence: ;
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3
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Aleshkina D, Iyyappan R, Lin CJ, Masek T, Pospisek M, Susor A. ncRNA BC1 influences translation in the oocyte. RNA Biol 2021; 18:1893-1904. [PMID: 33491548 PMCID: PMC8583082 DOI: 10.1080/15476286.2021.1880181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 01/06/2023] Open
Abstract
Regulation of translation is essential for the diverse biological processes involved in development. Particularly, mammalian oocyte development requires the precisely controlled translation of maternal transcripts to coordinate meiotic and early embryo progression while transcription is silent. It has been recently reported that key components of mRNA translation control are short and long noncoding RNAs (ncRNAs). We found that the ncRNABrain cytoplasmic 1 (BC1) has a role in the fully grown germinal vesicle (GV) mouse oocyte, where is highly expressed in the cytoplasm associated with polysomes. Overexpression of BC1 in GV oocyte leads to a minute decrease in global translation with a significant reduction of specific mRNA translation via interaction with the Fragile X Mental Retardation Protein (FMRP). BC1 performs a repressive role in translation only in the GV stage oocyte without forming FMRP or Poly(A) granules. In conclusion, BC1 acts as the translational repressor of specific mRNAs in the GV stage via its binding to a subset of mRNAs and physical interaction with FMRP. The results reported herein contribute to the understanding of the molecular mechanisms of developmental events connected with maternal mRNA translation.
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Affiliation(s)
- D. Aleshkina
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - R. Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Ch. J. Lin
- MRC Centre for Reproductive Health, The University of Edinburgh, Edinburgh, UK
| | - T. Masek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - M. Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - A. Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
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4
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Jang S, Shin H, Lee Y. Functional Analysis of RNA Motifs Essential for BC200 RNA-mediated Translational Regulation. BMB Rep 2020. [PMID: 31234958 PMCID: PMC7061212 DOI: 10.5483/bmbrep.2020.53.2.153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA) is proposed to act as a local translational modulator by inhibiting translation after being targeted to neuronal dendrites. However, the mechanism by which BC200 RNA inhibits translation is not fully understood. Although a detailed functional analysis of RNA motifs is essential for understanding the BC200 RNA-mediated translation-inhibition mechanism, there is little relevant research on the subject. Here, we performed a systematic domain-dissection analysis of BC200 RNA to identify functional RNA motifs responsible for its translational-inhibition activity. Various RNA variants were assayed for their ability to inhibit translation of luciferase mRNA in vitro. We found that the 111–200-nucleotide region consisting of part of the Alu domain as well as the A/C-rich domain (consisting of both the A-rich and C-rich domains) is most effective for translation inhibition. Surprisingly, we also found that individual A-rich, A/C-rich, and Alu domains can enhance translation but at different levels for each domain, and that these enhancing effects manifest as cap-dependent translation.
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Affiliation(s)
- Seonghui Jang
- Department of Chemistry, KAIST, Daejeon 34141, Korea
- Korea Food Research Institute, Wanju 55365, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea
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5
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Brain Cytoplasmic RNAs in Neurons: From Biosynthesis to Function. Biomolecules 2020; 10:biom10020313. [PMID: 32079202 PMCID: PMC7072442 DOI: 10.3390/biom10020313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
Flexibility in signal transmission is essential for high-level brain function. This flexibility is achieved through strict spatial and temporal control of gene expression in neurons. Given the key regulatory roles of a variety of noncoding RNAs (ncRNAs) in neurons, studying neuron-specific ncRNAs provides an important basis for understanding molecular principles of brain function. This approach will have wide use in understanding the pathogenesis of brain diseases and in the development of therapeutic agents in the future. Brain cytoplasmic RNAs (BC RNAs) are a leading paradigm for research on neuronal ncRNAs. Since the first confirmation of brain-specific expression of BC RNAs in 1982, their investigation has been an area of active research. In this review, we summarize key studies on the characteristics and functions of BC RNAs in neurons.
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6
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Neuronal BC RNA Transport Impairments Caused by Systemic Lupus Erythematosus Autoantibodies. J Neurosci 2019; 39:7759-7777. [PMID: 31405929 DOI: 10.1523/jneurosci.1657-18.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 05/02/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
The etiology of the autoimmune disorder systemic lupus erythematosus (SLE) remains poorly understood. In neuropsychiatric SLE (NPSLE), autoimmune responses against neural self-antigens find expression in neurological and cognitive alterations. SLE autoantibodies often target nucleic acids, including RNAs and specifically RNA domains with higher-order structural content. We report that autoantibodies directed against neuronal regulatory brain cytoplasmic (BC) RNAs were generated in a subset of SLE patients. By contrast, anti-BC RNA autoantibodies (anti-BC abs) were not detected in sera from patients with autoimmune diseases other than SLE (e.g., rheumatoid arthritis or multiple sclerosis) or in sera from healthy subjects with no evidence of disease. SLE anti-BC abs belong to the IgG class of immunoglobulins and target both primate BC200 RNA and rodent BC1 RNA. They are specifically directed at architectural motifs in BC RNA 5' stem-loop domains that serve as dendritic targeting elements (DTEs). SLE anti-BC abs effectively compete with RNA transport factor heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2) for DTE access and significantly diminish BC RNA delivery to synapto-dendritic sites of function. In vivo experiments with male BALB/c mice indicate that, upon lipopolysaccharide-induced opening of the blood-brain barrier, SLE anti-BC abs are taken up by CNS neurons where they significantly impede localization of endogenous BC1 RNA to synapto-dendritic domains. Lack of BC1 RNA causes phenotypic abnormalities including epileptogenic responses and cognitive dysfunction. The combined data indicate a role for anti-BC RNA autoimmunity in SLE and its neuropsychiatric manifestations.SIGNIFICANCE STATEMENT Although clinical manifestations of neuropsychiatric lupus are well recognized, the underlying molecular-cellular alterations have been difficult to determine. We report that sera of a subset of lupus patients contain autoantibodies directed at regulatory brain cytoplasmic (BC) RNAs. These antibodies, which we call anti-BC abs, target the BC RNA 5' domain noncanonical motif structures that specify dendritic delivery. Lupus anti-BC abs effectively compete with RNA transport factor heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2) for access to BC RNAs. As a result, hnRNP A2 is displaced, and BC RNAs are impaired in their ability to reach synapto-dendritic sites of function. The results reveal an unexpected link between BC RNA autoantibody recognition and dendritic RNA targeting. Cellular RNA dysregulation may thus be a contributing factor in the pathogenesis of neuropsychiatric lupus.
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7
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Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation. Biochem J 2018; 475:2727-2748. [PMID: 30072491 DOI: 10.1042/bcj20180239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 11/17/2022]
Abstract
Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.
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8
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Samson J, Cronin S, Dean K. BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer. Noncoding RNA Res 2018; 3:131-143. [PMID: 30175286 PMCID: PMC6114260 DOI: 10.1016/j.ncrna.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022] Open
Abstract
With the discovery that the level of RNA synthesis in human cells far exceeds what is required to express protein-coding genes, there has been a concerted scientific effort to identify, catalogue and uncover the biological functions of the non-coding transcriptome. Long, non-coding RNAs (lncRNAs) are a diverse group of RNAs with equally wide-ranging biological roles in the cell. An increasing number of studies have reported alterations in the expression of lncRNAs in various cancers, although unravelling how they contribute specifically to the disease is a bigger challenge. Originally described as a brain-specific, non-coding RNA, BC200 (BCYRN1) is a 200-nucleotide, predominantly cytoplasmic lncRNA that has been linked to neurodegenerative disease and several types of cancer. Here we summarise what is known about BC200, primarily from studies in neuronal systems, before turning to a review of recent work that aims to understand how this lncRNA contributes to cancer initiation, progression and metastasis, along with its possible clinical utility as a biomarker or therapeutic target.
