351
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Mammalian FMRP S499 Is Phosphorylated by CK2 and Promotes Secondary Phosphorylation of FMRP. eNeuro 2016; 3:eN-NWR-0092-16. [PMID: 27957526 PMCID: PMC5116651 DOI: 10.1523/eneuro.0092-16.2016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/29/2022] Open
Abstract
The fragile X mental retardation protein (FMRP) is an mRNA-binding regulator of protein translation that associates with 4-6% of brain transcripts and is central to neurodevelopment. Autism risk genes’ transcripts are overrepresented among FMRP-binding mRNAs, and FMRP loss-of-function mutations are responsible for fragile X syndrome, the most common cause of monogenetic autism. It is thought that FMRP-dependent translational repression is governed by the phosphorylation of serine residue 499 (S499). However, recent evidence suggests that S499 phosphorylation is not modulated by metabotropic glutamate receptor class I (mGluR-I) or protein phosphatase 2A (PP2A), two molecules shown to regulate FMRP translational repression. Moreover, the mammalian FMRP S499 kinase remains unknown. We found that casein kinase II (CK2) phosphorylates murine FMRP S499. Further, we show that phosphorylation of FMRP S499 permits phosphorylation of additional, nearby residues. Evidence suggests that these nearby residues are modulated by mGluR-I and PP2A pathways. These data support an alternative phosphodynamic model of FMRP that is harmonious with prior studies and serves as a framework for further investigation.
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352
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The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nat Genet 2016; 49:36-45. [PMID: 27841880 DOI: 10.1038/ng.3720] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/17/2016] [Indexed: 12/16/2022]
Abstract
Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.
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353
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Kloetgen A, Borkhardt A, Hoell JI, McHardy AC. The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ 2016; 4:e2619. [PMID: 27812418 PMCID: PMC5088580 DOI: 10.7717/peerj.2619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/27/2016] [Indexed: 01/13/2023] Open
Abstract
Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, respectively, under the GNU GPLv3 license.
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Affiliation(s)
- Andreas Kloetgen
- Department for Algorithmic Bioinformatics, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf , Düsseldorf , Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf , Düsseldorf , Germany
| | - Alice C McHardy
- Department for Algorithmic Bioinformatics, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
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354
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Yeh E, Weiss LA. If genetic variation could talk: What genomic data may teach us about the importance of gene expression regulation in the genetics of autism. Mol Cell Probes 2016; 30:346-356. [PMID: 27751841 DOI: 10.1016/j.mcp.2016.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 11/25/2022]
Abstract
Autism spectrum disorder (ASD) has been long known to have substantial genetic etiology. Much research has attempted to identify specific genes contributing to ASD risk with the goal of tying gene function to a molecular pathological explanation for ASD. A unifying molecular pathology would potentially increase understanding of what is going wrong during development, and could lead to diagnostic biomarkers or targeted preventative or therapeutic directions. We review past and current genetic mapping approaches and discuss major results, leading to the hypothesis that global dysregulation of gene or protein expression may be implicated in ASD rather than disturbance of brain-specific functions. If substantiated, this hypothesis might indicate the need for novel experimental and analytical approaches in order to understand this neurodevelopmental disorder, develop biomarkers, or consider treatment approaches.
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Affiliation(s)
- Erika Yeh
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Lauren A Weiss
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94143, USA.
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355
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Wang GX, Smith SJ, Mourrain P. Sub-synaptic, multiplexed analysis of proteins reveals Fragile X related protein 2 is mislocalized in Fmr1 KO synapses. eLife 2016; 5. [PMID: 27770568 PMCID: PMC5098911 DOI: 10.7554/elife.20560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022] Open
Abstract
The distribution of proteins within sub-synaptic compartments is an essential aspect of their neurological function. Current methodologies, such as electron microscopy (EM) and super-resolution imaging techniques, can provide the precise localization of proteins, but are often limited to a small number of one-time observations with narrow spatial and molecular coverage. The diversity of synaptic proteins and synapse types demands synapse analysis on a scale that is prohibitive with current methods. Here, we demonstrate SubSynMAP, a fast, multiplexed sub-synaptic protein analysis method using wide-field data from deconvolution array tomography (ATD). SubSynMAP generates probability distributions for that reveal the functional range of proteins within the averaged synapse of a particular class. This enables the differentiation of closely juxtaposed proteins. Using this method, we analyzed 15 synaptic proteins in normal and Fragile X mental retardation syndrome (FXS) model mouse cortex, and revealed disease-specific modifications of sub-synaptic protein distributions across synapse classes and cortical layers. DOI:http://dx.doi.org/10.7554/eLife.20560.001
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Affiliation(s)
- Gordon X Wang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, United States.,Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Stephen J Smith
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Allen Institute for Brain Science, Seattle, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, United States.,Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, United States.,INSERM 1024, Ecole Normale Supérieure, Paris, France
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356
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Wise TL. Changes in insulin-like growth factor signaling alter phenotypes in Fragile X Mice. GENES BRAIN AND BEHAVIOR 2016; 16:241-249. [DOI: 10.1111/gbb.12340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/30/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Affiliation(s)
- T. L. Wise
- Department of Human Genetics; New York State Institute for Basic Research in Developmental Disabilities; Staten Island NY USA
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357
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Lu P, Chen X, Feng Y, Zeng Q, Jiang C, Zhu X, Fan G, Xue Z. Integrated transcriptome analysis of human iPS cells derived from a fragile X syndrome patient during neuronal differentiation. SCIENCE CHINA. LIFE SCIENCES 2016; 59:1093-1105. [PMID: 27730449 DOI: 10.1007/s11427-016-0194-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/05/2016] [Indexed: 01/01/2023]
Abstract
Fragile X syndrome (FXS) patients carry the expansion of over 200 CGG repeats at the promoter of fragile X mental retardation 1 (FMR1), leading to decreased or absent expression of its encoded fragile X mental retardation protein (FMRP). However, the global transcriptional alteration by FMRP deficiency has not been well characterized at single nucleotide resolution, i.e., RNA-seq. Here, we performed in-vitro neuronal differentiation of human induced pluripotent stem (iPS) cells that were derived from fibroblasts of a FXS patient (FXS-iPSC). We then performed RNA-seq and examined the transcriptional misregulation at each intermediate stage during in-vitro differentiation of FXS-iPSC into neurons. After thoroughly analyzing the transcriptomic data and integrating them with those from other platforms, we found up-regulation of many genes encoding TFs for neuronal differentiation (WNT1, BMP4, POU3F4, TFAP2C, and PAX3), down-regulation of potassium channels (KCNA1, KCNC3, KCNG2, KCNIP4, KCNJ3, KCNK9, and KCNT1) and altered temporal regulation of SHANK1 and NNAT in FXS-iPSC derived neurons, indicating impaired neuronal differentiation and function in FXS patients. In conclusion, we demonstrated that the FMRP deficiency in FXS patients has significant impact on the gene expression patterns during development, which will help to discover potential targeting candidates for the cure of FXS symptoms.
