451
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Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell 2014; 157:869-81. [PMID: 24813610 DOI: 10.1016/j.cell.2014.03.040] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 02/04/2014] [Accepted: 03/20/2014] [Indexed: 01/18/2023]
Abstract
Fragile X syndrome, a common form of inherited intellectual disability, is caused by loss of the fragile X mental retardation protein FMRP. FMRP is present predominantly in the cytoplasm, where it regulates translation of proteins that are important for synaptic function. We identify FMRP as a chromatin-binding protein that functions in the DNA damage response (DDR). Specifically, we show that FMRP binds chromatin through its tandem Tudor (Agenet) domain in vitro and associates with chromatin in vivo. We also demonstrate that FMRP participates in the DDR in a chromatin-binding-dependent manner. The DDR machinery is known to play important roles in developmental processes such as gametogenesis. We show that FMRP occupies meiotic chromosomes and regulates the dynamics of the DDR machinery during mouse spermatogenesis. These findings suggest that nuclear FMRP regulates genomic stability at the chromatin interface and may impact gametogenesis and some developmental aspects of fragile X syndrome.
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Affiliation(s)
- Roman Alpatov
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bluma J Lesch
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mika Nakamoto-Kinoshita
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andres Blanco
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shuzhen Chen
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Stützer
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Karim J Armache
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew D Simon
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Chao Xu
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Muzaffar Ali
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jernej Murn
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sladjana Prisic
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Jinrong Min
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Robert E Kingston
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stephen T Warren
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David C Page
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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452
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Innate immune responses regulate morphogenesis and degeneration: roles of Toll-like receptors and Sarm1 in neurons. Neurosci Bull 2014; 30:645-54. [PMID: 24993772 DOI: 10.1007/s12264-014-1445-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022] Open
Abstract
The central nervous system is recognized as an immunoprivileged site because peripheral immune cells do not typically enter it. Microglial cells are thought to be the main immune cells in brain. However, recent reports have indicated that neurons express the key players of innate immunity, including Toll-like receptors (TLRs) and their adaptor proteins (Sarm1, Myd88, and Trif), and may produce cytokines in response to pathogen infection. In the absence of an immune challenge, neuronal TLRs can detect intrinsic danger signals and modulate neuronal morphology and function. In this article, we review the recent findings on the involvement of TLRs and Sarm1 in controlling neuronal morphogenesis and neurodegeneration. Abnormal behaviors in TLR- and Sarm1-deficient mice are also discussed.
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453
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Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T. Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. RNA (NEW YORK, N.Y.) 2014; 20:1090-102. [PMID: 24860013 PMCID: PMC4114688 DOI: 10.1261/rna.045005.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Recent studies implicated the RNA-binding protein with multiple splicing (RBPMS) family of proteins in oocyte, retinal ganglion cell, heart, and gastrointestinal smooth muscle development. These RNA-binding proteins contain a single RNA recognition motif (RRM), and their targets and molecular function have not yet been identified. We defined transcriptome-wide RNA targets using photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in HEK293 cells, revealing exonic mature and intronic pre-mRNA binding sites, in agreement with the nuclear and cytoplasmic localization of the proteins. Computational and biochemical approaches defined the RNA recognition element (RRE) as a tandem CAC trinucleotide motif separated by a variable spacer region. Similar to other mRNA-binding proteins, RBPMS family of proteins relocalized to cytoplasmic stress granules under oxidative stress conditions suggestive of a support function for mRNA localization in large and/or multinucleated cells where it is preferentially expressed.
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Affiliation(s)
- Thalia A. Farazi
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Carl S. Leonhardt
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Neelanjan Mukherjee
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Aleksandra Mihailovic
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Song Li
- Biology Department, Duke University, Durham, North Carolina 27708, USA
| | - Klaas E.A. Max
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Masashi Yamaji
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Pavol Cekan
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Nicholas C. Jacobs
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Stefanie Gerstberger
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Claudia Bognanni
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Erik Larsson
- Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
- Corresponding authorE-mail
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454
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Li Y, Zhao X. Concise review: Fragile X proteins in stem cell maintenance and differentiation. Stem Cells 2014; 32:1724-33. [PMID: 24648324 PMCID: PMC4255947 DOI: 10.1002/stem.1698] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 02/18/2014] [Accepted: 03/01/2014] [Indexed: 12/15/2022]
Abstract
Fragile X syndrome (FXS), the most common genetic form of autism spectrum disorder, is caused by deficiency of the fragile X mental retardation protein (FMRP). Despite extensive research and scientific progress, understanding how FMRP regulates brain development and function remains a major challenge. FMRP is a neuronal RNA-binding protein that binds about a third of messenger RNAs in the brain and controls their translation, stability, and cellular localization. The absence of FMRP results in increased protein synthesis, leading to enhanced signaling in a number of intracellular pathways, including the mTOR, mGLuR5, ERK, Gsk3β, PI3K, and insulin pathways. Until recently, FXS was largely considered a deficit of mature neurons; however, a number of new studies have shown that FMRP may also play important roles in stem cells, among them neural stem cells, germline stem cells, and pluripotent stem cells. In this review, we will cover these newly discovered functions of FMRP, as well as the other two fragile X-related proteins, in stem cells. We will also discuss the literature on the use of stem cells, particularly neural stem cells and induced pluripotent stem cells, as model systems for studying the functions of FMRP in neuronal development.
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Affiliation(s)
- Yue Li
- Waisman Center and Department of Neuroscience, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
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455
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Kloetgen A, Münch PC, Borkhardt A, Hoell JI, McHardy AC. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics 2014; 14:102-14. [PMID: 24951655 PMCID: PMC4471435 DOI: 10.1093/bfgp/elu020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Our understanding of transcriptional gene regulation has dramatically increased over the past decades, and many regulators of gene expression, such as transcription factors, have been analyzed extensively. Additionally, in recent years, deeper insights into the physiological roles of RNA have been obtained. More precisely, splicing, polyadenylation, various modifications, localization and the translation of messenger RNAs (mRNAs) are regulated by their interaction with RNA-binding proteins (RBPs). New technologies now enable the analysis of this regulation at different levels. A technique known as ultraviolet (UV) cross-linking and immunoprecipitation (CLIP) allows us to determine physical protein–RNA interactions on a genome-wide scale. UV cross-linking introduces covalent bonds between interacting RBPs and RNAs. In combination with immunoprecipitation and deep sequencing techniques, tens of millions of short reads (representing bound RNAs by an RBP of interest) are generated and are used to characterize the regulatory network mediated by an RBP. Other methods, such as mass spectrometry, can also be used for characterization of cross-linked RBPs and RNAs instead of CLIP methods. In this review, we discuss experimental and computational methods for the generation and analysis of CLIP data. The computational methods include short-read alignment, annotation and RNA-binding motif discovery. We describe the challenges of analyzing CLIP data and indicate areas where improvements are needed.
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Affiliation(s)
| | | | | | | | - Alice C McHardy
- Corresponding author. Alice C. McHardy, Heinrich-Heine University, Department of Algorithmic Bioinformatics, Universitaetsstrasse 1, 40225 Duesseldorf, Germany. Tel.: +49-211-8110427; Fax: +49-211-8113464; E-mail:
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456
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Yokoshi M, Li Q, Yamamoto M, Okada H, Suzuki Y, Kawahara Y. Direct binding of Ataxin-2 to distinct elements in 3' UTRs promotes mRNA stability and protein expression. Mol Cell 2014; 55:186-98. [PMID: 24954906 DOI: 10.1016/j.molcel.2014.05.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/19/2014] [Accepted: 05/15/2014] [Indexed: 01/22/2023]
Abstract
It has been proposed that Ataxin-2, a member of the like-Sm (LSm) protein family, participates in the regulation of RNA metabolism through interaction with PABPC1. However, the exact biological mechanism and in vivo targets remain unknown. Here, we report that Ataxin-2 binds directly to RNAs in a PABPC1-independent manner. High-throughput sequencing of Ataxin-2-bound RNAs prepared by PAR-CLIP revealed that Ataxin-2 binds predominantly to uridine-rich elements, including well-characterized cis-regulatory AU-rich elements, in the 3' UTRs of target mRNAs. Gene expression analysis after Ataxin-2 depletion or overexpression revealed that Ataxin-2 stabilizes target mRNAs and increases the abundance of the corresponding proteins. A tethering assay demonstrated that Ataxin-2 elicits this effect by direct interaction with mRNAs. We also found that disease-associated polyglutamine expansion downregulates the physiological activity of Ataxin-2. These findings suggest that Ataxin-2 is an RNA-binding protein that targets cis-regulatory elements in 3' UTRs to stabilize a subset of mRNAs and increase protein expression.