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Affiliation(s)
| | | | - K. Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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9
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Cawez F, Duray E, Hu Y, Vandenameele J, Romão E, Vincke C, Dumoulin M, Galleni M, Muyldermans S, Vandevenne M. Combinatorial Design of a Nanobody that Specifically Targets Structured RNAs. J Mol Biol 2018; 430:1652-1670. [PMID: 29654796 DOI: 10.1016/j.jmb.2018.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/08/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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10
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Muslimov IA, Eom T, Iacoangeli A, Chuang SC, Hukema RK, Willemsen R, Stefanov DG, Wong RKS, Tiedge H. BC RNA Mislocalization in the Fragile X Premutation. eNeuro 2018; 5:ENEURO.0091-18.2018. [PMID: 29766042 PMCID: PMC5952321 DOI: 10.1523/eneuro.0091-18.2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Fragile X premutation disorder is caused by CGG triplet repeat expansions in the 5' untranslated region of FMR1 mRNA. The question of how expanded CGG repeats cause disease is a subject of continuing debate. Our work indicates that CGG-repeat structures compete with regulatory BC1 RNA for access to RNA transport factor hnRNP A2. As a result, BC1 RNA is mislocalized in vivo, as its synapto-dendritic presence is severely diminished in brains of CGG-repeat knock-in animals (a premutation mouse model). Lack of BC1 RNA is known to cause seizure activity and cognitive dysfunction. Our working hypothesis thus predicted that absence, or significantly reduced presence, of BC1 RNA in synapto-dendritic domains of premutation animal neurons would engender cognate phenotypic alterations. Testing this prediction, we established epileptogenic susceptibility and cognitive impairments as major phenotypic abnormalities of CGG premutation mice. In CA3 hippocampal neurons of such animals, synaptic release of glutamate elicits neuronal hyperexcitability in the form of group I metabotropic glutamate receptor-dependent prolonged epileptiform discharges. CGG-repeat knock-in animals are susceptible to sound-induced seizures and are cognitively impaired as revealed in the Attentional Set Shift Task. These phenotypic disturbances occur in young-adult premutation animals, indicating that a neurodevelopmental deficit is an early-initial manifestation of the disorder. The data are consistent with the notion that RNA mislocalization can contribute to pathogenesis.
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Affiliation(s)
- Ilham A. Muslimov
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Taesun Eom
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Anna Iacoangeli
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Shih-Chieh Chuang
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Renate K. Hukema
- Department of Clinical Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Dimitre G. Stefanov
- Statistical Design and Analysis, Research Division, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Robert K. S. Wong
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
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11
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Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1. Sci Rep 2018; 8:3189. [PMID: 29453387 PMCID: PMC5816658 DOI: 10.1038/s41598-017-14908-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022] Open
Abstract
Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases. Here we present the secondary structure of the SINE B2 Transposable Element (TE) embedded in AS Uchl1. We find that specific structural regions, containing a short hairpin, are required for the ability of AS Uchl1 RNA to increase translation of its target mRNA. We also provide a high-resolution structure of the relevant hairpin, based on NMR observables. Our results highlight the importance of structural determinants in embedded TEs for their activity as functional domains in lncRNAs.
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12
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SMORE: Synteny Modulator of Repetitive Elements. Life (Basel) 2017; 7:life7040042. [PMID: 29088079 PMCID: PMC5745555 DOI: 10.3390/life7040042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 12/19/2022] Open
Abstract
Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available.
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13
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Maraia RJ, Arimbasseri AG. Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon-Codon Use. Biomolecules 2017; 7:biom7010026. [PMID: 28282871 PMCID: PMC5372738 DOI: 10.3390/biom7010026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/24/2017] [Indexed: 01/24/2023] Open
Abstract
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias. Here, we review convergent evidence that suggest that expansion of the eukaryotic tRNAome was supported by its dedicated RNA polymerase III transcription system and coupling to the precursor-tRNA chaperone, La protein. We also review aspects of eukaryotic tRNAome evolution involving G34/A34 anticodon-sparing, relation to A34 modification to inosine, biased codon use and regulatory information in the redundancy (synonymous) component of the genetic code. We then review interdependent anticodon loop modifications involving position 37 in eukaryotes. This includes the eukaryote-specific tRNA modification, 3-methylcytidine-32 (m3C32) and the responsible gene, TRM140 and homologs which were duplicated and subspecialized for isoacceptor-specific substrates and dependence on i6A37 or t6A37. The genetics of tRNA function is relevant to health directly and as disease modifiers.
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Affiliation(s)
- Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, 20016, USA.
| | - Aneeshkumar G Arimbasseri
- Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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14
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Shin H, Lee J, Kim Y, Jang S, Lee Y, Kim S, Lee Y. Knockdown of BC200 RNA expression reduces cell migration and invasion by destabilizing mRNA for calcium-binding protein S100A11. RNA Biol 2017; 14:1418-1430. [PMID: 28277927 DOI: 10.1080/15476286.2017.1297913] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Although BC200 RNA is best known as a neuron-specific non-coding RNA, it is overexpressed in various cancer cells. BC200 RNA was recently shown to contribute to metastasis in several cancer cell lines, but the underlying mechanism was not understood in detail. To examine this mechanism, we knocked down BC200 RNA in cancer cells, which overexpress the RNA, and examined cell motility, profiling of ribosome footprints, and the correlation between cell motility changes and genes exhibiting altered ribosome profiles. We found that BC200 RNA knockdown reduced cell migration and invasion, suggesting that BC200 RNA promotes cell motility. Our ribosome profiling analysis identified 29 genes whose ribosomal occupations were altered more than 2-fold by BC200 RNA knockdown. Many (> 30%) of them were directly or indirectly related to cancer progression. Among them, we focused on S100A11 (which showed a reduced ribosome footprint) because its expression was previously shown to increase cellular motility. S100A11 was decreased at both the mRNA and protein levels following knockdown of BC200 RNA. An actinomycin-chase experiment showed that BC200 RNA knockdown significantly decreased the stability of the S100A11 mRNA without changing its transcription rate, suggesting that the downregulation of S100A11 was mainly caused by destabilization of its mRNA. Finally, we showed that the BC200 RNA-knockdown-induced decrease in cell motility was mainly mediated by S100A11. Together, our results show that BC200 RNA promotes cell motility by stabilizing S100A11 transcripts.
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Affiliation(s)
- Heegwon Shin
- a Department of Chemistry , KAIST , Daejeon , Korea
| | - Jungmin Lee
- a Department of Chemistry , KAIST , Daejeon , Korea
| | - Youngmi Kim
- a Department of Chemistry , KAIST , Daejeon , Korea
| | | | - Yunhee Lee
- a Department of Chemistry , KAIST , Daejeon , Korea.,b Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon , Korea
| | - Semi Kim
- a Department of Chemistry , KAIST , Daejeon , Korea.,b Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon , Korea
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15
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Schein A, Zucchelli S, Kauppinen S, Gustincich S, Carninci P. Identification of antisense long noncoding RNAs that function as SINEUPs in human cells. Sci Rep 2016; 6:33605. [PMID: 27646849 PMCID: PMC5028707 DOI: 10.1038/srep33605] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/30/2016] [Indexed: 01/04/2023] Open
Abstract
Mammalian genomes encode numerous natural antisense long noncoding RNAs (lncRNAs) that regulate gene expression. Recently, an antisense lncRNA to mouse Ubiquitin carboxyl-terminal hydrolase L1 (Uchl1) was reported to increase UCHL1 protein synthesis, representing a new functional class of lncRNAs, designated as SINEUPs, for SINE element-containing translation UP-regulators. Here, we show that an antisense lncRNA to the human protein phosphatase 1 regulatory subunit 12A (PPP1R12A), named as R12A-AS1, which overlaps with the 5′ UTR and first coding exon of the PPP1R12A mRNA, functions as a SINEUP, increasing PPP1R12A protein translation in human cells. The SINEUP activity depends on the aforementioned sense-antisense interaction and a free right Alu monomer repeat element at the 3′ end of R12A-AS1. In addition, we identify another human antisense lncRNA with SINEUP activity. Our results demonstrate for the first time that human natural antisense lncRNAs can up-regulate protein translation, suggesting that endogenous SINEUPs may be widespread and present in many mammalian species.