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Affiliation(s)
- Ping Lu
- Tongji Stem Cell Research Center, Tongji University School of Medicine, Shanghai, 200092, China
| | - Xiaolong Chen
- Tongji University, School of Life Sciences and Technology, Shanghai, 200092, China
| | - Yun Feng
- Tongji Stem Cell Research Center, Tongji University School of Medicine, Shanghai, 200092, China
| | - Qiao Zeng
- Tongji Stem Cell Research Center, Tongji University School of Medicine, Shanghai, 200092, China
| | - Cizhong Jiang
- Tongji University, School of Life Sciences and Technology, Shanghai, 200092, China
| | - Xianmin Zhu
- Tongji University, School of Life Sciences and Technology, Shanghai, 200092, China.
| | - Guoping Fan
- Tongji University, School of Life Sciences and Technology, Shanghai, 200092, China.
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Zhigang Xue
- Tongji Stem Cell Research Center, Tongji University School of Medicine, Shanghai, 200092, China.
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China.
- Tongji University Suzhou Institute, Suzhou, 215101, China.
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358
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Rosario R, Filis P, Tessyman V, Kinnell H, Childs AJ, Gray NK, Anderson RA. FMRP Associates with Cytoplasmic Granules at the Onset of Meiosis in the Human Oocyte. PLoS One 2016; 11:e0163987. [PMID: 27695106 PMCID: PMC5047637 DOI: 10.1371/journal.pone.0163987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/16/2016] [Indexed: 01/09/2023] Open
Abstract
Germ cell development and primordial follicle formation during fetal life is critical in establishing the pool of oocytes that subsequently determines the reproductive lifespan of women. Fragile X-associated primary ovarian insufficiency (FXPOI) is caused by inheritance of the FMR1 premutation allele and approximately 20% of women with the premutation allele develop ovarian dysfunction and premature ovarian insufficiency. However, the underlying disease mechanism remains obscure, and a potential role of FMRP in human ovarian development has not been explored. We have characterised the expression of FMR1 and FMRP in the human fetal ovary at the time of germ cell entry into meiosis through to primordial follicle formation. FMRP expression is exclusively in germ cells in the human fetal ovary. Increased FMRP expression in germ cells coincides with the loss of pluripotency-associated protein expression, and entry into meiosis is associated with FMRP granulation. In addition, we have uncovered FMRP association with components of P-bodies and stress granules, suggesting it may have a role in mRNA metabolism at the time of onset of meiosis. Therefore, this data support the hypothesis that FMRP plays a role regulating mRNAs during pivotal maturational processes in fetal germ cells, and ovarian dysfunction resulting from FMR1 premutation may have its origins during these stages of oocyte development.
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Affiliation(s)
- Roseanne Rosario
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Panagiotis Filis
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Victoria Tessyman
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Hazel Kinnell
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Andrew J. Childs
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Nicola K. Gray
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Richard A. Anderson
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
- * E-mail:
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359
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Arsenault J, Gholizadeh S, Niibori Y, Pacey LK, Halder SK, Koxhioni E, Konno A, Hirai H, Hampson DR. FMRP Expression Levels in Mouse Central Nervous System Neurons Determine Behavioral Phenotype. Hum Gene Ther 2016; 27:982-996. [PMID: 27604541 PMCID: PMC5178026 DOI: 10.1089/hum.2016.090] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is absent or highly reduced in Fragile X Syndrome, a genetic disorder causing cognitive impairment and autistic behaviors. Previous proof-of-principle studies have demonstrated that restoring FMRP in the brain using viral vectors can improve pathological abnormalities in mouse models of fragile X. However, unlike small molecule drugs where the dose can readily be adjusted during treatment, viral vector–based biological therapeutic drugs present challenges in terms of achieving optimal dosing and expression levels. The objective of this study was to investigate the consequences of expressing varying levels of FMRP selectively in neurons of Fmr1 knockout and wild-type (WT) mice. A wide range of neuronal FMRP transgene levels was achieved in individual mice after intra-cerebroventricular administration of adeno-associated viral vectors coding for FMRP. In all treated knockout mice, prominent FMRP transgene expression was observed in forebrain structures, whereas lower levels were present in more caudal regions of the brain. Reduced levels of the synaptic protein PSD-95, elevated levels of the transcriptional modulator MeCP2, and abnormal motor activity, anxiety, and acoustic startle responses in Fmr1 knockout mice were fully or partially rescued after expression of FMRP at about 35–115% of WT expression, depending on the brain region examined. In the WT mouse, moderate FMRP over-expression of up to about twofold had little or no effect on PSD-95 and MeCP2 levels or on behavioral endophenotypes. In contrast, excessive over-expression in the Fmr1 knockout mouse forebrain (approximately 2.5–6-fold over WT) induced pathological motor hyperactivity and suppressed the startle response relative to WT mice. These results delineate a range of FMRP expression levels in the central nervous system that confer phenotypic improvement in fragile X mice. Collectively, these findings are pertinent to the development of long-term curative gene therapy strategies for treating Fragile X Syndrome and other neurodevelopmental disorders.