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Affiliation(s)
- Moe Yokoshi
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Quan Li
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Munetaka Yamamoto
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hitomi Okada
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-1 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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457
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Liu T, Wan RP, Tang LJ, Liu SJ, Li HJ, Zhao QH, Liao WP, Sun XF, Yi YH, Long YS. A MicroRNA Profile in Fmr1 Knockout Mice Reveals MicroRNA Expression Alterations with Possible Roles in Fragile X Syndrome. Mol Neurobiol 2014; 51:1053-63. [DOI: 10.1007/s12035-014-8770-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 06/01/2014] [Indexed: 01/01/2023]
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458
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Ji B, Higa KK, Kim M, Zhou L, Young JW, Geyer MA, Zhou X. Inhibition of protein translation by the DISC1-Boymaw fusion gene from a Scottish family with major psychiatric disorders. Hum Mol Genet 2014; 23:5683-705. [PMID: 24908665 DOI: 10.1093/hmg/ddu285] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The t(1; 11) translocation appears to be the causal genetic lesion with 70% penetrance for schizophrenia, major depression and other psychiatric disorders in a Scottish family. Molecular studies identified the disruption of the disrupted-in-schizophrenia 1 (DISC1) gene by chromosome translocation at chromosome 1q42. Our previous studies, however, revealed that the translocation also disrupted another gene, Boymaw (also termed DISC1FP1), on chromosome 11. After translocation, two fusion genes [the DISC1-Boymaw (DB7) and the Boymaw-DISC1 (BD13)] are generated between the DISC1 and Boymaw genes. In the present study, we report that expression of the DB7 fusion gene inhibits both intracellular NADH oxidoreductase activities and protein translation. We generated humanized DISC1-Boymaw mice with gene targeting to examine the in vivo functions of the fusion genes. Consistent with the in vitro studies on the DB7 fusion gene, protein translation activity is decreased in the hippocampus and in cultured primary neurons from the brains of the humanized mice. Expression of Gad67, Nmdar1 and Psd95 proteins are also reduced. The humanized mice display prolonged and increased responses to the NMDA receptor antagonist, ketamine, on various mouse genetic backgrounds. Abnormal information processing of acoustic startle and depressive-like behaviors are also observed. In addition, the humanized mice display abnormal erythropoiesis, which was reported to associate with depression in humans. Expression of the DB7 fusion gene may reduce protein translation to impair brain functions and thereby contribute to the pathogenesis of major psychiatric disorders.
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Affiliation(s)
- Baohu Ji
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kerin K Higa
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Minjung Kim
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lynn Zhou
- La Jolla High School, 750 Nautilus St., San Diego, CA 92037, USA and
| | - Jared W Young
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA, Research Service, VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, CA 92037, USA
| | - Mark A Geyer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA, Research Service, VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, CA 92037, USA
| | - Xianjin Zhou
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA, Research Service, VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, CA 92037, USA
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459
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Jung H, Gkogkas CG, Sonenberg N, Holt CE. Remote control of gene function by local translation. Cell 2014; 157:26-40. [PMID: 24679524 PMCID: PMC3988848 DOI: 10.1016/j.cell.2014.03.005] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/04/2014] [Accepted: 03/04/2014] [Indexed: 12/12/2022]
Abstract
The subcellular position of a protein is a key determinant of its function. Mounting evidence indicates that RNA localization, where specific mRNAs are transported subcellularly and subsequently translated in response to localized signals, is an evolutionarily conserved mechanism to control protein localization. On-site synthesis confers novel signaling properties to a protein and helps to maintain local proteome homeostasis. Local translation plays particularly important roles in distal neuronal compartments, and dysregulated RNA localization and translation cause defects in neuronal wiring and survival. Here, we discuss key findings in this area and possible implications of this adaptable and swift mechanism for spatial control of gene function.
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Affiliation(s)
- Hosung Jung
- Department of Anatomy, Brain Research Institute, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, South Korea
| | - Christos G Gkogkas
- Patrick Wild Centre, Centre for Integrative Physiology, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada.
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, Anatomy Building, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK.
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460
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Ding Q, Sethna F, Wang H. Behavioral analysis of male and female Fmr1 knockout mice on C57BL/6 background. Behav Brain Res 2014; 271:72-8. [PMID: 24886775 DOI: 10.1016/j.bbr.2014.05.046] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 11/17/2022]
Abstract
Fragile X syndrome (FXS) is a monogenic disease caused by mutations in the FMR1 gene. The Fmr1 knockout (KO) mice show many aspects of FXS-related phenotypes, and have been used as a major pre-clinical model for FXS. Although FXS occurs in both male and female patients, most studies on the mouse model use male animals. Few studies test whether gender affects the face validity of the mouse model. Here, we examined multiple behavioral phenotypes with male hemizygous and female homozygous Fmr1 KO mice on C57BL/6 background. For each behavioral paradigm, we examined multiple cohorts from different litters. We found that both male and female Fmr1 KO mice displayed significant audiogenic seizures, hyperactivity in the open field test, deficits in passive avoidance and contextual fear memory, and significant enhancement of PPI at low stimulus intensity. Male and female Fmr1 KO mice also showed more transitional movement between the lit and dark chambers in the light-dark tests. The lack of gender effects suggests that the Fmr1 KO mouse is a reasonable tool to test the efficacy of potential FXS therapies.
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Affiliation(s)
- Qi Ding
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Ferzin Sethna
- Genetics Program, Michigan State University, East Lansing, MI 48824, USA
| | - Hongbing Wang
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA.
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461
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Thomas MG, Pascual ML, Maschi D, Luchelli L, Boccaccio GL. Synaptic control of local translation: the plot thickens with new characters. Cell Mol Life Sci 2014; 71:2219-39. [PMID: 24212248 PMCID: PMC11113725 DOI: 10.1007/s00018-013-1506-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 10/11/2013] [Accepted: 10/21/2013] [Indexed: 12/18/2022]
Abstract
The production of proteins from mRNAs localized at the synapse ultimately controls the strength of synaptic transmission, thereby affecting behavior and cognitive functions. The regulated transcription, processing, and transport of mRNAs provide dynamic control of the dendritic transcriptome, which includes thousands of messengers encoding multiple cellular functions. Translation is locally modulated by synaptic activity through a complex network of RNA-binding proteins (RBPs) and various types of non-coding RNAs (ncRNAs) including BC-RNAs, microRNAs, piwi-interacting RNAs, and small interference RNAs. The RBPs FMRP and CPEB play a well-established role in synaptic translation, and additional regulatory factors are emerging. The mRNA repressors Smaug, Nanos, and Pumilio define a novel pathway for local translational control that affects dendritic branching and spines in both flies and mammals. Recent findings support a role for processing bodies and related synaptic mRNA-silencing foci (SyAS-foci) in the modulation of synaptic plasticity and memory formation. The SyAS-foci respond to different stimuli with changes in their integrity thus enabling regulated mRNA release followed by translation. CPEB, Pumilio, TDP-43, and FUS/TLS form multimers through low-complexity regions related to prion domains or polyQ expansions. The oligomerization of these repressor RBPs is mechanistically linked to the aggregation of abnormal proteins commonly associated with neurodegeneration. Here, we summarize the current knowledge on how specificity in mRNA translation is achieved through the concerted action of multiple pathways that involve regulatory ncRNAs and RBPs, the modification of translation factors, and mRNA-silencing foci dynamics.
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Affiliation(s)
- María Gabriela Thomas
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
| | - Malena Lucía Pascual
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
| | - Darío Maschi
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- Present Address: Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO USA
| | - Luciana Luchelli
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
| | - Graciela Lidia Boccaccio
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
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462
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Advances in Genetic Diagnosis of Autism Spectrum Disorders. CURRENT PEDIATRICS REPORTS 2014. [DOI: 10.1007/s40124-014-0042-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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463
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Suhl JA, Chopra P, Anderson BR, Bassell GJ, Warren ST. Analysis of FMRP mRNA target datasets reveals highly associated mRNAs mediated by G-quadruplex structures formed via clustered WGGA sequences. Hum Mol Genet 2014; 23:5479-91. [PMID: 24876161 DOI: 10.1093/hmg/ddu272] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fragile X syndrome, a common cause of intellectual disability and a well-known cause of autism spectrum disorder, is the result of loss or dysfunction of fragile X mental retardation protein (FMRP), a highly selective RNA-binding protein and translation regulator. A major research priority has been the identification of the mRNA targets of FMRP, particularly as recent studies suggest an excess of FMRP targets among genes implicated in idiopathic autism and schizophrenia. Several large-scale studies have attempted to identify mRNAs bound by FMRP through several methods, each generating a list of putative target genes, leading to distinct hypotheses by which FMRP recognizes its targets; namely, by RNA structure or sequence. However, no in depth analyses have been performed to identify the level of consensus among the studies. Here, we analyze four large FMRP target datasets to generate high-confidence consensus lists, and examine all datasets for sequence elements within the target RNAs to validate reported FMRP binding motifs (GACR, ACUK and WGGA). We found GACR to be highly enriched in FMRP datasets, while ACUK was not. The WGGA pattern was modestly enriched in several, but not all datasets. The previous association between FMRP and G-quadruplexes prompted the analysis of the distribution of WGGA in the target genes. Consistent with the requirements for G-quadruplex formation, we observed highly clustered WGGA motifs in FMRP targets compared with other genes, implicating both RNA structure and sequence in the recognition motif of FMRP. In addition, we generate a list of the top 40 FMRP targets associated with FXS-related phenotypes.