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Affiliation(s)
- Aleks Schein
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan.,Center for RNA Medicine, Department of Clinical Medicine, Aalborg University Campus Copenhagen, Copenhagen 2450 Denmark
| | - Silvia Zucchelli
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience, Trieste, Italy.,Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University Campus Copenhagen, Copenhagen 2450 Denmark
| | - Stefano Gustincich
- Scuola Internazionale Superiore di Studi Avanzati, Area of Neuroscience, Trieste, Italy.,Department of Neuroscience and Brain Technologies, Italian Institute of Technology, Genova, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
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16
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BC1 RNA motifs required for dendritic transport in vivo. Sci Rep 2016; 6:28300. [PMID: 27350115 PMCID: PMC4923876 DOI: 10.1038/srep28300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/20/2016] [Indexed: 12/26/2022] Open
Abstract
BC1 RNA is a small brain specific non-protein coding RNA. It is transported from the cell body into dendrites where it is involved in the fine-tuning translational control. Due to its compactness and established secondary structure, BC1 RNA is an ideal model for investigating the motifs necessary for dendritic localization. Previously, microinjection of in vitro transcribed BC1 RNA mutants into the soma of cultured primary neurons suggested the importance of RNA motifs for dendritic targeting. These ex vivo experiments identified a single bulged nucleotide (U22) and a putative K-turn (GA motif) structure required for dendritic localization or distal transport, respectively. We generated six transgenic mouse lines (three founders each) containing neuronally expressing BC1 RNA variants on a BC1 RNA knockout mouse background. In contrast to ex vivo data, we did not find indications of reduction or abolition of dendritic BC1 RNA localization in the mutants devoid of the GA motif or the bulged nucleotide. We confirmed the ex vivo data, which showed that the triloop terminal sequence had no consequence on dendritic transport. Interestingly, changing the triloop supporting structure completely abolished dendritic localization of BC1 RNA. We propose a novel RNA motif important for dendritic transport in vivo.
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17
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Vicario A, Colliva A, Ratti A, Davidovic L, Baj G, Gricman Ł, Colombrita C, Pallavicini A, Jones KR, Bardoni B, Tongiorgi E. Dendritic targeting of short and long 3' UTR BDNF mRNA is regulated by BDNF or NT-3 and distinct sets of RNA-binding proteins. Front Mol Neurosci 2015; 8:62. [PMID: 26578876 PMCID: PMC4624863 DOI: 10.3389/fnmol.2015.00062] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022] Open
Abstract
Sorting of mRNAs in neuronal dendrites relies upon inducible transport mechanisms whose molecular bases are poorly understood. We investigated here the mechanism of inducible dendritic targeting of rat brain-derived neurotrophic factor (BDNF) mRNAs as a paradigmatic example. BDNF encodes multiple mRNAs with either short or long 3' UTR, both hypothesized to harbor inducible dendritic targeting signals. However, the mechanisms of sorting of the two 3' UTR isoforms are controversial. We found that dendritic localization of BDNF mRNAs with short 3' UTR was induced by depolarization and NT3 in vitro or by seizures in vivo and required CPEB-1, -2 and ELAV-2, -4. Dendritic targeting of long 3' UTR was induced by activity or BDNF and required CPEB-1 and the relief of soma-retention signals mediated by ELAV-1, -3, -4, and FXR proteins. Thus, long and short 3' UTRs, by using different sets of RNA-binding proteins provide a mechanism of selective targeting in response to different stimuli which may underlay distinct roles of BDNF variants in neuronal development and plasticity.
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Affiliation(s)
- Annalisa Vicario
- Department of Life Sciences, University of Trieste Trieste, Italy
| | - Andrea Colliva
- Department of Life Sciences, University of Trieste Trieste, Italy
| | - Antonia Ratti
- Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano Milano, Italy ; Department of Pathophysiology and Transplantation, "Dino Ferrari Center", Università degli Studi di Milano Milano, Italy
| | | | - Gabriele Baj
- Department of Life Sciences, University of Trieste Trieste, Italy
| | - Łukasz Gricman
- Department of Life Sciences, University of Trieste Trieste, Italy
| | - Claudia Colombrita
- Laboratory of Neuroscience - IRCCS Istituto Auxologico Italiano Milano, Italy ; Department of Pathophysiology and Transplantation, "Dino Ferrari Center", Università degli Studi di Milano Milano, Italy
| | | | - Kevin R Jones
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder CO, USA
| | | | - Enrico Tongiorgi
- Department of Life Sciences, University of Trieste Trieste, Italy
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18
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Sosińska P, Mikuła-Pietrasik J, Książek K. The double-edged sword of long non-coding RNA: The role of human brain-specific BC200 RNA in translational control, neurodegenerative diseases, and cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 766:58-67. [DOI: 10.1016/j.mrrev.2015.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/29/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022]
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19
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Muslimov IA, Tuzhilin A, Tang TH, Wong RKS, Bianchi R, Tiedge H. Interactions of noncanonical motifs with hnRNP A2 promote activity-dependent RNA transport in neurons. ACTA ACUST UNITED AC 2014; 205:493-510. [PMID: 24841565 PMCID: PMC4033767 DOI: 10.1083/jcb.201310045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ca2+-dependent RNA–protein interactions enable activity-inducible RNA transport in dendrites. A key determinant of neuronal functionality and plasticity is the targeted delivery of select ribonucleic acids (RNAs) to synaptodendritic sites of protein synthesis. In this paper, we ask how dendritic RNA transport can be regulated in a manner that is informed by the cell’s activity status. We describe a molecular mechanism in which inducible interactions of noncanonical RNA motif structures with targeting factor heterogeneous nuclear ribonucleoprotein (hnRNP) A2 form the basis for activity-dependent dendritic RNA targeting. High-affinity interactions between hnRNP A2 and conditional GA-type RNA targeting motifs are critically dependent on elevated Ca2+ levels in a narrow concentration range. Dendritic transport of messenger RNAs that carry such GA motifs is inducible by influx of Ca2+ through voltage-dependent calcium channels upon β-adrenergic receptor activation. The combined data establish a functional correspondence between Ca2+-dependent RNA–protein interactions and activity-inducible RNA transport in dendrites. They also indicate a role of genomic retroposition in the phylogenetic development of RNA targeting competence.
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Affiliation(s)
- Ilham A Muslimov
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Aliya Tuzhilin
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Thean Hock Tang
- Advanced Medical and Dental Institute, Universiti Sains Malaysi, 13200 Kepala Batas, Penang, Malaysia
| | - Robert K S Wong
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Riccardo Bianchi
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
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20
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Di Liegro CM, Schiera G, Di Liegro I. Regulation of mRNA transport, localization and translation in the nervous system of mammals (Review). Int J Mol Med 2014; 33:747-62. [PMID: 24452120 PMCID: PMC3976132 DOI: 10.3892/ijmm.2014.1629] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/09/2013] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional control of mRNA trafficking and metabolism plays a critical role in the actualization and fine tuning of the genetic program of cells, both in development and in differentiated tissues. Cis-acting signals, responsible for post-transcriptional regulation, reside in the RNA message itself, usually in untranslated regions, 5′ or 3′ to the coding sequence, and are recognized by trans-acting factors: RNA-binding proteins (RBPs) and/or non-coding RNAs (ncRNAs). ncRNAs bind short mRNA sequences usually present in the 3′-untranslated (3′-UTR) region of their target messages. RBPs recognize specific nucleotide sequences and/or secondary/tertiary structures. Most RBPs assemble on mRNA at the moment of transcription and shepherd it to its destination, somehow determining its final fate. Regulation of mRNA localization and metabolism has a particularly important role in the nervous system where local translation of pre-localized mRNAs has been implicated in developing axon and dendrite pathfinding, and in synapse formation. Moreover, activity-dependent mRNA trafficking and local translation may underlie long-lasting changes in synaptic efficacy, responsible for learning and memory. This review focuses on the role of RBPs in neuronal development and plasticity, as well as possible connections between ncRNAs and RBPs.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Italia Di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo, I-90127 Palermo, Italy
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21
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Iacoangeli A, Tiedge H. Translational control at the synapse: role of RNA regulators. Trends Biochem Sci 2012; 38:47-55. [PMID: 23218750 DOI: 10.1016/j.tibs.2012.11.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 11/01/2012] [Accepted: 11/05/2012] [Indexed: 12/31/2022]
Abstract
Translational control of gene expression is instrumental in the regulation of eukaryotic cellular form and function. Neurons in particular rely on this form of control because their numerous synaptic connections need to be independently modulated in an input-specific manner. Brain cytoplasmic (BC) RNAs implement translational control at neuronal synapses. BC RNAs regulate protein synthesis by interacting with eIF4 translation initiation factors. Recent evidence suggests that such regulation is required to control synaptic strength, and that dysregulation of local protein synthesis precipitates neuronal hyperexcitability and a propensity for epileptogenic responses. A similar phenotype results from lack of fragile X mental retardation protein (FMRP), indicating that BC RNAs and FMRP use overlapping and convergent modes of action in neuronal translational regulation.