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Affiliation(s)
- Jason Arsenault
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Shervin Gholizadeh
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Yosuke Niibori
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Laura K Pacey
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Sebok K Halder
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Enea Koxhioni
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ayumu Konno
- 2 Department of Neurophysiology and Neural Repair, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hirokazu Hirai
- 2 Department of Neurophysiology and Neural Repair, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - David R Hampson
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,3 Department of Pharmacology, Faculty of Medicine, University of Toronto , Toronto, Ontario, Canada
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360
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Tabet R, Vitale N, Moine H. Fragile X syndrome: Are signaling lipids the missing culprits? Biochimie 2016; 130:188-194. [PMID: 27597551 DOI: 10.1016/j.biochi.2016.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
Abstract
Fragile X syndrome (FXS) is the most common cause of inherited intellectual disability and autism. FXS results from the absence of FMRP, an RNA binding protein associated to ribosomes that influences the translation of specific mRNAs in post-synaptic compartments of neurons. The main molecular consequence of the absence of FMRP is an excessive translation of neuronal protein in several areas of the brain. This local protein synthesis deregulation is proposed to underlie the defect in synaptic plasticity responsible for FXS. Recent findings in neurons of the fragile X mouse model (Fmr1-KO) uncovered another consequence of the lack of FMRP: a deregulation of the diacylglycerol (DAG)/phosphatidic acid (PA) homeostasis. DAG and PA are two interconvertible lipids that influence membrane architecture and that act as essential signaling molecules that activate various downstream effectors, including master regulators of local protein synthesis and actin polymerization. As a consequence, DAG and PA govern a variety of cellular processes, including cell proliferation, vesicle/membrane trafficking and cytoskeletal organization. At the synapse, the level of these lipids is proposed to influence the synaptic activation status. FMRP appears as a master regulator of this neuronal process by controlling the translation of a diacylglycerol kinase enzyme that converts DAG into PA. The deregulated levels of DAG and PA caused by the absence of FMRP could represent a novel therapeutic target for the treatment of FXS.
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Affiliation(s)
- Ricardos Tabet
- Mass General Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicolas Vitale
- Institut des Neurosciences Cellulaires et Intégratives, UPR3212 CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Hervé Moine
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67084 Strasbourg, France.
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361
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Telias M, Mayshar Y, Amit A, Ben-Yosef D. Molecular mechanisms regulating impaired neurogenesis of fragile X syndrome human embryonic stem cells. Stem Cells Dev 2016; 24:2353-65. [PMID: 26393806 DOI: 10.1089/scd.2015.0220] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common form of inherited cognitive impairment. It is caused by developmental inactivation of the FMR1 gene and the absence of its encoded protein FMRP, which plays pivotal roles in brain development and function. In FXS embryos with full FMR1 mutation, FMRP is expressed during early embryogenesis and is gradually downregulated at the third trimester of pregnancy. FX-human embryonic stem cells (FX-hESCs), derived from FX human blastocysts, demonstrate the same pattern of developmentally regulated FMR1 inactivation when subjected to in vitro neural differentiation (IVND). In this study, we used this in vitro human platform to explore the molecular mechanisms downstream to FMRP in the context of early human embryonic neurogenesis. Our results show a novel role for the SOX superfamily of transcription factors, specifically for SOX2 and SOX9, which could explain the reduced and delayed neurogenesis observed in FX cells. In addition, we assess in this study the "GSK3β theory of FXS" for the first time in a human-based model. We found no evidence for a pathological increase in GSK3β protein levels upon cellular loss of FMRP, in contrast to what was found in the brain of Fmr1 knockout mice. Our study adds novel data on potential downstream targets of FMRP and highlights the importance of the FX-hESC IVND system.
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Affiliation(s)
- Michael Telias
- 1 The Wolfe PGD-SC Lab, Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center , Tel Aviv, Israel .,2 Department of Cell and Developmental Biology Sackler Medical School, Tel Aviv University , Tel Aviv, Israel
| | - Yoav Mayshar
- 1 The Wolfe PGD-SC Lab, Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center , Tel Aviv, Israel
| | - Ami Amit
- 1 The Wolfe PGD-SC Lab, Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center , Tel Aviv, Israel
| | - Dalit Ben-Yosef
- 1 The Wolfe PGD-SC Lab, Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center , Tel Aviv, Israel .,2 Department of Cell and Developmental Biology Sackler Medical School, Tel Aviv University , Tel Aviv, Israel
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362
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Cheng C, Lau SKM, Doering LC. Astrocyte-secreted thrombospondin-1 modulates synapse and spine defects in the fragile X mouse model. Mol Brain 2016; 9:74. [PMID: 27485117 PMCID: PMC4971702 DOI: 10.1186/s13041-016-0256-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/15/2016] [Indexed: 01/24/2023] Open
Abstract
Astrocytes are key participants in various aspects of brain development and function, many of which are executed via secreted proteins. Defects in astrocyte signaling are implicated in neurodevelopmental disorders characterized by abnormal neural circuitry such as Fragile X syndrome (FXS). In animal models of FXS, the loss in expression of the Fragile X mental retardation 1 protein (FMRP) from astrocytes is associated with delayed dendrite maturation and improper synapse formation; however, the effect of astrocyte-derived factors on the development of neurons is not known. Thrombospondin-1 (TSP-1) is an important astrocyte-secreted protein that is involved in the regulation of spine development and synaptogenesis. In this study, we found that cultured astrocytes isolated from an Fmr1 knockout (Fmr1 KO) mouse model of FXS displayed a significant decrease in TSP-1 protein expression compared to the wildtype (WT) astrocytes. Correspondingly, Fmr1 KO hippocampal neurons exhibited morphological deficits in dendritic spines and alterations in excitatory synapse formation following long-term culture. All spine and synaptic abnormalities were prevented in the presence of either astrocyte-conditioned media or a feeder layer derived from FMRP-expressing astrocytes, or following the application of exogenous TSP-1. Importantly, this work demonstrates the integral role of astrocyte-secreted signals in the establishment of neuronal communication and identifies soluble TSP-1 as a potential therapeutic target for Fragile X syndrome.
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Affiliation(s)
- Connie Cheng
- McMaster Integrative Neuroscience Discovery and Study Program (MINDS), McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada.,Department of Pathology and Molecular Medicine, McMaster University, 1200 Main Street West, HSC 1R15A, Hamilton, Ontario, L8N 3Z5, Canada
| | - Sally K M Lau
- Department of Pathology and Molecular Medicine, McMaster University, 1200 Main Street West, HSC 1R15A, Hamilton, Ontario, L8N 3Z5, Canada
| | - Laurie C Doering
- McMaster Integrative Neuroscience Discovery and Study Program (MINDS), McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada. .,Department of Pathology and Molecular Medicine, McMaster University, 1200 Main Street West, HSC 1R15A, Hamilton, Ontario, L8N 3Z5, Canada.