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Affiliation(s)
| | | | | | | | - Stephen T Warren
- Department of Human Genetics, Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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464
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Bartley CM, O’Keefe RA, Bordey A. FMRP S499 is phosphorylated independent of mTORC1-S6K1 activity. PLoS One 2014; 9:e96956. [PMID: 24806451 PMCID: PMC4013076 DOI: 10.1371/journal.pone.0096956] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/08/2014] [Indexed: 11/18/2022] Open
Abstract
Hyperactive mammalian target of rapamycin (mTOR) is associated with cognitive deficits in several neurological disorders including tuberous sclerosis complex (TSC). The phosphorylation of the mRNA-binding protein FMRP reportedly depends on mTOR complex 1 (mTORC1) activity via p70 S6 kinase 1 (S6K1). Because this phosphorylation is thought to regulate the translation of messages important for synaptic plasticity, we explored whether FMRP phosphorylation of the S6K1-dependent residue (S499) is altered in TSC and states of dysregulated TSC-mTORC1 signaling. Surprisingly, we found that FMRP S499 phosphorylation was unchanged in heterozygous and conditional Tsc1 knockout mice despite significantly elevated mTORC1-S6K1 activity. Neither up- nor down-regulation of the mTORC1-S6K1 axis in vivo or in vitro had any effect on phospho-FMRP S499 levels. In addition, FMRP S499 phosphorylation was unaltered in S6K1-knockout mice. Collectively, these data strongly suggest that FMRP S499 phosphorylation is independent of mTORC1-S6K1 activity and is not altered in TSC.
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Affiliation(s)
- Christopher M. Bartley
- Departments of Neurosurgery, and Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Rachel A. O’Keefe
- Departments of Neurosurgery, and Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Angélique Bordey
- Departments of Neurosurgery, and Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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465
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Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, Thiruvahindrapuram B, Xu X, Ziman R, Wang Z, Vorstman JAS, Thompson A, Regan R, Pilorge M, Pellecchia G, Pagnamenta AT, Oliveira B, Marshall CR, Magalhaes TR, Lowe JK, Howe JL, Griswold AJ, Gilbert J, Duketis E, Dombroski BA, De Jonge MV, Cuccaro M, Crawford EL, Correia CT, Conroy J, Conceição IC, Chiocchetti AG, Casey JP, Cai G, Cabrol C, Bolshakova N, Bacchelli E, Anney R, Gallinger S, Cotterchio M, Casey G, Zwaigenbaum L, Wittemeyer K, Wing K, Wallace S, van Engeland H, Tryfon A, Thomson S, Soorya L, Rogé B, Roberts W, Poustka F, Mouga S, Minshew N, McInnes LA, McGrew SG, Lord C, Leboyer M, Le Couteur AS, Kolevzon A, Jiménez González P, Jacob S, Holt R, Guter S, Green J, Green A, Gillberg C, Fernandez BA, Duque F, Delorme R, Dawson G, Chaste P, Café C, Brennan S, Bourgeron T, Bolton PF, Bölte S, Bernier R, Baird G, Bailey AJ, Anagnostou E, Almeida J, Wijsman EM, Vieland VJ, Vicente AM, Schellenberg GD, Pericak-Vance M, Paterson AD, Parr JR, Oliveira G, Nurnberger JI, Monaco AP, Maestrini E, Klauck SM, Hakonarson H, Haines JL, Geschwind DH, Freitag CM, Folstein SE, Ennis S, Coon H, Battaglia A, Szatmari P, Sutcliffe JS, Hallmayer J, Gill M, Cook EH, Buxbaum JD, Devlin B, Gallagher L, Betancur C, Scherer SW. Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. Am J Hum Genet 2014; 94:677-94. [PMID: 24768552 PMCID: PMC4067558 DOI: 10.1016/j.ajhg.2014.03.018] [Citation(s) in RCA: 659] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/25/2014] [Indexed: 12/15/2022] Open
Abstract
Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10−5) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10−15, ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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Affiliation(s)
- Dalila Pinto
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elsa Delaby
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Daniele Merico
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Mafalda Barbosa
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alison Merikangas
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Bhooma Thiruvahindrapuram
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Xiao Xu
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Ziman
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Zhuozhi Wang
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Jacob A S Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Regina Regan
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Marion Pilorge
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Giovanna Pellecchia
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | | | - Bárbara Oliveira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Christian R Marshall
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Tiago R Magalhaes
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Jennifer K Lowe
- Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer L Howe
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - John Gilbert
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Eftichia Duketis
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Beth A Dombroski
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maretha V De Jonge
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Michael Cuccaro
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Emily L Crawford
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Catarina T Correia
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Judith Conroy
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; Children's University Hospital Temple Street, Dublin 1, Ireland
| | - Inês C Conceição
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Jillian P Casey
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Guiqing Cai
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christelle Cabrol
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Nadia Bolshakova
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Richard Anney
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6B 2H3, Canada
| | | | - Kirsty Wing
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Simon Wallace
- Department of Psychiatry, University of Oxford and Warneford Hospital, Oxford OX3 7JX, UK
| | - Herman van Engeland
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Ana Tryfon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susanne Thomson
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Latha Soorya
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernadette Rogé
- Unité de Recherche Interdisciplinaire Octogone, Centre d'Etudes et de Recherches en Psychopathologie, Toulouse 2 University, 31058 Toulouse, France
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Susana Mouga
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Nancy Minshew
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - L Alison McInnes
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susan G McGrew
- Department of Pediatrics, Vanderbilt University, Nashville, TN 37232, USA
| | - Catherine Lord
- NewYork-Presbyterian/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Marion Leboyer
- FondaMental Foundation, 94010 Créteil, France; Institut National de la Santé et de la Recherche U955, Psychiatrie Génétique, 94010 Créteil, France; Faculté de Médecine, Université Paris Est, 94010 Créteil, France; Department of Psychiatry, Henri Mondor-Albert Chenevier Hospital, Assistance Publique - Hôpitaux de Paris, 94010 Créteil, France
| | - Ann S Le Couteur
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne NE1 4LP, UK
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patricia Jiménez González
- Child Developmental and Behavioral Unit, Hospital Nacional de Niños Dr. Sáenz Herrera, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Suma Jacob
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA; Institute of Translational Neuroscience and Department of Psychiatry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Stephen Guter
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Jonathan Green
- Institute of Brain, Behaviour, and Mental Health, University of Manchester, Manchester M13 9PL, UK; Manchester Academic Health Sciences Centre, Manchester M13 9NT, UK
| | - Andrew Green
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, 41119 Gothenburg, Sweden
| | - Bridget A Fernandez
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Richard Delorme
- FondaMental Foundation, 94010 Créteil, France; Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015 Paris, France; Centre National de la Recherche Scientifique URA 2182 (Genes, Synapses, and Cognition), Institut Pasteur, 75015 Paris, France; Department of Child and Adolescent Psychiatry, Robert Debré Hospital, Assistance Publique - Hôpitaux de Paris, 75019 Paris, France
| | - Geraldine Dawson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; FondaMental Foundation, 94010 Créteil, France
| | - Cátia Café
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Sean Brennan
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Thomas Bourgeron
- FondaMental Foundation, 94010 Créteil, France; Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015 Paris, France; Centre National de la Recherche Scientifique URA 2182 (Genes, Synapses, and Cognition), Institut Pasteur, 75015 Paris, France; University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Patrick F Bolton
- Institute of Psychiatry, King's College London, London SE5 8AF, UK; South London & Maudsley Biomedical Research Centre for Mental Health, London SE5 8AF, UK
| | - Sven Bölte
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University of Frankfurt, 60528 Frankfurt, Germany
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gillian Baird
- Paediatric Neurodisability, King's Health Partners, King's College London, London WC2R 2LS, UK
| | - Anthony J Bailey
- Department of Psychiatry, University of Oxford and Warneford Hospital, Oxford OX3 7JX, UK
| | - Evdokia Anagnostou
- Bloorview Research Institute, University of Toronto, Toronto, ON M4G 1R8, Canada
| | - Joana Almeida
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Veronica J Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Astrid M Vicente
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Gerard D Schellenberg
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Andrew D Paterson
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Dalla Lana School of Public Health, Toronto, ON M5T 3M7, Canada
| | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - John I Nurnberger
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics and Program in Medical Neuroscience, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Office of the President, Tufts University, Medford, MA 02155, USA
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Sabine M Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (Deutsches Krebsforschungszentrum), 69120 Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan L Haines
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel H Geschwind
- Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Susan E Folstein
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Hilary Coon
- Utah Autism Research Program, Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Agatino Battaglia
- Stella Maris Clinical Research Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - James S Sutcliffe
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Joachim Hallmayer
- Department of Psychiatry, Stanford University Medical School, Stanford, CA 94305, USA
| | - Michael Gill
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Louise Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Catalina Betancur
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada.