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Affiliation(s)
- Anna Iacoangeli
- Department of Physiology and Pharmacology, The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
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22
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Koval AP, Gogolevskaya IK, Tatosyan KA, Kramerov DA. Complementarity of end regions increases the lifetime of small RNAs in mammalian cells. PLoS One 2012; 7:e44157. [PMID: 22984470 PMCID: PMC3440375 DOI: 10.1371/journal.pone.0044157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/30/2012] [Indexed: 11/22/2022] Open
Abstract
Two RNAs (4.5SH and 4.5SI) with unknown functions share a number of features: short length (about 100 nt), transcription by RNA polymerase III, predominately nuclear localization, the presence in various tissues, and relatively narrow taxonomic distribution (4 and 3 rodent families, respectively). It was reported that 4.5SH RNA turns over rapidly, whereas 4.5SI RNA is stable in the cell, but their lifetimes remained unknown. We showed that 4.5SH is indeed short-lived (t1/2∼18 min) and 4.5SI is long-lived (t1/2∼22 h) in Krebs ascites carcinoma cells. The RNA structures specifying rapid or slow decay of different small cellular RNAs remain unstudied. We searched for RNA structural features that determine the short lifetime of 4.5SH in comparison with the long lifetime of 4.5SI RNA. The sequences of genes of 4.5SH and 4.5SI RNAs were altered and human cells (HeLa) were transfected with these genes. The decay rate of the original and altered RNAs was measured. The complementarity of 16-nt end regions of 4.5SI RNA proved to contribute to its stability in cells, whereas the lack of such complementarity in 4.5SH RNA caused its rapid decay. Possible mechanisms of the phenomenon are discussed.
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Affiliation(s)
| | | | | | - Dmitri A. Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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23
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Lessa FA, Raiol T, Brigido MM, Martins Neto DSB, Walter MEMT, Stadler PF. Clustering rfam 10.1: clans, families, and classes. Genes (Basel) 2012; 3:378-90. [PMID: 24704975 PMCID: PMC3899987 DOI: 10.3390/genes3030378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/04/2012] [Accepted: 06/15/2012] [Indexed: 11/16/2022] Open
Abstract
The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its “decimal release”. In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to Genes 2012, 3 379 well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes.
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Affiliation(s)
- Felipe A Lessa
- Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil.
| | - Tainá Raiol
- Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil.
| | - Marcelo M Brigido
- Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil.
| | | | - Maria Emília M T Walter
- Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
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24
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Lacoux C, Di Marino D, Boyl PP, Zalfa F, Yan B, Ciotti MT, Falconi M, Urlaub H, Achsel T, Mougin A, Caizergues-Ferrer M, Bagni C. BC1-FMRP interaction is modulated by 2'-O-methylation: RNA-binding activity of the tudor domain and translational regulation at synapses. Nucleic Acids Res 2012; 40:4086-96. [PMID: 22238374 PMCID: PMC3351191 DOI: 10.1093/nar/gkr1254] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The brain cytoplasmic RNA, BC1, is a small non-coding RNA that is found in different RNP particles, some of which are involved in translational control. One component of BC1-containing RNP complexes is the fragile X mental retardation protein (FMRP) that is implicated in translational repression. Peptide mapping and computational simulations show that the tudor domain of FMRP makes specific contacts to BC1 RNA. Endogenous BC1 RNA is 2′-O-methylated in nucleotides that contact the FMRP interface, and methylation can affect this interaction. In the cell body BC1 2′-O-methylations are present in both the nucleus and the cytoplasm, but they are virtually absent at synapses where the FMRP–BC1–mRNA complex exerts its function. These results strongly suggest that subcellular region-specific modifications of BC1 affect the binding to FMRP and the interaction with its mRNA targets. We finally show that BC1 RNA has an important role in translation of certain mRNAs associated to FMRP. All together these findings provide further insights into the translational regulation by the FMRP–BC1 complex at synapses.
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Affiliation(s)
- Caroline Lacoux
- Department of Experimental Medicine and Biochemical Sciences, Faculty of Medicine, University of Rome Tor Vergata, Via Montpellier, 1. 00133, Rome, Italy
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25
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Abstract
In higher eukaryotes, increasing evidence suggests, gene expression is to a large degree controlled by RNA. Regulatory RNAs have been implicated in the management of neuronal function and plasticity in mammalian brains. However, much of the molecular-mechanistic framework that enables neuronal regulatory RNAs to control gene expression remains poorly understood. Here, we establish molecular mechanisms that underlie the regulatory capacity of neuronal BC RNAs in the translational control of gene expression. We report that regulatory BC RNAs employ a two-pronged approach in translational control. One of two distinct repression mechanisms is mediated by C-loop motifs in BC RNA 3' stem-loop domains. These C-loops bind to eIF4B and prevent the factor's interaction with 18S rRNA of the small ribosomal subunit. In the second mechanism, the central A-rich domains of BC RNAs target eIF4A, specifically inhibiting its RNA helicase activity. Thus, BC RNAs repress translation initiation in a bimodal mechanistic approach. As BC RNA functionality has evolved independently in rodent and primate lineages, our data suggest that BC RNA translational control was necessitated and implemented during mammalian phylogenetic development of complex neural systems.
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26
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Muslimov IA, Patel MV, Rose A, Tiedge H. Spatial code recognition in neuronal RNA targeting: role of RNA-hnRNP A2 interactions. ACTA ACUST UNITED AC 2011; 194:441-57. [PMID: 21807882 PMCID: PMC3153643 DOI: 10.1083/jcb.201010027] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Recognition of non-canonical purine•purine RNA motifs by hnRNP A2 mediates targeted delivery of neuronal RNAs to dendrites. In neurons, regulation of gene expression occurs in part through translational control at the synapse. A fundamental requirement for such local control is the targeted delivery of select neuronal mRNAs and regulatory RNAs to distal dendritic sites. The nature of spatial RNA destination codes, and the mechanism by which they are interpreted for dendritic delivery, remain poorly understood. We find here that in a key dendritic RNA transport pathway (exemplified by BC1 RNA, a dendritic regulatory RNA, and protein kinase M ζ [PKMζ] mRNA, a dendritic mRNA), noncanonical purine•purine nucleotide interactions are functional determinants of RNA targeting motifs. These motifs are specifically recognized by heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2), a trans-acting factor required for dendritic delivery. Binding to hnRNP A2 and ensuing dendritic delivery are effectively competed by RNAs with CGG triplet repeat expansions. CGG repeats, when expanded in the 5′ untranslated region of fragile X mental retardation 1 (FMR1) mRNA, cause fragile X–associated tremor/ataxia syndrome. The data suggest that cellular dysregulation observed in the presence of CGG repeat RNA may result from molecular competition in neuronal RNA transport pathways.