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363
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Cooperativity in RNA–protein interactions: the complex is more than the sum of its partners. Curr Opin Neurobiol 2016; 39:146-51. [DOI: 10.1016/j.conb.2016.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 12/13/2022]
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364
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Anderson BR, Chopra P, Suhl JA, Warren ST, Bassell GJ. Identification of consensus binding sites clarifies FMRP binding determinants. Nucleic Acids Res 2016; 44:6649-59. [PMID: 27378784 PMCID: PMC5001617 DOI: 10.1093/nar/gkw593] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function.
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Affiliation(s)
- Bart R Anderson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joshua A Suhl
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
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365
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Gross C. Defective phosphoinositide metabolism in autism. J Neurosci Res 2016; 95:1161-1173. [PMID: 27376697 DOI: 10.1002/jnr.23797] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/26/2016] [Accepted: 06/01/2016] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are essential components of lipid membranes and crucial regulators of many cellular functions, including signal transduction, vesicle trafficking, membrane receptor localization and activity, and determination of membrane identity. These functions depend on the dynamic and highly regulated metabolism of phosphoinositides and require finely balanced activity of specific phosphoinositide kinases and phosphatases. There is increasing evidence from genetic and functional studies that these enzymes are often dysregulated or mutated in autism spectrum disorders; in particular, phosphoinositide 3-kinases and their regulatory subunits appear to be affected frequently. Examples of autism spectrum disorders with defective phosphoinositide metabolism are fragile X syndrome and autism disorders associated with mutations in the phosphoinositide 3-phosphatase tensin homolog deleted on chromosome 10 (PTEN), but recent genetic analyses also suggest that select nonsyndromic, idiopathic forms of autism may have altered activity of phosphoinositide kinases and phosphatases. Isoform-specific inhibitors for some of the phosphoinositide kinases have already been developed for cancer research and treatment, and a few are being evaluated for use in humans. Altogether, this offers exciting opportunities to explore altered phosphoinositide metabolism as a therapeutic target in individuals with certain forms of autism. This review summarizes genetic and functional studies identifying defects in phosphoinositide metabolism in autism and related disorders, describes published preclinical work targeting phosphoinositide 3-kinases in neurological diseases, and discusses the opportunities and challenges ahead to translate these findings from animal models and human cells into clinical application in humans. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Christina Gross
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
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366
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Tabet R, Moutin E, Becker JAJ, Heintz D, Fouillen L, Flatter E, Krężel W, Alunni V, Koebel P, Dembélé D, Tassone F, Bardoni B, Mandel JL, Vitale N, Muller D, Le Merrer J, Moine H. Fragile X Mental Retardation Protein (FMRP) controls diacylglycerol kinase activity in neurons. Proc Natl Acad Sci U S A 2016; 113:E3619-28. [PMID: 27233938 PMCID: PMC4932937 DOI: 10.1073/pnas.1522631113] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragile X syndrome (FXS) is caused by the absence of the Fragile X Mental Retardation Protein (FMRP) in neurons. In the mouse, the lack of FMRP is associated with an excessive translation of hundreds of neuronal proteins, notably including postsynaptic proteins. This local protein synthesis deregulation is proposed to underlie the observed defects of glutamatergic synapse maturation and function and to affect preferentially the hundreds of mRNA species that were reported to bind to FMRP. How FMRP impacts synaptic protein translation and which mRNAs are most important for the pathology remain unclear. Here we show by cross-linking immunoprecipitation in cortical neurons that FMRP is mostly associated with one unique mRNA: diacylglycerol kinase kappa (Dgkκ), a master regulator that controls the switch between diacylglycerol and phosphatidic acid signaling pathways. The absence of FMRP in neurons abolishes group 1 metabotropic glutamate receptor-dependent DGK activity combined with a loss of Dgkκ expression. The reduction of Dgkκ in neurons is sufficient to cause dendritic spine abnormalities, synaptic plasticity alterations, and behavior disorders similar to those observed in the FXS mouse model. Overexpression of Dgkκ in neurons is able to rescue the dendritic spine defects of the Fragile X Mental Retardation 1 gene KO neurons. Together, these data suggest that Dgkκ deregulation contributes to FXS pathology and support a model where FMRP, by controlling the translation of Dgkκ, indirectly controls synaptic proteins translation and membrane properties by impacting lipid signaling in dendritic spine.
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Affiliation(s)
- Ricardos Tabet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Enora Moutin
- Department of Basic Neuroscience, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jérôme A J Becker
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Plateforme Métabolomique, Unité Propre de Recherche (UPR) 2357 CNRS, Université de Strasbourg, 67082 Strasbourg, France
| | - Laetitia Fouillen
- Laboratoire de Biogènese Membranaire; UMR 5200 CNRS, Plateforme Métabolome, Université de Bordeaux, 33140 Villenave D'Ornon, France
| | - Eric Flatter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Wojciech Krężel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Violaine Alunni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Pascale Koebel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Doulaye Dembélé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Flora Tassone
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis Medical Center, Sacramento, CA 95817
| | - Barbara Bardoni
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, University of Nice Sophia-Antipolis, CNRS Laboratoire International Associé (LIA) Neogenex, 06560 Valbonne, France
| | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France; Collège de France, 75005 Paris, France
| | - Nicolas Vitale
- Institut des Neurosciences Cellulaires et Intégratives, UPR3212 CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Dominique Muller
- Department of Basic Neuroscience, University of Geneva, 1211 Geneva 4, Switzerland
| | - Julie Le Merrer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Hervé Moine
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France;
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367
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RNA Secondary Structure Modulates FMRP's Bi-Functional Role in the MicroRNA Pathway. Int J Mol Sci 2016; 17:ijms17060985. [PMID: 27338369 PMCID: PMC4926514 DOI: 10.3390/ijms17060985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/23/2016] [Accepted: 06/14/2016] [Indexed: 11/28/2022] Open
Abstract
MicroRNAs act by post-transcriptionally regulating the gene expression of 30%–60% of mammalian genomes. MicroRNAs are key regulators in all cellular processes, though the mechanism by which the cell activates or represses microRNA-mediated translational regulation is poorly understood. In this review, we discuss the RNA binding protein Fragile X Mental Retardation Protein (FMRP) and its role in microRNA-mediated translational regulation. Historically, FMRP is known to function as a translational suppressor. However, emerging data suggests that FMRP has both an agonistic and antagonistic role in regulating microRNA-mediated translational suppression. This bi-functional role is dependent on FMRP’s interaction with the RNA helicase Moloney leukemia virus 10 (MOV10), which modifies the structural landscape of bound mRNA, therefore facilitating or inhibiting its association with the RNA-Induced Silencing Complex.