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466
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Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Mol Cell 2014; 54:407-417. [PMID: 24746697 DOI: 10.1016/j.molcel.2014.03.023] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/18/2014] [Accepted: 03/10/2014] [Indexed: 11/23/2022]
Abstract
Fragile X syndrome (FXS) is the most common form of inherited mental retardation, and it is caused by loss of function of the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein that is involved in the translational regulation of several neuronal mRNAs. However, the precise mechanism of translational inhibition by FMRP is unknown. Here, we show that FMRP inhibits translation by binding directly to the L5 protein on the 80S ribosome. Furthermore, cryoelectron microscopic reconstruction of the 80S ribosome⋅FMRP complex shows that FMRP binds within the intersubunit space of the ribosome such that it would preclude the binding of tRNA and translation elongation factors on the ribosome. These findings suggest that FMRP inhibits translation by blocking the essential components of the translational machinery from binding to the ribosome.
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467
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Romano D, Nicolau M, Quintin EM, Mazaika PK, Lightbody AA, Cody Hazlett H, Piven J, Carlsson G, Reiss AL. Topological methods reveal high and low functioning neuro-phenotypes within fragile X syndrome. Hum Brain Mapp 2014; 35:4904-15. [PMID: 24737721 DOI: 10.1002/hbm.22521] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/24/2014] [Accepted: 03/20/2014] [Indexed: 11/06/2022] Open
Abstract
Fragile X syndrome (FXS), due to mutations of the FMR1 gene, is the most common known inherited cause of developmental disability as well as the most common single-gene risk factor for autism. Our goal was to examine variation in brain structure in FXS with topological data analysis (TDA), and to assess how such variation is associated with measures of IQ and autism-related behaviors. To this end, we analyzed imaging and behavioral data from young boys (n = 52; aged 1.57-4.15 years) diagnosed with FXS. Application of topological methods to structural MRI data revealed two large subgroups within the study population. Comparison of these subgroups showed significant between-subgroup neuroanatomical differences similar to those previously reported to distinguish children with FXS from typically developing controls (e.g., enlarged caudate). In addition to neuroanatomy, the groups showed significant differences in IQ and autism severity scores. These results suggest that despite arising from a single gene mutation, FXS may encompass two biologically, and clinically separable phenotypes. In addition, these findings underscore the potential of TDA as a powerful tool in the search for biological phenotypes of neuropsychiatric disorders.
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Affiliation(s)
- David Romano
- Center for Interdisciplinary Brain Sciences Research, Stanford University Medical School, Stanford, California
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468
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Wang T, Chen B, Kim M, Xie Y, Xiao G. A model-based approach to identify binding sites in CLIP-Seq data. PLoS One 2014; 9:e93248. [PMID: 24714572 PMCID: PMC3979666 DOI: 10.1371/journal.pone.0093248] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/02/2014] [Indexed: 11/18/2022] Open
Abstract
Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present a novel model-based approach (MiClip) to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize subsequent validation experiments. The MiClip algorithm has been tested in both HITS-CLIP and PAR-CLIP datasets. In the HITS-CLIP dataset, the signal/noise ratios of miRNA seed motif enrichment produced by the MiClip approach are between 17% and 301% higher than those by the ad hoc method for the top 10 most enriched miRNAs. In the PAR-CLIP dataset, the MiClip approach can identify ∼50% more validated binding targets than the original ad hoc method and two recently published methods. To facilitate the application of the algorithm, we have released an R package, MiClip (http://cran.r-project.org/web/packages/MiClip/index.html), and a public web-based graphical user interface software (http://galaxy.qbrc.org/tool_runner?tool_id=mi_clip) for customized analysis.
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Affiliation(s)
- Tao Wang
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Beibei Chen
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - MinSoo Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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469
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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470
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Lin CW, Hsueh YP. Sarm1, a neuronal inflammatory regulator, controls social interaction, associative memory and cognitive flexibility in mice. Brain Behav Immun 2014; 37:142-51. [PMID: 24321214 DOI: 10.1016/j.bbi.2013.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/16/2013] [Accepted: 12/01/2013] [Indexed: 12/31/2022] Open
Abstract
Impaired neurodevelopment leads to several psychiatric disorders, including autism, schizophrenia and attention deficiency hyperactivity disorder. Our prior study showed that sterile alpha and TIR motif-containing 1 protein (Sarm1) regulates neuronal morphogenesis through at least two pathways. Sarm1 controls neuronal morphogenesis, including dendritic arborization, axonal outgrowth and establishment of neuronal polarity, through the MKK-JNK pathway. Neuronally expressed Sarm1 also regulates the expression of inflammatory cytokines in the brain, which have also been shown to impact brain development and function. Because the reduction of Sarm1 expression negatively influences neuronal development, here we investigated whether Sarm1 controls mouse behaviors. We analyzed two independent Sarm1 transgenic mouse lines using a series of behavioral assays, and found that the reduction of Sarm1 protein levels had a limited effect on locomotion and anxiety. However, Sarm1 knockdown mice exhibited impairments in cued and contextual fear conditioning as well as cognitive flexibility. Moreover, the three-chambered social test, reciprocal social interaction and social transmission of food preference further illustrated deficiencies in Sarm1 knockdown mice in social interaction. These findings suggest that Sarm1, a molecule that regulates innate immunity and neuronal morphogenesis, regulates social behaviors and cognition. We conclude that Sarm1 is involved in immune response, neural development and psychiatric disorders.
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Affiliation(s)
- Chia-Wen Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
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471
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Kleijer KTE, Schmeisser MJ, Krueger DD, Boeckers TM, Scheiffele P, Bourgeron T, Brose N, Burbach JPH. Neurobiology of autism gene products: towards pathogenesis and drug targets. Psychopharmacology (Berl) 2014; 231:1037-62. [PMID: 24419271 DOI: 10.1007/s00213-013-3403-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 12/14/2013] [Indexed: 12/22/2022]
Abstract
RATIONALE The genetic heterogeneity of autism spectrum disorders (ASDs) is enormous, and the neurobiology of proteins encoded by genes associated with ASD is very diverse. Revealing the mechanisms on which different neurobiological pathways in ASD pathogenesis converge may lead to the identification of drug targets. OBJECTIVE The main objective is firstly to outline the main molecular networks and neuronal mechanisms in which ASD gene products participate and secondly to answer the question how these converge. Finally, we aim to pinpoint drug targets within these mechanisms. METHOD Literature review of the neurobiological properties of ASD gene products with a special focus on the developmental consequences of genetic defects and the possibility to reverse these by genetic or pharmacological interventions. RESULTS The regulation of activity-dependent protein synthesis appears central in the pathogenesis of ASD. Through sequential consequences for axodendritic function, neuronal disabilities arise expressed as behavioral abnormalities and autistic symptoms in ASD patients. Several known ASD gene products have their effect on this central process by affecting protein synthesis intrinsically, e.g., through enhancing the mammalian target of rapamycin (mTOR) signal transduction pathway or through impairing synaptic function in general. These are interrelated processes and can be targeted by compounds from various directions: inhibition of protein synthesis through Lovastatin, mTOR inhibition using rapamycin, or mGluR-related modulation of synaptic activity. CONCLUSIONS ASD gene products may all feed into a central process of translational control that is important for adequate glutamatergic regulation of dendritic properties. This process can be modulated by available compounds but may also be targeted by yet unexplored routes.
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Affiliation(s)
- Kristel T E Kleijer
- Department Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3984 CG, Utrecht, The Netherlands
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472
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Weidner J, Wang C, Prescianotto-Baschong C, Estrada AF, Spang A. The polysome-associated proteins Scp160 and Bfr1 prevent P body formation under normal growth conditions. J Cell Sci 2014; 127:1992-2004. [PMID: 24569876 DOI: 10.1242/jcs.142083] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Numerous mRNAs are degraded in processing bodies (P bodies) in Saccharomyces cerevisiae. In logarithmically growing cells, only 0-1 P bodies per cell are detectable. However, the number and appearance of P bodies change once the cell encounters stress. Here, we show that the polysome-associated mRNA-binding protein Scp160 interacts with P body components, such as the decapping protein Dcp2 and the scaffold protein Pat1, presumably, on polysomes. Loss of either Scp160 or its interaction partner Bfr1 caused the formation of Dcp2-positive structures. These Dcp2-positive foci contained mRNA, because their formation was inhibited by the presence of cycloheximide. In addition, Scp160 was required for proper P body formation because only a subset of bona fide P body components could assemble into the Dcp2-positive foci in Δscp160 cells. In either Δbfr1 or Δscp160 cells, P body formation was uncoupled from translational attenuation as the polysome profile remained unchanged. Collectively, our data suggest that Bfr1 and Scp160 prevent P body formation under normal growth conditions.