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Affiliation(s)
- Ilham A Muslimov
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn, USA
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27
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Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS. The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome. RNA (NEW YORK, N.Y.) 2011; 17:1357-1366. [PMID: 21610211 PMCID: PMC3138571 DOI: 10.1261/rna.2682311] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
New deep RNA sequencing methodologies in transcriptome analyses identified a wealth of novel nonprotein-coding RNAs (npcRNAs). Recently, deep sequencing was used to delineate the small npcRNA transcriptome of the human pathogen Vibrio cholerae and 627 novel npcRNA candidates were identified. Here, we report the detection of 223 npcRNA candidates in V. cholerae by different cDNA library construction and conventional sequencing methods. Remarkably, only 39 of the candidates were common to both surveys. We therefore examined possible biasing influences in the transcriptome analyses. Key steps, including tailing and adapter ligations for generating cDNA, contribute qualitatively and quantitatively to the discrepancies between data sets. In addition, the state of 5'-end phosphorylation influences the efficiency of adapter ligation and C-tailing at the 3'-end of the RNA. Finally, our data indicate that the inclusion of sample-specific molecular identifier sequences during ligation steps also leads to biases in cDNA representation. In summary, even deep sequencing is unlikely to identify all RNA species, and caution should be used for meta-analyses among alternatively generated data sets.
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Affiliation(s)
- Carsten A. Raabe
- Institute of Experimental Pathology, University of Muenster, 48149 Muenster, Germany
| | - Chee Hock Hoe
- Infectious Diseases Cluster, Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
| | - Gerrit Randau
- Institute of Experimental Pathology, University of Muenster, 48149 Muenster, Germany
| | - Juergen Brosius
- Institute of Experimental Pathology, University of Muenster, 48149 Muenster, Germany
| | - Thean Hock Tang
- Infectious Diseases Cluster, Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
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28
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Yan X, Denman RB. Conformational-dependent and independent RNA binding to the fragile x mental retardation protein. J Nucleic Acids 2011; 2011:246127. [PMID: 21772992 PMCID: PMC3136132 DOI: 10.4061/2011/246127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 03/16/2011] [Indexed: 01/13/2023] Open
Abstract
The interaction between the fragile X mental retardation protein (FMRP) and BC1 RNA has been the subject of controversy. We probed the parameters of RNA binding to FMRP in several ways. Nondenaturing agarose gel analysis showed that BC1 RNA transcripts produced by in vitro transcription contain a population of conformers, which can be modulated by preannealing. Accordingly, FMRP differentially binds to the annealed and unannealed conformer populations. Using partial RNase digestion, we demonstrate that annealed BC1 RNA contains a unique conformer that FMRP likely binds. We further demonstrate that this interaction is 100-fold weaker than that the binding of eEF-1A mRNA and FMRP, and that preannealing is not a general requirement for FMRP's interaction with RNA. In addition, binding does not require the N-terminal 204 amino acids of FMRP, methylated arginine residues and can be recapitulated by both fragile X paralogs. Altogether, our data continue to support a model in which BC1 RNA functions independently of FMRP.
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Affiliation(s)
- Xin Yan
- CSI/IBR Center for Developmental Neuroscience, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | - Robert B. Denman
- Biochemical Molecular Neurobiology Laboratory, Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
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29
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Abstract
Whole genome transcriptomic analyses have identified large numbers of dynamically expressed long non-protein-coding RNAs (lncRNAs) in mammals and other animals whose functions are, as yet, largely unknown. Here we summarize the growing evidence that lncRNAs, like mRNAs, can be trafficked to and function in a wide variety of subcellular locations. Investigation of the subcellular distribution of lncRNAs has the potential to greatly expand our knowledge not only of the function of lncRNAs but also of cell biology by identifying previously unknown subcellular structures and novel constituents of known cellular organelles.
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Bermudez-Santana C, Attolini CSO, Kirsten T, Engelhardt J, Prohaska SJ, Steigele S, Stadler PF. Genomic organization of eukaryotic tRNAs. BMC Genomics 2010; 11:270. [PMID: 20426822 PMCID: PMC2888827 DOI: 10.1186/1471-2164-11-270] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 04/28/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Surprisingly little is known about the organization and distribution of tRNA genes and tRNA-related sequences on a genome-wide scale. While tRNA gene complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNA gene in Entamoeba histolytica have been described in some detail, systematic comparative studies are rare and mostly restricted to bacteria. We therefore set out to survey the genomic arrangement of tRNA genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. RESULTS In line with previous reports, we find that tRNA complements evolve rapidly and tRNA gene and pseudogene locations are subject to rapid turnover. At phylum level, the distributions of the number of tRNA genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. Even among closely related species we observe dramatic changes in local organization. For instance, 65% and 87% of the tRNA genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. Among basal metazoa, Trichoplax adherens has hardly any duplicated tRNA gene, while the sea anemone Nematostella vectensis boasts more than 17000 tRNA genes and pseudogenes. Dramatic variations are observed even within the eutherian mammals. Higher primates, for instance, have 616 +/- 120 tRNA genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby Otolemur garnetti has 45225 tRNA genes and pseudogenes of which only 5.6% appear in clusters. In contrast, the distribution is surprisingly uniform across plant genomes. Consistent with this variability, syntenic conservation of tRNA genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. Despite this large variation in abundance in Eukarya we observe a significant correlation between the number of tRNA genes, tRNA pseudogenes, and genome size. CONCLUSIONS The genomic organization of tRNA genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the tRNAs themselves. The comprehensive analysis of the genomic organization of tRNA genes and pseudogenes in Eukarya provides a basis for further studies into the interplay of tRNA gene arrangements and genome organization in general.
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Affiliation(s)
- Clara Bermudez-Santana
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
- Department of Biology, Universidad Nacional de Colombia. Carrera45 # 26-85 - Edificio Uriel Gutiérrez, Bogotá D.C., Colombia
| | - Camille Stephan-Otto Attolini
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
- Biostatistics and Bioinformatics unit, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Toralf Kirsten
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Jan Engelhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Sonja J Prohaska
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | | | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraß 22 D-04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany
- Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
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31
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Mourier T, Willerslev E. Retrotransposons and non-protein coding RNAs. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:493-501. [PMID: 19729447 DOI: 10.1093/bfgp/elp036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Retrotransposons constitute a significant fraction of mammalian genomes. Considering the finding of widespread transcriptional activity across entire genomes, it is not surprising that retrotransposons contribute to the collective RNA pool. However, the transcriptional output from retrotransposons does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review the emerging understanding of how retrotransposons themselves are regulated by small RNAs.
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Affiliation(s)
- Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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Cognat V, Deragon JM, Vinogradova E, Salinas T, Remacle C, Maréchal-Drouard L. On the evolution and expression of Chlamydomonas reinhardtii nucleus-encoded transfer RNA genes. Genetics 2008; 179:113-23. [PMID: 18493044 PMCID: PMC2390591 DOI: 10.1534/genetics.107.085688] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 03/18/2008] [Indexed: 11/18/2022] Open
Abstract
In Chlamydomonas reinhardtii, 259 tRNA genes were identified and classified into 49 tRNA isoaccepting families. By constructing phylogenetic trees, we determined the evolutionary history for each tRNA gene family. The majority of the tRNA sequences are more closely related to their plant counterparts than to animals ones. Northern experiments also permitted us to show that at least one member of each tRNA isoacceptor family is transcribed and correctly processed in vivo. A short stretch of T residues known to be a signal for termination of polymerase III transcription was found downstream of most tRNA genes. It allowed us to propose that the vast majority of the tRNA genes are expressed and to confirm that numerous tRNA genes separated by short spacers are indeed cotranscribed. Interestingly, in silico analyses and hybridization experiments show that the cellular tRNA abundance is correlated with the number of tRNA genes and is adjusted to the codon usage to optimize translation efficiency. Finally, we studied the origin of SINEs, short interspersed elements related to tRNAs, whose presence in Chlamydomonas is exceptional. Phylogenetic analysis strongly suggests that tRNA(Asp)-related SINEs originate from a prokaryotic-type tRNA either horizontally transferred from a bacterium or originally present in mitochondria or chloroplasts.