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368
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Stepniak B, Kästner A, Poggi G, Mitjans M, Begemann M, Hartmann A, Van der Auwera S, Sananbenesi F, Krueger-Burg D, Matuszko G, Brosi C, Homuth G, Völzke H, Benseler F, Bagni C, Fischer U, Dityatev A, Grabe HJ, Rujescu D, Fischer A, Ehrenreich H. Accumulated common variants in the broader fragile X gene family modulate autistic phenotypes. EMBO Mol Med 2016; 7:1565-79. [PMID: 26612855 PMCID: PMC4693501 DOI: 10.15252/emmm.201505696] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Fragile X syndrome (FXS) is mostly caused by a CGG triplet expansion in the fragile X mental retardation 1 gene (FMR1). Up to 60% of affected males fulfill criteria for autism spectrum disorder (ASD), making FXS the most frequent monogenetic cause of syndromic ASD. It is unknown, however, whether normal variants (independent of mutations) in the fragile X gene family (FMR1, FXR1, FXR2) and in FMR2 modulate autistic features. Here, we report an accumulation model of 8 SNPs in these genes, associated with autistic traits in a discovery sample of male patients with schizophrenia (N = 692) and three independent replicate samples: patients with schizophrenia (N = 626), patients with other psychiatric diagnoses (N = 111) and a general population sample (N = 2005). For first mechanistic insight, we contrasted microRNA expression in peripheral blood mononuclear cells of selected extreme group subjects with high‐ versus low‐risk constellation regarding the accumulation model. Thereby, the brain‐expressed miR‐181 species emerged as potential “umbrella regulator”, with several seed matches across the fragile X gene family and FMR2. To conclude, normal variation in these genes contributes to the continuum of autistic phenotypes.
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Affiliation(s)
- Beata Stepniak
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Anne Kästner
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Giulia Poggi
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Marina Mitjans
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Martin Begemann
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Annette Hartmann
- Department of Psychiatry and Psychotherapy, University of Halle, Halle, Germany
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Farahnaz Sananbenesi
- Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Dilja Krueger-Burg
- Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Gabriela Matuszko
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Cornelia Brosi
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Fritz Benseler
- Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Claudia Bagni
- KU Leuven, Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, Leuven, Belgium Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Alexander Dityatev
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, University of Halle, Halle, Germany
| | - Andre Fischer
- Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany Department of Psychiatry & Psychotherapy, University of Göttingen, Göttingen, Germany
| | - Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
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369
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Promiscuous or discriminating: Has the favored mRNA target of Fragile X Mental Retardation Protein been overlooked? Proc Natl Acad Sci U S A 2016; 113:7009-11. [PMID: 27317743 DOI: 10.1073/pnas.1607665113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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370
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Kashima R, Roy S, Ascano M, Martinez-Cerdeno V, Ariza-Torres J, Kim S, Louie J, Lu Y, Leyton P, Bloch KD, Kornberg TB, Hagerman PJ, Hagerman R, Lagna G, Hata A. Augmented noncanonical BMP type II receptor signaling mediates the synaptic abnormality of fragile X syndrome. Sci Signal 2016; 9:ra58. [PMID: 27273096 DOI: 10.1126/scisignal.aaf6060] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Epigenetic silencing of fragile X mental retardation 1 (FMR1) causes fragile X syndrome (FXS), a common inherited form of intellectual disability and autism. FXS correlates with abnormal synapse and dendritic spine development, but the molecular link between the absence of the FMR1 product FMRP, an RNA binding protein, and the neuropathology is unclear. We found that the messenger RNA encoding bone morphogenetic protein type II receptor (BMPR2) is a target of FMRP. Depletion of FMRP increased BMPR2 abundance, especially that of the full-length isoform that bound and activated LIM domain kinase 1 (LIMK1), a component of the noncanonical BMP signal transduction pathway that stimulates actin reorganization to promote neurite outgrowth and synapse formation. Heterozygosity for BMPR2 rescued the morphological abnormalities in neurons both in Drosophila and in mouse models of FXS, as did the postnatal pharmacological inhibition of LIMK1 activity. Compared with postmortem prefrontal cortex tissue from healthy subjects, the amount of full-length BMPR2 and of a marker of LIMK1 activity was increased in this brain region from FXS patients. These findings suggest that increased BMPR2 signal transduction is linked to FXS and that the BMPR2-LIMK1 pathway is a putative therapeutic target in patients with FXS and possibly other forms of autism.
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Affiliation(s)
- Risa Kashima
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sougata Roy
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Veronica Martinez-Cerdeno
- Institute for Pediatric Regenerative Medicine, Department of Pathology, University of California, Davis, Davis, CA 95817, USA. MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California, Davis, Davis, CA 95817, USA
| | - Jeanelle Ariza-Torres
- Institute for Pediatric Regenerative Medicine, Department of Pathology, University of California, Davis, Davis, CA 95817, USA
| | - Sunghwan Kim
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Justin Louie
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yao Lu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patricio Leyton
- Anesthesia and Critical Care, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kenneth D Bloch
- Anesthesia and Critical Care, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Thomas B Kornberg
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Randi Hagerman
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California, Davis, Davis, CA 95817, USA
| | - Giorgio Lagna
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
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371
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Abstract
Fragile X syndrome is the most common inherited form of intellectual disability and results from a loss of function of the translational repressor FMRP. In this issue of Science Signaling, Kashima et al find that FMRP binds to and represses a specific isoform of BMPR2, a type II bone morphogenetic protein (BMP) receptor. Reducing signaling through this BMP pathway reverses neuroanatomical defects observed in fragile X models.