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Affiliation(s)
- Julie Weidner
- Growth & Development, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
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473
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Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis. Mol Autism 2014; 5:16. [PMID: 24564913 PMCID: PMC3940253 DOI: 10.1186/2040-2392-5-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 02/04/2014] [Indexed: 12/31/2022] Open
Abstract
Background Fragile X syndrome and tuberous sclerosis are genetic syndromes that both have a high rate of comorbidity with autism spectrum disorder (ASD). Several lines of evidence suggest that these two monogenic disorders may converge at a molecular level through the dysfunction of activity-dependent synaptic plasticity. Methods To explore the characteristics of transcriptomic changes in these monogenic disorders, we profiled genome-wide gene expression levels in cerebellum and blood from murine models of fragile X syndrome and tuberous sclerosis. Results Differentially expressed genes and enriched pathways were distinct for the two murine models examined, with the exception of immune response-related pathways. In the cerebellum of the Fmr1 knockout (Fmr1-KO) model, the neuroactive ligand receptor interaction pathway and gene sets associated with synaptic plasticity such as long-term potentiation, gap junction, and axon guidance were the most significantly perturbed pathways. The phosphatidylinositol signaling pathway was significantly dysregulated in both cerebellum and blood of Fmr1-KO mice. In Tsc2 heterozygous (+/−) mice, immune system-related pathways, genes encoding ribosomal proteins, and glycolipid metabolism pathways were significantly changed in both tissues. Conclusions Our data suggest that distinct molecular pathways may be involved in ASD with known but different genetic causes and that blood gene expression profiles of Fmr1-KO and Tsc2+/− mice mirror some, but not all, of the perturbed molecular pathways in the brain.
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474
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Yun J, Wang T, Xiao G. Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP. Biometrics 2014; 70:430-40. [PMID: 24571656 DOI: 10.1111/biom.12147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/01/2013] [Accepted: 12/01/2013] [Indexed: 11/30/2022]
Abstract
The photoactivatable ribonucleoside enhanced cross-linking immunoprecipitation (PAR-CLIP) has been increasingly used for the global mapping of RNA-protein interaction sites. There are two key features of the PAR-CLIP experiments: The sequence read tags are likely to form an enriched peak around each RNA-protein interaction site; and the cross-linking procedure is likely to introduce a specific mutation in each sequence read tag at the interaction site. Several ad hoc methods have been developed to identify the RNA-protein interaction sites using either sequence read counts or mutation counts alone; however, rigorous statistical methods for analyzing PAR-CLIP are still lacking. In this article, we propose an integrative model to establish a joint distribution of observed read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we developed a novel modeling approach that adopts non-homogeneous hidden Markov models to incorporate the nucleotide sequence at each genomic location. Both simulation studies and data application showed that our method outperforms the ad hoc methods, and provides reliable inferences for the RNA-protein binding sites from PAR-CLIP data.
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Affiliation(s)
- Jonghyun Yun
- Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75290, USA
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475
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Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N, Roussos P, O’Dushlaine C, Chambert K, Bergen SE, Kähler A, Duncan L, Stahl E, Genovese G, Fernández E, Collins MO, Komiyama NH, Choudhary JS, Magnusson PKE, Banks E, Shakir K, Garimella K, Fennell T, de Pristo M, Grant SG, Haggarty S, Gabriel S, Scolnick EM, Lander ES, Hultman C, Sullivan PF, McCarroll SA, Sklar P. A polygenic burden of rare disruptive mutations in schizophrenia. Nature 2014; 506:185-90. [PMID: 24463508 PMCID: PMC4136494 DOI: 10.1038/nature12975] [Citation(s) in RCA: 1015] [Impact Index Per Article: 101.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/24/2013] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a common disease with a complex aetiology, probably involving multiple and heterogeneous genetic factors. Here, by analysing the exome sequences of 2,536 schizophrenia cases and 2,543 controls, we demonstrate a polygenic burden primarily arising from rare (less than 1 in 10,000), disruptive mutations distributed across many genes. Particularly enriched gene sets include the voltage-gated calcium ion channel and the signalling complex formed by the activity-regulated cytoskeleton-associated scaffold protein (ARC) of the postsynaptic density, sets previously implicated by genome-wide association and copy-number variation studies. Similar to reports in autism, targets of the fragile X mental retardation protein (FMRP, product of FMR1) are enriched for case mutations. No individual gene-based test achieves significance after correction for multiple testing and we do not detect any alleles of moderately low frequency (approximately 0.5 to 1 per cent) and moderately large effect. Taken together, these data suggest that population-based exome sequencing can discover risk alleles and complements established gene-mapping paradigms in neuropsychiatric disease.
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Affiliation(s)
- Shaun M. Purcell
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Jennifer L. Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Menachem Fromer
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Douglas Ruderfer
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nadia Solovieff
- Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Panos Roussos
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Colm O’Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Sarah E. Bergen
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
- Department of Medical Epidemiology and Biostatisics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Anna Kähler
- Department of Medical Epidemiology and Biostatisics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Laramie Duncan
- Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Eli Stahl
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Esperanza Fernández
- Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium; VIB Center for Biology of Disease, 3000 Leuven, Belgium
| | - Mark O Collins
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Noboru H. Komiyama
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Jyoti S. Choudhary
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatisics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Eric Banks
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Khalid Shakir
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Kiran Garimella
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Tim Fennell
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Mark de Pristo
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Seth G.N. Grant
- Genes to Cognition Programme, Centre for Clinical Brain Sciences and Centre for Neuroregeneration, The University of Edinburgh, Edinburgh, UK
| | - Stephen Haggarty
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Stacey Gabriel
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Edward M. Scolnick
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Eric S. Lander
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatisics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599-7264, USA
| | - Steven A. McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
- Medical & Population Genetics Program, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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476
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Glutamatergic candidate genes in autism spectrum disorder: an overview. J Neural Transm (Vienna) 2014; 121:1081-106. [PMID: 24493018 DOI: 10.1007/s00702-014-1161-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/13/2014] [Indexed: 12/22/2022]
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental disorders with early onset in childhood. Most of the risk for ASD can be explained by genetic variants that act in interaction with biological environmental risk factors. However, the architecture of the genetic components is still unclear. Genetic studies and subsequent systems biological approaches described converging functional effects of identified genes towards pathways relevant for neuronal signalling. Mouse models suggest an aberrant synaptic plasticity at the neuropathological level, which is believed to be conferred by dysregulation of long-term potentiation or depression of neuronal connections. A central pathway regulating these mechanisms is glutamatergic signalling. Here, we hypothesized that susceptibility genes for ASD are enriched for components of this pathway. To further understand the impact of ASD risk genes on the glutamatergic pathway, we performed a systematic review using the literature database "pubmed" and the "AutismKB" knowledgebase. We provide an overview of the glutamatergic system in typical brain function and development, and summarize findings from linkage, association, copy number variants, and sequencing studies in ASD to provide a comprehensive picture of the glutamatergic landscape of ASD genetics. Genetic variants associated with ASD were enriched in glutamatergic pathways, affecting receptor signalling, metabolism and transport. Furthermore, in genetically modified mouse models for ASD, pharmacological compounds acting on ionotropic or metabotropic receptor activity are able to rescue ASD reminscent phenotypes. We conclude that glutamatergic genetic risk factors for ASD show a complex pattern and further studies are needed to fully understand its mechanisms, before translation of findings into clinical applications and individualized treatment approaches will be possible.
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477
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Wittkowski KM, Sonakya V, Bigio B, Tonn MK, Shic F, Ascano M, Nasca C, Gold-Von Simson G. A novel computational biostatistics approach implies impaired dephosphorylation of growth factor receptors as associated with severity of autism. Transl Psychiatry 2014; 4:e354. [PMID: 24473445 PMCID: PMC3905234 DOI: 10.1038/tp.2013.124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/16/2013] [Accepted: 11/25/2013] [Indexed: 01/05/2023] Open
Abstract
The prevalence of autism spectrum disorders (ASDs) has increased 20-fold over the past 50 years to >1% of US children. Although twin studies attest to a high degree of heritability, the genetic risk factors are still poorly understood. We analyzed data from two independent populations using u-statistics for genetically structured wide-locus data and added data from unrelated controls to explore epistasis. To account for systematic, but disease-unrelated differences in (non-randomized) genome-wide association studies (GWAS), a correlation between P-values and minor allele frequency with low granularity data and for conducting multiple tests in overlapping genetic regions, we present a novel study-specific criterion for 'genome-wide significance'. From recent results in a comorbid disease, childhood absence epilepsy, we had hypothesized that axonal guidance and calcium signaling are involved in autism as well. Enrichment of the results in both studies with related genes confirms this hypothesis. Additional ASD-specific variations identified in this study suggest protracted growth factor signaling as causing more severe forms of ASD. Another cluster of related genes suggests chloride and potassium ion channels as additional ASD-specific drug targets. The involvement of growth factors suggests the time of accelerated neuronal growth and pruning at 9-24 months of age as the period during which treatment with ion channel modulators would be most effective in preventing progression to more severe forms of autism. By extension, the same computational biostatistics approach could yield profound insights into the etiology of many common diseases from the genetic data collected over the last decade.