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Affiliation(s)
- Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionnée avec l'Université Louis Pasteur (Strasbourg 1), Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France
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33
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Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol Cell Biol 2008; 28:3008-19. [PMID: 18316401 DOI: 10.1128/mcb.01800-07] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Translational repressors, increasing evidence suggests, participate in the regulation of protein synthesis at the synapse, thus providing a basis for the long-term plastic modulation of synaptic strength. Dendritic BC1 RNA is a non-protein-coding RNA that represses translation at the level of initiation. However, the molecular mechanism of BC1 repression has remained unknown. Here we identify the catalytic activity of eukaryotic initiation factor 4A (eIF4A), an ATP-dependent RNA helicase, as a target of BC1-mediated translational control. BC1 RNA specifically blocks the RNA duplex unwinding activity of eIF4A but, at the same time, stimulates its ATPase activity. BC200 RNA, the primate-specific BC1 counterpart, targets eIF4A activity in identical fashion, as a result decoupling ATP hydrolysis from RNA duplex unwinding. In vivo, BC1 RNA represses translation of a reporter mRNA with 5' secondary structure. The eIF4A mechanism places BC RNAs in a central position to modulate protein synthesis in neurons.
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Abstract
The fragile X mental retardation protein (FMRP), the functional absence of which causes fragile X syndrome, is an RNA-binding protein that has been implicated in the regulation of local protein synthesis at the synapse. The mechanism of FMRP's interaction with its target mRNAs, however, has remained controversial. In one model, it has been proposed that BC1 RNA, a small non-protein-coding RNA that localizes to synaptodendritic domains, operates as a requisite adaptor by specifically binding to both FMRP and, via direct base-pairing, to FMRP target mRNAs. Other models posit that FMRP interacts with its target mRNAs directly, i.e., in a BC1-independent manner. Here five laboratories independently set out to test the BC1-FMRP model. We report that specific BC1-FMRP interactions could be documented neither in vitro nor in vivo. Interactions between BC1 RNA and FMRP target mRNAs were determined to be of a nonspecific nature. Significantly, the association of FMRP with bona fide target mRNAs was independent of the presence of BC1 RNA in vivo. The combined experimental evidence is discordant with a proposed scenario in which BC1 RNA acts as a bridge between FMRP and its target mRNAs and rather supports a model in which BC1 RNA and FMRP are translational repressors that operate independently.
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35
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Khanam T, Raabe CA, Kiefmann M, Handel S, Skryabin BV, Brosius J. Can ID repetitive elements serve as cis-acting dendritic targeting elements? An in vivo study. PLoS One 2007; 2:e961. [PMID: 17896001 PMCID: PMC1978531 DOI: 10.1371/journal.pone.0000961] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 07/05/2007] [Indexed: 11/19/2022] Open
Abstract
Dendritic localization of mRNA/RNA involves interaction of cis-elements and trans-factors. Small, non-protein coding dendritic BC1 RNA is thought to regulate translation in dendritic microdomains. Following microinjections into cultured cells, BC1 RNA fused to larger mRNAs appeared to impart transport competence to these chimeras, and its 5' ID region was proposed as the cis-acting dendritic targeting element. As these ID elements move around rodent genomes and, if transcribed, form a long RNA stem-loop, they might, thereby, lead to new localizations for targeted gene products. To test their targeting ability in vivo we created transgenic mice expressing various ID elements fused to the 3' UTR of reporter mRNA for Enhanced Green Fluorescent Protein. In vivo, neither ID elements nor the BC1 RNA coding region were capable of transporting EGFP RNA to dendrites, although the 3' UTR of alpha-CaMKII mRNA, an established cis-acting element did produce positive results. Other mRNAs containing naturally inserted ID elements are also not found in neuronal dendrites. We conclude that the 5' ID domain from BC1 RNA is not a sufficient dendritic targeting element for mRNAs in vivo.
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Affiliation(s)
- Tasneem Khanam
- Institute of Experimental Pathology, University of Münster, Münster, Germany
- * To whom correspondence should be addressed. E-mail: (TK); (JB)
| | - Carsten A. Raabe
- Institute of Experimental Pathology, University of Münster, Münster, Germany
| | - Martin Kiefmann
- Institute of Experimental Pathology, University of Münster, Münster, Germany
| | - Sergej Handel
- Institute of Experimental Pathology, University of Münster, Münster, Germany
| | - Boris V. Skryabin
- Institute of Experimental Pathology, University of Münster, Münster, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology, University of Münster, Münster, Germany
- * To whom correspondence should be addressed. E-mail: (TK); (JB)
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36
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Centonze D, Rossi S, Napoli I, Mercaldo V, Lacoux C, Ferrari F, Ciotti MT, De Chiara V, Prosperetti C, Maccarrone M, Fezza F, Calabresi P, Bernardi G, Bagni C. The brain cytoplasmic RNA BC1 regulates dopamine D2 receptor-mediated transmission in the striatum. J Neurosci 2007; 27:8885-92. [PMID: 17699670 PMCID: PMC6672174 DOI: 10.1523/jneurosci.0548-07.2007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 06/07/2007] [Accepted: 06/22/2007] [Indexed: 11/21/2022] Open
Abstract
Dopamine D(2) receptor (D(2)DR)-mediated transmission in the striatum is remarkably flexible, and changes in its efficacy have been heavily implicated in a variety of physiological and pathological conditions. Although receptor-associated proteins are clearly involved in specific forms of synaptic plasticity, the molecular mechanisms regulating the sensitivity of D(2) receptors in this brain area are essentially obscure. We have studied the physiological responses of the D(2)DR stimulations in mice lacking the brain cytoplasmic RNA BC1, a small noncoding dendritically localized RNA that is supposed to play a role in mRNA translation. We show that the efficiency of D(2)-mediated transmission regulating striatal GABA synapses is under the control of BC1 RNA, through a negative influence on D(2) receptor protein level affecting the functional pool of receptors. Ablation of the BC1 gene did not result in widespread dysregulation of synaptic transmission, because the sensitivity of cannabinoid CB(1) receptors was intact in the striatum of BC1 knock-out (KO) mice despite D(2) and CB(1) receptors mediated similar electrophysiological actions. Interestingly, the fragile X mental retardation protein FMRP, one of the multiple BC1 partners, is not involved in the BC1 effects on the D(2)-mediated transmission. Because D(2)DR mRNA is apparently equally translated in the BC1-KO and wild-type mice, whereas the protein level is higher in BC1-KO mice, we suggest that BC1 RNA controls D(2)DR indirectly, probably regulating translation of molecules involved in D(2)DR turnover and/or stability.