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Affiliation(s)
- Heather T Broihier
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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372
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Sensory-Derived Glutamate Regulates Presynaptic Inhibitory Terminals in Mouse Spinal Cord. Neuron 2016; 90:1189-1202. [DOI: 10.1016/j.neuron.2016.05.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/03/2016] [Accepted: 05/02/2016] [Indexed: 11/18/2022]
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373
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Le Tonqueze O, Kollu S, Lee S, Al-Salah M, Truesdell SS, Vasudevan S. Regulation of monocyte induced cell migration by the RNA binding protein, FXR1. Cell Cycle 2016; 15:1874-82. [PMID: 27229378 DOI: 10.1080/15384101.2016.1189040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
FXR1 belongs to a family of RNA-binding proteins that play critical roles in post-transcriptional regulation of gene expression in immunity, development and cancer. FXR1 is associated with regulation of specific mRNAs in myocytes and macrophages. In quiescent cells (> 24 h of extended serum-starvation, ∼30-48 h or more), a spliced isoform of FXR1, FXR1a, promotes translation of the cytokine TNFα, independent of the effects of RNA levels. Here we examined the role of FXR1 in THP1 human monocytic leukemic cells that were grown in serum, as well as in early (24 h) serum-starvation conditions that demonstrates differences in gene expression mechanisms and is distinct from quiescent (> 24 h extended serum-starvation) cells. Global RNA profiling, conducted to investigate the role of FXR1 on mRNA levels, revealed that FXR1 affects levels of specific mRNAs in serum-grown and in early 24 h serum-starvation conditions. FXR1 decreases levels of several mRNAs, including as previously identified, CDKN1A (p21CIP1 or p21) mRNA in serum-grown cells. Interestingly, we find that FXR1 positively regulates mRNA levels of specific cytokines and chemokines in serum-grown and in early 24 h serum-starvation conditions. These include IL1β and CCL2 that control cell migration. Accordingly, depletion and overexpression of FXR1 decreased and increased levels of CCL2 mRNA. Consistent with the reduced levels of IL1β, CCL2 and other chemokines upon FXR1 depletion, our data reveal that depletion of FXR1 decreases the ability of these cells to induce cell migration of neighboring monocytic cells. These data reveal a new role of FXR1 in controlling induction of monocyte migration.
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Affiliation(s)
- O Le Tonqueze
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - S Kollu
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - S Lee
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - M Al-Salah
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - S S Truesdell
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - S Vasudevan
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
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374
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Sourial M, Doering LC. Astrocyte-Secreted Factors Selectively Alter Neural Stem and Progenitor Cell Proliferation in the Fragile X Mouse. Front Cell Neurosci 2016; 10:126. [PMID: 27242437 PMCID: PMC4870401 DOI: 10.3389/fncel.2016.00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/29/2016] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED An increasing body of evidence indicates that astrocytes contribute to the governance and fine tuning of stem and progenitor cell production during brain development. The effect of astrocyte function in cell production in neurodevelopmental disorders is unknown. We used the Neural Colony Forming Cell assay to determine the effect of astrocyte conditioned media (ACM) on the generation of neurospheres originating from either progenitor cells or functional stem cells in the knock out (KO) Fragile X mouse model. ACM from both normal and Fmr1-KO mice generated higher percentages of smaller neurospheres indicative of restricted proliferation of the progenitor cell population in Fmr1-KO brains. Wild type (WT) neurospheres, but not KO neurospheres, showed enhanced responses to ACM from the Fmr1-KO mice. In particular, Fmr1-KO ACM increased the percentage of large neurospheres generated, representative of spheres produced from neural stem cells. We also used 2D DIGE to initiate identification of the astrocyte-secreted proteins with differential expression between Fmr1-KO and WT cortices and hippocampi. The results further support the critical role of astrocytes in governing neural cell production in brain development and point to significant alterations in neural cell proliferation due to astrocyte secreted factors from the Fragile X brain. HIGHLIGHTS • We studied the proliferation of neural stem and progenitor cells in Fragile X.• We examined the role of astrocyte-secreted factors in neural precursor cell biology.• Astrocyte-secreted factors with differential expression in Fragile X identified.
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Affiliation(s)
- Mary Sourial
- McMaster Integrative Neuroscience Discovery and Study, McMaster University, HamiltonON, Canada; Pathology and Molecular Medicine, McMaster University, HamiltonON, Canada
| | - Laurie C Doering
- McMaster Integrative Neuroscience Discovery and Study, McMaster University, HamiltonON, Canada; Pathology and Molecular Medicine, McMaster University, HamiltonON, Canada
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375
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Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. Sci Rep 2016; 6:25711. [PMID: 27161996 PMCID: PMC4861959 DOI: 10.1038/srep25711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.
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376
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Spencer KB, Mulholland PJ, Chandler LJ. FMRP Mediates Chronic Ethanol-Induced Changes in NMDA, Kv4.2, and KChIP3 Expression in the Hippocampus. Alcohol Clin Exp Res 2016; 40:1251-61. [PMID: 27147118 DOI: 10.1111/acer.13060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/04/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Exposure to chronic ethanol (EtOH) results in changes in the expression of proteins that regulate neuronal excitability. This study examined whether chronic EtOH alters the hippocampal expression and function of fragile X mental retardation protein (FMRP) and the role of FMRP in the modulation of chronic EtOH-induced changes in the expression of NMDA receptors and Kv4.2 channels. METHODS For in vivo studies, C57BL/6J mice underwent a chronic intermittent EtOH (CIE) vapor exposure procedure. After CIE, hippocampal tissue was collected and subjected to immunoblot blot analysis of NMDA receptor subunits (GluN1, GluN2B), Kv4.2, and its accessory protein KChIP3. For in vitro studies, hippocampal slice cultures were exposed to 75 mM EtOH for 8 days. Following EtOH exposure, mRNAs bound to FMRP was measured. In a separate set of studies, cultures were exposed to an inhibitor of S6K1 (PF-4708671 [PF], 6 μM) in order to assess whether EtOH-induced homeostatic changes in protein expression depend upon changes in FMRP activity. RESULTS Immunoblot blot analysis revealed increases in GluN1 and GluN2B but reductions in Kv4.2 and KChIP3. Analysis of mRNAs bound to FMRP revealed a similar bidirectional change observed as reduction of GluN2B and increase in Kv4.2 and KChIP3 mRNA transcripts. Analysis of FMRP further revealed that while chronic EtOH did not alter the expression of FMRP, it significantly increased phosphorylation of FMRP at the S499 residue that is known to critically regulate its activity. Inhibition of S6K1 prevented the chronic EtOH-induced increase in phospho-FMRP and changes in NMDA subunits, Kv4.2, and KChIP3. In contrast, PF had no effect in the absence of alcohol, indicating it was specific for the chronic EtOH-induced changes. CONCLUSIONS These findings demonstrate that chronic EtOH exposure enhances translational control of plasticity-related proteins by FMRP, and that S6K1 and FMRP activities are required for expression of chronic EtOH-induced homeostatic plasticity at glutamatergic synapses in the hippocampus.