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Affiliation(s)
- K M Wittkowski
- The Rockefeller University, Center for Clinical and Translational Science, New York, NY, USA
| | - V Sonakya
- The Rockefeller University, Center for Clinical and Translational Science, New York, NY, USA
| | - B Bigio
- The Rockefeller University, Center for Clinical and Translational Science, New York, NY, USA
| | - M K Tonn
- Hochschule Koblenz, RheinAhrCampus, Joseph-Rovan-Allee 2, Remagen, Germany
| | - F Shic
- Yale School of Medicine, Yale Autism Program, New Haven, CT, USA
| | - M Ascano
- Tuschl Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - C Nasca
- McEwen Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
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478
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Maurin T, Zongaro S, Bardoni B. Fragile X Syndrome: from molecular pathology to therapy. Neurosci Biobehav Rev 2014; 46 Pt 2:242-55. [PMID: 24462888 DOI: 10.1016/j.neubiorev.2014.01.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 02/09/2023]
Abstract
Fragile X Syndrome (FXS) is the most common form of inherited intellectual disability due to the silencing of the FMR1 gene encoding FMRP (Fragile X Mental Retardation Protein), an RNA-binding protein involved in different steps of RNA metabolism. Of particular interest is the key role of FMRP in translational regulation. Since the first functional characterizations of FMRP, its role has been underlined by its association with actively translating polyribosomes. Furthermore, a plethora of mRNA targets of FMRP have been identified. In the absence of FMRP the deregulation of translation/transport/stability of these mRNAs has a cascade effect on many pathways, resulting into the final phenotype. We review here a set of targets of FMRP (mRNAs and proteins) that may have an impact on the FXS phenotype by deregulating some key cellular processes, such as translation, cytoskeleton remodeling and oxidative stress. The manipulation of these abnormal pathways by specific drugs may represent new therapeutic opportunities for FXS patients.
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Affiliation(s)
- Thomas Maurin
- Institute of Molecular and Cellular Pharmacology, CNRS UMR7275, University of Nice Sophia Antipolis, Route des Lucioles, 06560 Valbonne, France
| | - Samantha Zongaro
- Institute of Molecular and Cellular Pharmacology, CNRS UMR7275, University of Nice Sophia Antipolis, Route des Lucioles, 06560 Valbonne, France
| | - Barbara Bardoni
- Institute of Molecular and Cellular Pharmacology, CNRS UMR7275, University of Nice Sophia Antipolis, Route des Lucioles, 06560 Valbonne, France.
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479
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Fukunaga T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H. CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biol 2014; 15:R16. [PMID: 24447569 PMCID: PMC4053987 DOI: 10.1186/gb-2014-15-1-r16] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/21/2014] [Indexed: 12/02/2022] Open
Abstract
RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP–RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts. CapR is available at https://sites.google.com/site/fukunagatsu/software/capr.
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480
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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: 79] [Impact Index Per Article: 7.9] [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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481
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Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol 2014; 15:R12. [PMID: 24401661 PMCID: PMC4053807 DOI: 10.1186/gb-2014-15-1-r12] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 01/08/2013] [Indexed: 02/05/2023] Open
Abstract
Background ZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embryonic kidney cells, and examined the combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Results Targets bound and negatively regulated by ZFP36 include transcripts encoding proteins necessary for immune function and cancer, and transcripts encoding other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance upon ZFP36 overexpression independent of effects from confounding features. Genes with increased mRNA half-lives in ZFP36 knockout versus wild-type mouse cells were significantly enriched for our human ZFP36 targets. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes, and found that ZFP36 degrades transcripts through specific AU-rich sequences, representing a subset of the U-rich sequences ELAVL1 interacts with to stabilize transcripts. Conclusions ZFP36-RNA target specificities in vivo are quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to unravel in vivo combinatorial regulation by RNA-binding proteins.
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482
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Wang T, Xie Y, Xiao G. dCLIP: a computational approach for comparative CLIP-seq analyses. Genome Biol 2014; 15:R11. [PMID: 24398258 PMCID: PMC4054096 DOI: 10.1186/gb-2014-15-1-r11] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 01/07/2014] [Indexed: 12/13/2022] Open
Abstract
Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.
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483
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Friedersdorf MB, Keene JD. Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biol 2014; 15:R2. [PMID: 24393468 PMCID: PMC4053780 DOI: 10.1186/gb-2014-15-1-r2] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 01/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequence specific RNA binding proteins are important regulators of gene expression. Several related crosslinking-based, high-throughput sequencing methods, including PAR-CLIP, have recently been developed to determine direct binding sites of global protein-RNA interactions. However, no studies have quantitatively addressed the contribution of background binding to datasets produced by these methods. RESULTS We measured non-specific RNA background in PAR-CLIP data, demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal among laboratories. We show that quantitative determination of background is essential for identifying targets of most RNA-binding proteins and can substantially improve motif analysis. We also demonstrate that by applying background correction to an RNA binding protein of unknown binding specificity, Caprin1, we can identify a previously unrecognized RNA recognition element not otherwise apparent in a PAR-CLIP study. CONCLUSIONS Empirical background measurements of global RNA-protein crosslinking are a necessary addendum to other experimental controls, such as performing replicates, because covalently crosslinked background signals are reproducible and otherwise unavoidable. Recognizing and quantifying the contribution of background extends the utility of PAR-CLIP and can improve mechanistic understanding of protein-RNA specificity, protein-RNA affinity and protein-RNA association dynamics.
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484
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The Fragile X mental retardation protein regulates matrix metalloproteinase 9 mRNA at synapses. J Neurosci 2014; 33:18234-41. [PMID: 24227732 DOI: 10.1523/jneurosci.2207-13.2013] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Activity-dependent protein synthesis at synapses is dysregulated in the Fragile X syndrome (FXS). This process contributes to dendritic spine dysmorphogenesis and synaptic dysfunction in FXS. Matrix Metalloproteinase 9 (MMP-9) is an enzyme involved in activity-dependent reorganization of dendritic spine architecture and was shown to regulate spine morphology in a mouse model of FXS, the Fmr1 knock-out mice. Here we show that MMP-9 mRNA is part of the FMRP complex and colocalizes in dendrites. In the absence of FMRP MMP-9 mRNA translation is increased at synapses, suggesting that this mechanism contributes to the increased metalloproteinase level at synapses of Fmr1 knock-out mice. We propose that such a local effect can contribute to the aberrant dendritic spine morphology observed in the Fmr1 knock-out mice and in patients with FXS.
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485
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Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
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Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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486
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Li Y, Tang W, Zhang LR, Zhang CY. FMRP regulates miR196a-mediated repression of HOXB8 via interaction with the AGO2 MID domain. MOLECULAR BIOSYSTEMS 2014; 10:1757-64. [DOI: 10.1039/c4mb00066h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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487
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Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:1-55. [PMID: 25201102 DOI: 10.1007/978-1-4939-1221-6_1] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.
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488
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Jacquemont S, Berry-Kravis E, Hagerman R, von Raison F, Gasparini F, Apostol G, Ufer M, Des Portes V, Gomez-Mancilla B. The challenges of clinical trials in fragile X syndrome. Psychopharmacology (Berl) 2014; 231:1237-50. [PMID: 24173622 PMCID: PMC3932172 DOI: 10.1007/s00213-013-3289-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/05/2013] [Indexed: 11/28/2022]
Abstract
RATIONALE Advances in understanding the underlying mechanisms of conditions such as fragile X syndrome (FXS) and autism spectrum disorders have revealed heterogeneous populations. Recent trials of novel FXS therapies have highlighted several challenges including subpopulations with possibly differential therapeutic responses, the lack of specific outcome measures capturing the full range of improvements of patients with FXS, and a lack of biomarkers that can track whether a specific mechanism is responsive to a new drug and whether the response correlates with clinical improvement. OBJECTIVES We review the phenotypic heterogeneity of FXS and the implications for clinical research in FXS and other neurodevelopmental disorders. RESULTS Residual levels of fragile X mental retardation protein (FMRP) expression explain in part the heterogeneity in the FXS phenotype; studies indicate a correlation with both cognitive and behavioral deficits. However, this does not fully explain the extent of phenotypic variance observed or the variability of drug response. Post hoc analyses of studies involving the selective mGluR5 antagonist mavoglurant and the GABAB agonist arbaclofen have uncovered significant therapeutic responses following patient stratification according to FMR1 promoter methylation patterns or baseline severity of social withdrawal, respectively. Future studies designed to quantify disease modification will need to develop new strategies to track changes effectively over time and in multiple symptom domains. CONCLUSION Appropriate selection of patients and outcome measures is central to optimizing future clinical investigations of these complex disorders.