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MESH Headings
- Animals
- Animals, Newborn
- Biphenyl Compounds/pharmacology
- Cells, Cultured
- Corpus Striatum/cytology
- Dopamine D2 Receptor Antagonists
- Glutamate Decarboxylase/metabolism
- Guanosine 5'-O-(3-Thiotriphosphate)/pharmacokinetics
- In Vitro Techniques
- Inhibitory Postsynaptic Potentials/drug effects
- Inhibitory Postsynaptic Potentials/physiology
- Isoenzymes/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microtubule-Associated Proteins/metabolism
- Neurons/drug effects
- Neurons/physiology
- Oligonucleotides/pharmacology
- Patch-Clamp Techniques/methods
- Piperazines/pharmacology
- RNA, Long Noncoding
- RNA, Messenger/biosynthesis
- RNA, Untranslated
- Receptors, Dopamine D2/agonists
- Receptors, Dopamine D2/chemistry
- Receptors, Dopamine D2/physiology
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Ribonucleoproteins, Small Cytoplasmic/deficiency
- Ribonucleoproteins, Small Cytoplasmic/physiology
- Synaptic Transmission/drug effects
- Synaptic Transmission/physiology
- gamma-Aminobutyric Acid/metabolism
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Affiliation(s)
- Diego Centonze
- Clinica Neurologica, Dipartimento di Neuroscienze
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Silvia Rossi
- Clinica Neurologica, Dipartimento di Neuroscienze
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Ilaria Napoli
- Dipartimento di Biologia, and
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Valentina Mercaldo
- Dipartimento di Biologia, and
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Caroline Lacoux
- Dipartimento di Biologia, and
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Francesca Ferrari
- Dipartimento di Biologia, and
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Maria Teresa Ciotti
- Dipartimento di Biologia, and
- Consiglio Nazionale delle Ricerche/CERC, 00143 Rome, Italy
| | - Valentina De Chiara
- Clinica Neurologica, Dipartimento di Neuroscienze
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Chiara Prosperetti
- Clinica Neurologica, Dipartimento di Neuroscienze
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Mauro Maccarrone
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
- Dipartimento di Scienze Biomediche Comparate, Università degli Studi di Teramo, 64100 Teramo, Italy, and
| | - Filomena Fezza
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università Tor Vergata, 00133 Rome, Italy
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Paolo Calabresi
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
- Clinica Neurologica, Università di Perugia, Ospedale Silvestrini, 06156 Perugia, Italy
| | - Giorgio Bernardi
- Clinica Neurologica, Dipartimento di Neuroscienze
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
| | - Claudia Bagni
- Dipartimento di Biologia, and
- Fondazione Santa Lucia/Centro Europeo per la Ricerca sul Cervello (CERC), 00143 Rome, Italy
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37
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Thyagarajan A, Strong MJ, Szaro BG. Post-transcriptional control of neurofilaments in development and disease. Exp Cell Res 2007; 313:2088-97. [PMID: 17428473 DOI: 10.1016/j.yexcr.2007.02.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/15/2007] [Accepted: 02/20/2007] [Indexed: 02/05/2023]
Abstract
Tight coordination of the expression of neurofilament subunits is integral to the normal development and function of the nervous system. Imbalances in their expression are increasingly implicated in the induction of neurodegeneration in which formation of neurofilamentous aggregates is central to the pathology. Neurofilament expression can be controlled not only at the transcriptional level but also through post-transcriptional regulation of mRNA localization, stability, and translational efficiency. The critical role that post-transcriptional mechanisms play in maintaining neurofilament homeostasis is highlighted, for example, by the human disease amyotrophic lateral sclerosis, in which selective destabilization of NF-L mRNA (or failure to stabilize it) is associated with the formation of neurofilamentous aggregates - a hallmark of the disease process. This review discusses the post-transcriptional regulatory mechanisms and associated ribonucleoproteins that have been implicated to date in controlling neurofilament expression during normal development and in disrupting neurofilament homeostasis during neurodegenerative disease.
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Affiliation(s)
- Amar Thyagarajan
- Department of Biological Sciences and the Neuroscience Research Center, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
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38
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Jambhekar A, Derisi JL. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA (NEW YORK, N.Y.) 2007; 13:625-42. [PMID: 17449729 PMCID: PMC1852811 DOI: 10.1261/rna.262607] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Asymmetric subcellular distribution of RNA is used by many organisms to establish cell polarity, differences in cell fate, or to sequester protein activity. Accurate localization of RNA requires specific sequence and/or structural elements in the localized RNA, as well as proteins that recognize these elements and link the RNA to the appropriate molecular motors. Recent advances in biochemistry, molecular biology, and cell imaging have enabled the identification of many RNA localization elements, or "zipcodes," from a variety of systems. This review focuses on the mechanisms by which various zipcodes direct RNA transport and on the known sequence/structural requirements for their recognition by transport complexes. Computational and experimental methods for predicting and identifying zipcodes are also discussed.
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Affiliation(s)
- Ashwini Jambhekar
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA.
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39
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Sun FJ, Fleurdépine S, Bousquet-Antonelli C, Caetano-Anollés G, Deragon JM. Common evolutionary trends for SINE RNA structures. Trends Genet 2006; 23:26-33. [PMID: 17126948 DOI: 10.1016/j.tig.2006.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 10/10/2006] [Accepted: 11/10/2006] [Indexed: 10/23/2022]
Abstract
Short interspersed elements (SINEs) and long interspersed elements (LINEs) are transposable elements in eukaryotic genomes that mobilize through an RNA intermediate. Understanding their evolution is important because of their impact on the host genome. Most eukaryotic SINEs are ancestrally related to tRNA genes, although the typical tRNA cloverleaf structure is not apparent for most SINE consensus RNAs. Using a cladistic method where RNA structural components were coded as polarized and ordered multistate characters, we showed that related structural motifs are present in most SINE RNAs from mammals, fishes and plants, suggesting common selective constraints imposed at the SINE RNA structural level. Based on these results, we propose a general multistep model for the evolution of tRNA-related SINEs in eukaryotes.
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Affiliation(s)
- Feng-Jie Sun
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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40
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Abstract
Three-dimensional architectural motifs are increasingly recognized as determinants of RNA functionality. We submit that such motifs can encode spatial information. RNAs are targeted to subcellular localities in many eukaryotic cell types, and especially in neuronal and glial cells, RNAs can be transported over long distances to their final destination sites. Such RNAs contain cis-acting long-range targeting elements, and recent evidence suggests that kink-turn motifs within such elements may act as spatial codes to direct transport. Kink-turns are complex RNA motifs that feature double- and single-stranded components and introduce a signature three-dimensional structure into helical stems. We propose that the overall architectural design as well as the individual character--as specified by nucleotide identity and arrangement--of kink-turn motifs can serve as RNA targeting determinants.
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Affiliation(s)
- Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn, Brooklyn, New York 11203, USA.
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41
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Abstract
BC1 RNA is a dendritic untranslated RNA that has been implicated in local translational control mechanisms in neurons. Prerequisite for a functional role of the RNA in synaptodendritic domains is its targeted delivery along the dendritic extent. We report here that the targeting-competent 5' BC1 domain carries two dendritic targeting codes. One code, specifying somatic export, is located in the medial-basal region of the 5' BC1 stem-loop structure. It is defined by an export-determinant stem-bulge motif. The second code, specifying long-range dendritic delivery, is located in the apical part of the 5' stem-loop domain. This element features a GA kink-turn (KT) motif that is indispensable for distal targeting. It specifically interacts with heterogeneous nuclear ribonucleoprotein A2, a trans-acting targeting factor that has previously been implicated in the transport of MBP mRNA in oligodendrocytes and neurons. Our work suggests that a BC1 KT motif encodes distal targeting via the A2 pathway and that architectural RNA elements, such as KT motifs, may function as spatial codes in neural cells.
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Affiliation(s)
- Ilham A Muslimov
- Department of Physiology and Pharmacology, The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
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42
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Abstract
Small non coding RNAs are a group of very different RNA molecules, present in virtually all cells, with a wide spectrum of regulatory functions which include RNA modification and regulation of protein synthesis. They have been isolated and characterized in all organisms and tissues, from Archaeobacteria to mammals. In mammalian brain there are a number of these small molecules, which are involved in neuronal differentiation as well as, possibly, in learning and memory. In this manuscript, we analyze the present knowledge about the function of the most important groups of small non-coding RNA present in brain: small nucleolar RNAs, small cytoplasmic RNAs, and microRNAs. The last ones, in particular, appear to be critical for dictating neuronal cell identity during development and to play an important role in neurite growth, synaptic development and neuronal plasticity.
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Affiliation(s)
- Carlo Presutti
- Dipartimento di Genetica e Biologia Molecolare, Moro 5, 00185 Roma, Italy
| | - Jessica Rosati
- IBPM CNR, Università La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Sara Vincenti
- Dipartimento di Genetica e Biologia Molecolare, Moro 5, 00185 Roma, Italy
| | - Sergio Nasi
- IBPM CNR, Università La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
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43
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Wang H, Iacoangeli A, Lin D, Williams K, Denman RB, Hellen CUT, Tiedge H. Dendritic BC1 RNA in translational control mechanisms. ACTA ACUST UNITED AC 2006; 171:811-21. [PMID: 16330711 PMCID: PMC1828541 DOI: 10.1083/jcb.200506006] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translational control at the synapse is thought to be a key determinant of neuronal plasticity. How is such control implemented? We report that small untranslated BC1 RNA is a specific effector of translational control both in vitro and in vivo. BC1 RNA, expressed in neurons and germ cells, inhibits a rate-limiting step in the assembly of translation initiation complexes. A translational repression element is contained within the unique 3' domain of BC1 RNA. Interactions of this domain with eukaryotic initiation factor 4A and poly(A) binding protein mediate repression, indicating that the 3' BC1 domain targets a functional interaction between these factors. In contrast, interactions of BC1 RNA with the fragile X mental retardation protein could not be documented. Thus, BC1 RNA modulates translation-dependent processes in neurons and germs cells by directly interacting with translation initiation factors.