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Affiliation(s)
- Kathryn B Spencer
- Department of Neurosciences, Medical University of South Carolina, Charleston, South Carolina
| | - Patrick J Mulholland
- Department of Neurosciences, Medical University of South Carolina, Charleston, South Carolina
| | - L Judson Chandler
- Department of Neurosciences, Medical University of South Carolina, Charleston, South Carolina
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377
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Järvelin AI, Noerenberg M, Davis I, Castello A. The new (dis)order in RNA regulation. Cell Commun Signal 2016; 14:9. [PMID: 27048167 PMCID: PMC4822317 DOI: 10.1186/s12964-016-0132-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
RNA-binding proteins play a key role in the regulation of all aspects of RNA metabolism, from the synthesis of RNA to its decay. Protein-RNA interactions have been thought to be mostly mediated by canonical RNA-binding domains that form stable secondary and tertiary structures. However, a number of pioneering studies over the past decades, together with recent proteome-wide data, have challenged this view, revealing surprising roles for intrinsically disordered protein regions in RNA binding. Here, we discuss how disordered protein regions can mediate protein-RNA interactions, conceptually grouping these regions into RS-rich, RG-rich, and other basic sequences, that can mediate both specific and non-specific interactions with RNA. Disordered regions can also influence RNA metabolism through protein aggregation and hydrogel formation. Importantly, protein-RNA interactions mediated by disordered regions can influence nearly all aspects of co- and post-transcriptional RNA processes and, consequently, their disruption can cause disease. Despite growing interest in disordered protein regions and their roles in RNA biology, their mechanisms of binding, regulation, and physiological consequences remain poorly understood. In the coming years, the study of these unorthodox interactions will yield important insights into RNA regulation in cellular homeostasis and disease.
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Affiliation(s)
- Aino I. Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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378
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McMahon AC, Rahman R, Jin H, Shen JL, Fieldsend A, Luo W, Rosbash M. TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins. Cell 2016; 165:742-53. [PMID: 27040499 DOI: 10.1016/j.cell.2016.03.007] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/15/2016] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
Abstract
RNA transcripts are bound and regulated by RNA-binding proteins (RBPs). Current methods for identifying in vivo targets of an RBP are imperfect and not amenable to examining small numbers of cells. To address these issues, we developed TRIBE (targets of RNA-binding proteins identified by editing), a technique that couples an RBP to the catalytic domain of the Drosophila RNA-editing enzyme ADAR and expresses the fusion protein in vivo. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. We have used TRIBE to identify the targets of three RBPs (Hrp48, dFMR1, and NonA). TRIBE compares favorably to other methods, including CLIP, and we have identified RBP targets from as little as 150 specific fly neurons. TRIBE can be performed without an antibody and in small numbers of specific cells.
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Affiliation(s)
- Aoife C McMahon
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Hua Jin
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - James L Shen
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Allegra Fieldsend
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Weifei Luo
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
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379
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Leung C, Jia Z. Mouse Genetic Models of Human Brain Disorders. Front Genet 2016; 7:40. [PMID: 27047540 PMCID: PMC4803727 DOI: 10.3389/fgene.2016.00040] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/08/2016] [Indexed: 01/29/2023] Open
Abstract
Over the past three decades, genetic manipulations in mice have been used in neuroscience as a major approach to investigate the in vivo function of genes and their alterations. In particular, gene targeting techniques using embryonic stem cells have revolutionized the field of mammalian genetics and have been at the forefront in the generation of numerous mouse models of human brain disorders. In this review, we will first examine childhood developmental disorders such as autism, intellectual disability, Fragile X syndrome, and Williams-Beuren syndrome. We will then explore psychiatric disorders such as schizophrenia and lastly, neurodegenerative disorders including Alzheimer’s disease and Parkinson’s disease. We will outline the creation of these mouse models that range from single gene deletions, subtle point mutations to multi-gene manipulations, and discuss the key behavioral phenotypes of these mice. Ultimately, the analysis of the models outlined in this review will enhance our understanding of the in vivo role and underlying mechanisms of disease-related genes in both normal brain function and brain disorders, and provide potential therapeutic targets and strategies to prevent and treat these diseases.