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Affiliation(s)
- Sébastien Jacquemont
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Elizabeth Berry-Kravis
- Departments of Pediatrics, Neurological Sciences and Biochemistry, Rush University Medical Center, Chicago, IL 60612 USA
| | - Randi Hagerman
- MIND Institute and Department of Pediatrics, UC Davis Health System, Sacramento, CA 95817 USA
| | | | - Fabrizio Gasparini
- Novartis Institutes for BioMedical Research Basel, Forum 1, Novartis Campus, 4056 Basel, Switzerland
| | - George Apostol
- Neuroscience Development, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Mike Ufer
- Novartis Institutes for BioMedical Research Basel, Forum 1, Novartis Campus, 4056 Basel, Switzerland
| | - Vincent Des Portes
- National Reference Center for Fragile X and Other XLMR, Hospices Civils de Lyon, Université de Lyon and CNRS UMR 5304 (L2C2), Bron, France
| | - Baltazar Gomez-Mancilla
- Novartis Institutes for BioMedical Research Basel, Forum 1, Novartis Campus, 4056 Basel, Switzerland
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489
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Sethna F, Moon C, Wang H. From FMRP function to potential therapies for fragile X syndrome. Neurochem Res 2013; 39:1016-31. [PMID: 24346713 DOI: 10.1007/s11064-013-1229-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/03/2013] [Accepted: 12/12/2013] [Indexed: 12/12/2022]
Abstract
Fragile X syndrome (FXS) is caused by mutations in the fragile X mental retardation 1 (FMR1) gene. Most FXS cases occur due to the expansion of the CGG trinucleotide repeats in the 5' un-translated region of FMR1, which leads to hypermethylation and in turn silences the expression of FMRP (fragile X mental retardation protein). Numerous studies have demonstrated that FMRP interacts with both coding and non-coding RNAs and represses protein synthesis at dendritic and synaptic locations. In the absence of FMRP, the basal protein translation is enhanced and not responsive to neuronal stimulation. The altered protein translation may contribute to functional abnormalities in certain aspects of synaptic plasticity and intracellular signaling triggered by Gq-coupled receptors. This review focuses on the current understanding of FMRP function and potential therapeutic strategies that are mainly based on the manipulation of FMRP targets and knowledge gained from FXS pathophysiology.
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Affiliation(s)
- Ferzin Sethna
- Genetics Program, Michigan State University, East Lansing, MI, 48824, USA
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490
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Derlig K, Gießl A, Brandstätter JH, Enz R, Dahlhaus R. Identification and characterisation of Simiate, a novel protein linked to the fragile X syndrome. PLoS One 2013; 8:e83007. [PMID: 24349419 PMCID: PMC3859600 DOI: 10.1371/journal.pone.0083007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/07/2013] [Indexed: 11/19/2022] Open
Abstract
A strict regulation of protein expression during developmental stages and in response to environmental signals is essential to every cell and organism. Recent research has shown that the mammalian brain is particularly sensitive to alterations in expression patterns of specific proteins and cognitive deficits as well as autistic behaviours have been linked to dysregulated protein expression. An intellectual disability characterised by changes in the expression of a variety of proteins is the fragile X syndrome. Due to the loss of a single mRNA binding protein, the Fragile X Mental Retardation Protein FMRP, vast misregulation of the mRNA metabolism is taking place in the disease. Here, we present the identification and characterisation of a novel protein named Simiate, whose mRNA contains several FMRP recognition motifs and associates with FMRP upon co-precipitation. Sequence analysis revealed that the protein evolved app. 1.7 billion years ago when eukaryotes developed. Applying antibodies generated against Simiate, the protein is detected in a variety of tissues, including the mammalian brain. On the subcellular level, Simiate localises to somata and nuclear speckles. We show that Simiate and nuclear speckles experience specific alterations in FMR1(-/-) mice. An antibody-based block of endogenous Simiate revealed that the protein is essential for cell survival. These findings suggest not only an important role for Simiate in gene transcription and/or RNA splicing, but also provide evidence for a function of nuclear speckles in the fragile X syndrome. Indeed, transcription and splicing are two fundamental mechanisms to control protein expression, that underlie not only synaptic plasticity and memory formation, but are also affected in several diseases associated with mental disabilities.
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Affiliation(s)
- Kristin Derlig
- Institute for Biochemistry, Emil-Fischer Centre, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Andreas Gießl
- Department of Biology, Animal Physiology, University of Erlangen- Nuremberg, Erlangen, Germany
| | | | - Ralf Enz
- Institute for Biochemistry, Emil-Fischer Centre, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Regina Dahlhaus
- Institute for Biochemistry, Emil-Fischer Centre, University of Erlangen-Nuremberg, Erlangen, Germany
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491
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Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L, Jia G, Yu M, Lu Z, Deng X, Dai Q, Chen W, He C. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol 2013; 10:93-5. [PMID: 24316715 PMCID: PMC3911877 DOI: 10.1038/nchembio.1432] [Citation(s) in RCA: 2113] [Impact Index Per Article: 192.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 12/02/2013] [Indexed: 01/13/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent and reversible internal modification in mammalian messenger and non-coding RNAs. We report here that human METTL14 catalyzes m6A RNA methylation. Together with METTL3, the only previously known m6A methyltransferase, these two proteins form a stable heterodimer core complex of METTL3-14 that functions in cellular m6A deposition on mammalian nuclear RNAs. WTAP, a mammalian splicing factor, can interact with this complex and affect this methylation.
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Affiliation(s)
- Jianzhao Liu
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA. [3]
| | - Yanan Yue
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA. [3]
| | - Dali Han
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Xiao Wang
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Ye Fu
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Liang Zhang
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Guifang Jia
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Miao Yu
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Zhike Lu
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Xin Deng
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Qing Dai
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Weizhong Chen
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Chuan He
- 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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492
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Li X, Kazan H, Lipshitz HD, Morris QD. Finding the target sites of RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:111-30. [PMID: 24217996 PMCID: PMC4253089 DOI: 10.1002/wrna.1201] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 12/15/2022]
Abstract
RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201
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Affiliation(s)
- Xiao Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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493
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Steinberg J, Webber C. The roles of FMRP-regulated genes in autism spectrum disorder: single- and multiple-hit genetic etiologies. Am J Hum Genet 2013; 93:825-39. [PMID: 24207117 DOI: 10.1016/j.ajhg.2013.09.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 09/21/2013] [Accepted: 09/26/2013] [Indexed: 11/26/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable complex neurodevelopmental condition characterized by impairments in social interaction and communication and restricted and repetitive behaviors. Although roles for both de novo and familial genetic variation have been documented, the underlying disease mechanisms remain poorly elucidated. In this study, we defined and explored distinct etiologies of genetic variants that affect genes regulated by Fragile-X mental retardation protein (FMRP), thought to play a key role in neuroplasticity and neuronal translation, in ASD-affected individuals. In particular, we developed the Trend test, a pathway-association test that is able to robustly detect multiple-hit etiologies and is more powerful than existing approaches. Exploiting detailed spatiotemporal maps of gene expression within the human brain, we identified four discrete FMRP-target subpopulations that exhibit distinct functional biases and contribute to ASD via different types of genetic variation. We also demonstrated that FMRP target genes are more likely than other genes with similar expression patterns to contribute to disease. We developed the hypothesis that FMRP targets contribute to ASD via two distinct etiologies: (1) ultra-rare and highly penetrant single disruptions of embryonically upregulated FMRP targets ("single-hit etiology") or (2) the combination of multiple less penetrant disruptions of nonembryonic, synaptic FMRP targets ("multiple-hit etiology"). The Trend test provides rigorous support for a multiple-hit genetic etiology in a subset of autism cases and is easily extendible to combining information from multiple types of genetic variation (i.e., copy-number and exome variants), increasing its value to next-generation sequencing approaches.
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494
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Nolze A, Schneider J, Keil R, Lederer M, Hüttelmaier S, Kessels MM, Qualmann B, Hatzfeld M. FMRP regulates actin filament organization via the armadillo protein p0071. RNA (NEW YORK, N.Y.) 2013; 19:1483-96. [PMID: 24062571 PMCID: PMC3851716 DOI: 10.1261/rna.037945.112] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Loss of fragile X mental retardation protein (FMRP) causes synaptic dysfunction and intellectual disability. FMRP is an RNA-binding protein that controls the translation or turnover of a subset of mRNAs. Identifying these target transcripts is an important step toward understanding the pathology of the disease. Here, we show that FMRP regulates actin organization and neurite outgrowth via the armadillo protein p0071. In mouse embryonic fibroblasts (MEFs) lacking FMRP (Fmr1-), the actin cytoskeleton was markedly reorganized with reduced stress fibers and F-actin/G-actin ratios compared to fibroblasts re-expressing the protein. FMRP interfered with the translation of the p0071 mRNA in a 3'-UTR-dependent manner. Accordingly, FMRP-depleted cells revealed elevated levels of p0071 protein. The knockdown of p0071 in Fmr1- fibroblasts restored stress fibers and an elongated cell shape, thus rescuing the Fmr1- phenotype, whereas overexpression of p0071 in Fmr1+ cells mimicked the Fmr1- phenotype. Moreover, p0071 and FMRP regulated neurite outgrowth and branching in a diametrically opposed way in agreement with the negative regulation of p0071 by FMRP. These results identify p0071 as an important and novel FMRP target and strongly suggest that impaired actin cytoskeletal functions mediated by an excess of p0071 are key aspects underlying the fragile X syndrome.