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Affiliation(s)
- Huidong Wang
- Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
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44
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Kawagoe-Takaki H, Nameki N, Kajikawa M, Okada N. Probing the secondary structure of salmon SmaI SINE RNA. Gene 2006; 365:67-73. [PMID: 16356664 DOI: 10.1016/j.gene.2005.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/11/2005] [Accepted: 09/07/2005] [Indexed: 11/24/2022]
Abstract
SmaI is a short interspersed element (SINE) of the salmon genome, and is derived from tRNA(Lys). We probed the secondary structure of SmaI SINE RNA by enzymatic cleavage and found that the RNA structure comprises three separate domains. The 5'-terminal region (the 5' domain) forms a tRNA-like cloverleaf structure, whereas the 3'-terminal region (the 3' domain) forms an extended stem-loop. The loop region is thought to be recognized by the reverse transcriptase (RT) encoded by the long interspersed element (LINE). The two structural domains are linked by a single-stranded region (the linker domain). Our melting profile analyses indicated the presence of two structural domains having different thermal stabilities, thus supporting the domain composition described above. Based on these results, we discuss the structural generality and evolutionary advantage of the domain composition of SINE RNA.
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Affiliation(s)
- Hiroko Kawagoe-Takaki
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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Kondrashov AV, Kiefmann M, Ebnet K, Khanam T, Muddashetty RS, Brosius J. Inhibitory effect of naked neural BC1 RNA or BC200 RNA on eukaryotic in vitro translation systems is reversed by poly(A)-binding protein (PABP). J Mol Biol 2005; 353:88-103. [PMID: 16154588 DOI: 10.1016/j.jmb.2005.07.049] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 07/08/2005] [Accepted: 07/18/2005] [Indexed: 11/19/2022]
Abstract
Regulated protein biosynthesis in dendrites of neurons might be a key mechanism underlying learning and memory. Neuronal dendritic BC1 RNA and BC200 RNA and similar small untranslated RNAs inhibit protein translation in vitro systems, such as rabbit reticulocyte lysate. Likewise, co-transfection of these RNAs with reporter mRNA suppressed translation levels in HeLa cells. The oligo(A)-rich region of all active small RNAs were identified as the RNA domains chiefly responsible for the inhibitory effects. Addition of recombinant human poly(A)-binding protein (PABP) significantly compensated the inhibitory effect of the small oligo(A)-rich RNA. In vivo, all BC1 RNA appears to be complexed with PABP. Nevertheless, in the micro-environment of dendritic spines of neuronal cells, BC1 RNPs or BC200 RNPs might mediate regulatory functions by differential interactions with locally limited PABP and/or directly or indirectly, with other translation initiation factors.
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Affiliation(s)
- Alexander V Kondrashov
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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Kobayashi S, Higuchi T, Anzai K. Application of the BC1 RNA gene promoter for short hairpin RNA expression in cultured neuronal cells. Biochem Biophys Res Commun 2005; 334:1305-9. [PMID: 16054886 DOI: 10.1016/j.bbrc.2005.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 07/06/2005] [Indexed: 11/28/2022]
Abstract
BC1 RNA is a neuronal cell-specific non-messenger RNA transcribed by RNA polymerase III (Pol III). We previously reported that the transcription of BC1 RNA is controlled both by intragenic promoters for Pol III and by a 5'-flanking region containing several unique cis-elements that are possible members of the Pol II transcription system. In this study, we chose beta-secretase (BACE1) as a target and applied the promoter to produce a short hairpin RNA (shRNA) for RNA interference (RNAi) in cultured neuronal cells. A plasmid vector in which the promoter was linked to a target sequence functioned in rodent NG108-15 cells and suppressed BACE1 protein expression, but did not function in non-neuronal NIH3T3 cells. It was also effective in rat primary hippocampal neurons. We further showed that the promoter can be active in human neuroblastoma SH-SY5Y cells and reduced expression of targeted protein, although the BC1 RNA gene is a rodent-specific gene. The use of this vector-based system for shRNA expression may be an important component of future development of neuronal cell-selective RNAi in both transgenic and therapeutic applications.
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Affiliation(s)
- Shunsuke Kobayashi
- Department of Biochemistry, College of Pharmacy, Nihon University, Narashinodai, Funabashi, Chiba 274-8555, Japan.
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Bagni C, Greenough WT. From mRNP trafficking to spine dysmorphogenesis: the roots of fragile X syndrome. Nat Rev Neurosci 2005; 6:376-87. [PMID: 15861180 DOI: 10.1038/nrn1667] [Citation(s) in RCA: 368] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mental retardation protein FMRP is involved in the transport of mRNAs and their translation at synapses. Patients with fragile X syndrome, in whom FMRP is absent or mutated, show deficits in learning and memory that might reflect impairments in the translational regulation of a subset of neuronal mRNAs. The study of FMRP provides important insights into the regulation and functions of local protein synthesis in the neuronal periphery, and increases our understanding of how these functions can produce specific effects at individual synapses.
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Affiliation(s)
- Claudia Bagni
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, Roma, Italy.
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Zhang X, Wessler SR. BoS: A Large and Diverse Family of Short Interspersed Elements (SINEs) in Brassica oleracea. J Mol Evol 2005; 60:677-87. [PMID: 15983875 DOI: 10.1007/s00239-004-0259-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Accepted: 10/11/2004] [Indexed: 10/25/2022]
Abstract
Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, 30602, USA
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Muslimov IA, Nimmrich V, Hernandez AI, Tcherepanov A, Sacktor TC, Tiedge H. Dendritic transport and localization of protein kinase Mzeta mRNA: implications for molecular memory consolidation. J Biol Chem 2004; 279:52613-22. [PMID: 15371429 PMCID: PMC1828843 DOI: 10.1074/jbc.m409240200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Protein kinase Mzeta (PKMzeta) is an atypical protein kinase C isoform that has been implicated in the protein synthesis-dependent maintenance of long term potentiation and memory storage in the brain. Synapse-associated kinases are uniquely positioned to promote enduring consolidation of structural and functional modifications at the synapse, provided that kinase mRNA is available on site for local input-specific translation. We now report that the mRNA encoding PKMzeta is rapidly transported and specifically localized to synaptodendritic neuronal domains. Transport of PKMzeta mRNA is specified by two cis-acting dendritic targeting elements (Mzeta DTEs). Mzeta DTE1, located at the interface of the 5'-untranslated region and the open reading frame, directs somato-dendritic export of the mRNA. Mzeta DTE2, in contrast, is located in the 3'-untranslated region and is required for delivery of the mRNA to distal dendritic segments. Colocalization with translational repressor BC1 RNA in hippocampal dendrites suggests that PKMzeta mRNA may be subject to translational control in local domains. Dendritic localization of PKMzeta mRNA provides a molecular basis for the functional integration of synaptic signal transduction and translational control pathways.
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Affiliation(s)
- Ilham Aliagaevich Muslimov
- Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn, Brooklyn, New York 11203, USA
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Abstract
Learning and memory difficulties observed in patients with fragile X syndrome, as well as in a mouse model for the syndrome, are partially due to impaired translational regulation of neuronal mRNAs encoding key molecules for the synaptic structure and function. There has been intense interest in characterizing the mRNAs that are regulated by the fragile X mental retardation protein (FMRP) in the neuronal cell. A large number of candidate FMRP-interacting mRNAs has been identified over the last few years and three models have been described so far to explain the specificity of these interactions. Here, we report our vision on how they could work in the same and/or in different pathways and suggest that the three mechanisms may not be mutually exclusive.
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Affiliation(s)
- Massimiliano Veneri
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, Roma, Italy
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