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Affiliation(s)
- Alexander Nolze
- Institute of Molecular Medicine, Division of Pathobiochemistry, Martin-Luther-University of Halle, 06114 Halle, Germany
| | - Jacqueline Schneider
- Institute for Biochemistry I, Jena University Hospital–Friedrich Schiller University Jena, 07743 Jena, Germany
| | - René Keil
- Institute of Molecular Medicine, Division of Pathobiochemistry, Martin-Luther-University of Halle, 06114 Halle, Germany
| | - Marcell Lederer
- Institute of Molecular Medicine, Division of Cell Biology, Martin-Luther-University of Halle, 06120 Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Division of Cell Biology, Martin-Luther-University of Halle, 06120 Halle, Germany
| | - Michael M. Kessels
- Institute for Biochemistry I, Jena University Hospital–Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Britta Qualmann
- Institute for Biochemistry I, Jena University Hospital–Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mechthild Hatzfeld
- Institute of Molecular Medicine, Division of Pathobiochemistry, Martin-Luther-University of Halle, 06114 Halle, Germany
- Corresponding authorE-mail
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495
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Kroon T, Sierksma MC, Meredith RM. Investigating mechanisms underlying neurodevelopmental phenotypes of autistic and intellectual disability disorders: a perspective. Front Syst Neurosci 2013; 7:75. [PMID: 24198768 PMCID: PMC3814085 DOI: 10.3389/fnsys.2013.00075] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/15/2013] [Indexed: 12/24/2022] Open
Abstract
Brain function and behavior undergo significant plasticity and refinement, particularly during specific critical and sensitive periods. In autistic and intellectual disability (ID) neurodevelopmental disorders (NDDs) and their corresponding genetic mouse models, impairments in many neuronal and behavioral phenotypes are temporally regulated and in some cases, transient. However, the links between neurobiological mechanisms governing typically normal brain and behavioral development (referred to also as "neurotypical" development) and timing of NDD impairments are not fully investigated. This perspective highlights temporal patterns of synaptic and neuronal impairment, with a restricted focus on autism and ID types of NDDs. Given the varying known genetic and environmental causes for NDDs, this perspective proposes two strategies for investigation: (1) a focus on neurobiological mechanisms underlying known critical periods in the (typically) normal-developing brain; (2) investigation of spatio-temporal expression profiles of genes implicated in monogenic syndromes throughout affected brain regions. This approach may help explain why many NDDs with differing genetic causes can result in overlapping phenotypes at similar developmental stages and better predict vulnerable periods within these disorders, with implications for both therapeutic rescue and ultimately, prevention.
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Affiliation(s)
- Tim Kroon
- Department of Integrative Neurophysiology, Centre for Neurogenomics and Cognitive Research (CNCR), Neuroscience Campus Amsterdam, VU University Amsterdam, Netherlands
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496
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Fernández E, Rajan N, Bagni C. The FMRP regulon: from targets to disease convergence. Front Neurosci 2013; 7:191. [PMID: 24167470 PMCID: PMC3807044 DOI: 10.3389/fnins.2013.00191] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/04/2013] [Indexed: 01/08/2023] Open
Abstract
The fragile X mental retardation protein (FMRP) is an RNA-binding protein that regulates mRNA metabolism. FMRP has been largely studied in the brain, where the absence of this protein leads to fragile X syndrome, the most frequent form of inherited intellectual disability. Since the identification of the FMRP gene in 1991, many studies have primarily focused on understanding the function/s of this protein. Hundreds of potential FMRP mRNA targets and several interacting proteins have been identified. Here, we report the identification of FMRP mRNA targets in the mammalian brain that support the key role of this protein during brain development and in regulating synaptic plasticity. We compared the genes from databases and genome-wide association studies with the brain FMRP transcriptome, and identified several FMRP mRNA targets associated with autism spectrum disorders, mood disorders and schizophrenia, showing a potential common pathway/s for these apparently different disorders.
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Affiliation(s)
- Esperanza Fernández
- Center for the Biology of Disease, Vlaams Institut voor Biotechnologie Leuven, Belgium ; Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven Leuven, Belgium
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497
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Oldenburg AR, Delbarre E, Thiede B, Vigouroux C, Collas P. Deregulation of Fragile X-related protein 1 by the lipodystrophic lamin A p.R482W mutation elicits a myogenic gene expression program in preadipocytes. Hum Mol Genet 2013; 23:1151-62. [PMID: 24108105 DOI: 10.1093/hmg/ddt509] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The nuclear lamina is implicated in the regulation of various nuclear functions. Several laminopathy-causing mutations in the LMNA gene, notably the p.R482W substitution linked to familial partial lipodystrophy type 2 (FPLD2), are clustered in the immunoglobulin fold of lamin A. We report a functional association between lamin A and fragile X-related protein 1 (FXR1P), a protein of the fragile X-related family involved in fragile X syndrome. Searching for proteins differentially interacting with the immunoglobulin fold of wild-type and R482W mutant lamin A, we identify FXR1P as a novel component of the lamin A protein network. The p.R482W mutation abrogates interaction of FXR1P with lamin A. Fibroblasts from FPLD2 patients display elevated levels of FXR1P and delocalized FXR1P. In human adipocyte progenitors, deregulation of lamin A expression leads to FXR1P up-regulation, impairment of adipogenic differentiation and induction of myogenin expression. FXR1P overexpression also stimulates a myogenic gene expression program in these cells. Our results demonstrate a cross-talk between proteins hitherto implicated in two distinct mesodermal pathologies. We propose a model where the FPLD2 lamin A p.R482W mutation elicits, through up-regulation of FXR1P, a remodeling of an adipogenic differentiation program into a myogenic program.
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Affiliation(s)
- Anja R Oldenburg
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences and Norwegian Center for Stem Cell Research, Faculty of Medicine, University of Oslo, PO Box 1112, Blindern, Oslo 0317, Norway
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498
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Chang KT, Ro H, Wang W, Min KT. Meeting at the crossroads: common mechanisms in Fragile X and Down syndrome. Trends Neurosci 2013; 36:685-94. [PMID: 24075449 DOI: 10.1016/j.tins.2013.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 10/26/2022]
Abstract
Intellectual disability is characterized by significantly impaired cognitive abilities and is due to various etiological factors, including both genetic and non-genetic causes. Two of the most common genetic forms of intellectual disability are Fragile X syndrome (FXS) and Down syndrome (DS). Recent studies have shown that proteins altered in FXS and DS can physically interact and participate in common signaling pathways regulating dendritic spine development and local protein synthesis, thus supporting the notion that spine dysmorphogenesis and abnormal local protein synthesis may be molecular underpinnings of intellectual disability. Here we review the molecular constituents regulating local protein synthesis and spine morphology and their alterations in FXS and DS. We argue that these changes might ultimately affect synaptic homeostasis and alter cognitive performance.
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Affiliation(s)
- Karen T Chang
- Zilkha Neurogenetic Institute and Department of Cell and Neurobiology, University of Southern California, Los Angeles, CA 90033, USA
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499
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Bagni C, Oostra BA. Fragile X syndrome: From protein function to therapy. Am J Med Genet A 2013; 161A:2809-21. [PMID: 24115651 DOI: 10.1002/ajmg.a.36241] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/28/2013] [Indexed: 12/23/2022]
Abstract
Fragile X syndrome (FXS) is the leading monogenic cause of intellectual disability and autism. The FMR1 gene contains a CGG repeat present in the 5'-untranslated region which can be unstable upon transmission to the next generation. The repeat is up to 55 CGGs long in the normal population. In patients with fragile X syndrome (FXS), a repeat length exceeding 200 CGGs generally leads to methylation of the repeat and the promoter region, which is accompanied by silencing of the FMR1 gene. The disease is a result of lack of expression of the fragile X mental retardation protein leading to severe symptoms, including intellectual disability, hyperactivity, and autistic-like behavior. The FMR1 protein (FMRP) has a number of functions. The translational dysregulation of a subset of mRNAs targeted by FMRP is probably the major contribution to FXS. FMRP is also involved in mRNA transport to synapses where protein synthesis occurs. For some FMRP-bound mRNAs, FMRP is a direct modulator of mRNA stability either by sustaining or preventing mRNA decay. Increased knowledge about the role of FMRP has led to the identification of potential treatments for fragile X syndrome that were often tested first in the different animal models. This review gives an overview about the present knowledge of the function of FMRP and the therapeutic strategies in mouse and man.
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Affiliation(s)
- Claudia Bagni
- VIB Center for the Biology of Disease, Catholic University of Leuven, Leuven, Belgium; Department of Biomedicine and Prevention, University of Rome, Tor Vergata, Italy
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500
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Panda AC, Grammatikakis I, Yoon JH, Abdelmohsen K. Posttranscriptional regulation of insulin family ligands and receptors. Int J Mol Sci 2013; 14:19202-29. [PMID: 24051403 PMCID: PMC3794829 DOI: 10.3390/ijms140919202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/17/2013] [Accepted: 09/06/2013] [Indexed: 01/02/2023] Open
Abstract
Insulin system including ligands (insulin and IGFs) and their shared receptors (IR and IGFR) are critical regulators of insulin signaling and glucose homeostasis. Altered insulin system is associated with major pathological conditions like diabetes and cancer. The mRNAs encoding for these ligands and their receptors are posttranscriptionally controlled by three major groups of regulators; (i) alternative splicing regulatory factors; (ii) turnover and translation regulator RNA-binding proteins (TTR-RBPs); and (iii) non-coding RNAs including miRNAs and long non-coding RNAs (lncRNAs). In this review, we discuss the influence of these regulators on alternative splicing, mRNA stability and translation. Due to the pathological impacts of insulin system, we also discussed the possibilities of discovering new potential regulators which will improve understanding of insulin system and associated diseases.
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Affiliation(s)
- Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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