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Affiliation(s)
- Celeste Leung
- The Hospital for Sick Children, Program in Neurosciences and Mental Health, Peter Gilgan Centre for Research and Learning, TorontoON, Canada; Program in Physiology, University of Toronto, TorontoON, Canada
| | - Zhengping Jia
- The Hospital for Sick Children, Program in Neurosciences and Mental Health, Peter Gilgan Centre for Research and Learning, TorontoON, Canada; Program in Physiology, University of Toronto, TorontoON, Canada
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380
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Conca Dioguardi C, Uslu B, Haynes M, Kurus M, Gul M, Miao DQ, De Santis L, Ferrari M, Bellone S, Santin A, Giulivi C, Hoffman G, Usdin K, Johnson J. Granulosa cell and oocyte mitochondrial abnormalities in a mouse model of fragile X primary ovarian insufficiency. Mol Hum Reprod 2016; 22:384-96. [PMID: 26965313 DOI: 10.1093/molehr/gaw023] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/04/2016] [Indexed: 11/13/2022] Open
Abstract
STUDY HYPOTHESIS We hypothesized that the mitochondria of granulosa cells (GC) and/or oocytes might be abnormal in a mouse model of fragile X premutation (FXPM). STUDY FINDING Mice heterozygous and homozygous for the FXPM have increased death (atresia) of large ovarian follicles, fewer corpora lutea with a gene dosage effect manifesting in decreased litter size(s). Furthermore, granulosa cells (GC) and oocytes of FXPM mice have decreased mitochondrial content, structurally abnormal mitochondria, and reduced expression of critical mitochondrial genes. Because this mouse allele produces the mutant Fragile X mental retardation 1 (Fmr1) transcript and reduced levels of wild-type (WT) Fmr1 protein (FMRP), but does not produce a Repeat Associated Non-ATG Translation (RAN)-translation product, our data lend support to the idea that Fmr1 mRNA with large numbers of CGG-repeats is intrinsically deleterious in the ovary. WHAT IS KNOWN ALREADY Mitochondrial dysfunction has been detected in somatic cells of human and mouse FX PM carriers and mitochondria are essential for oogenesis and ovarian follicle development, FX-associated primary ovarian insufficiency (FXPOI) is seen in women with FXPM alleles. These alleles have 55-200 CGG repeats in the 5' UTR of an X-linked gene known as FMR1. The molecular basis of the pathology seen in this disorder is unclear but is thought to involve either some deleterious consequence of overexpression of RNA with long CGG-repeat tracts or of the generation of a repeat-associated non-AUG translation (RAN translation) product that is toxic. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Analysis of ovarian function in a knock-in FXPM mouse model carrying 130 CGG repeats was performed as follows on WT, PM/+, and PM/PM genotypes. Histomorphometric assessment of follicle and corpora lutea numbers in ovaries from 8-month-old mice was executed, along with litter size analysis. Mitochondrial DNA copy number was quantified in oocytes and GC using quantitative PCR, and cumulus granulosa mitochondrial content was measured by flow cytometric analysis after staining of cells with Mitotracker dye. Transmission electron micrographs were prepared of GC within small growing follicles and mitochondrial architecture was compared. Quantitative RT-PCR analysis of key genes involved in mitochondrial structure and recycling was performed. MAIN RESULTS AND THE ROLE OF CHANCE A defect was found in follicle survival at the large antral stage in PM/+ and PM/PM mice. Litter size was significantly decreased in PM/PM mice, and corpora lutea were significantly reduced in mice of both mutant genotypes. Mitochondrial DNA copy number was significantly decreased in GC and metaphase II eggs in mutants. Flow cytometric analysis revealed that PM/+ and PM/PM animals lack the cumulus GC that harbor the greatest mitochondrial content as found in wild-type animals. Electron microscopic evaluation of GC of small growing follicles revealed mitochondrial structural abnormalities, including disorganized and vacuolar cristae. Finally, aberrant mitochondrial gene expression was detected. Mitofusin 2 (Mfn2) and Optic atrophy 1 (Opa1), genes involved in mitochondrial fusion and structure, respectively, were significantly decreased in whole ovaries of both mutant genotypes. Mitochondrial fission factor 1 (Mff1) was significantly decreased in PM/+ and PM/PM GC and eggs compared with wild-type controls. LIMITATIONS, REASONS FOR CAUTION Data from the mouse model used for these studies should be viewed with some caution when considering parallels to the human FXPOI condition. WIDER IMPLICATIONS OF THE FINDINGS Our data lend support to the idea that Fmr1 mRNA with large numbers of CGG-repeats is intrinsically deleterious in the ovary. FXPM disease states, including FXPOI, may share mitochondrial dysfunction as a common underlying mechanism. LARGE SCALE DATA Not applicable. STUDY FUNDING AND COMPETING INTERESTS Studies were supported by NIH R21 071873 (J.J./G.H), The Albert McKern Fund for Perinatal Research (J.J.), NIH Intramural Funds (K.U.), and a TUBITAK Research Fellowship Award (B.U.). No conflict(s) of interest or competing interest(s) are noted.
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Affiliation(s)
- Carola Conca Dioguardi
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Reproductive Endocrinology and Infertility, Yale School of Medicine, New Haven, CT, USA Vita-Salute San Raffaele University/IRCCS San Raffaele Hospital, Milan, Italy
| | - Bahar Uslu
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Reproductive Endocrinology and Infertility, Yale School of Medicine, New Haven, CT, USA
| | - Monique Haynes
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Reproductive Endocrinology and Infertility, Yale School of Medicine, New Haven, CT, USA
| | - Meltem Kurus
- Department of Histology & Embryology, Izmir Katip Celebi University School of Medicine, Izmir, Turkey
| | - Mehmet Gul
- Department of Histology & Embryology, Inonu University School of Medicine, Malatya, Turkey
| | - De-Qiang Miao
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Reproductive Endocrinology and Infertility, Yale School of Medicine, New Haven, CT, USA
| | - Lucia De Santis
- Department of Obstetrics & Gynecology, IVF Unit, Vita-Salute San Raffaele University/IRCCS San Raffaele Hospital, Milan, Italy
| | - Maurizio Ferrari
- Laboratory of Clinical Molecular Biology and Cytogenetics, Vita-Salute San Raffaele University/IRCCS San Raffaele Hospital, Milan, Italy
| | - Stefania Bellone
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Gynecologic Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Alessandro Santin
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Gynecologic Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, M.I.N.D. Institute, University of California-Davis, Davis, CA, USA
| | - Gloria Hoffman
- Department of Biology, Morgan State University, Baltimore, MD, USA
| | - Karen Usdin
- Laboratory of Cellular and Molecular Biology, NIH/NIDDK, Bethesda, MD, USA
| | - Joshua Johnson
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA Division of Reproductive Endocrinology and Infertility, Yale School of Medicine, New Haven, CT, USA
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381
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Tekcan A. In Silico Analysis of FMR1 Gene Missense SNPs. Cell Biochem Biophys 2016; 74:109-27. [PMID: 26880065 DOI: 10.1007/s12013-016-0722-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/27/2016] [Indexed: 12/17/2022]
Abstract
The FMR1 gene, a member of the fragile X-related gene family, is responsible for fragile X syndrome (FXS). Missense single-nucleotide polymorphisms (SNPs) are responsible for many complex diseases. The effect of FMR1 gene missense SNPs is unknown. The aim of this study, using in silico techniques, was to analyze all known missense mutations that can affect the functionality of the FMR1 gene, leading to mental retardation (MR) and FXS. Data on the human FMR1 gene were collected from the Ensembl database (release 81), National Centre for Biological Information dbSNP Short Genetic Variations database, 1000 Genomes Browser, and NHLBI Exome Sequencing Project Exome Variant Server. In silico analysis was then performed. One hundred-twenty different missense SNPs of the FMR1 gene were determined. Of these, 11.66 % of the FMR1 gene missense SNPs were in highly conserved domains, and 83.33 % were in domains with high variety. The results of the in silico prediction analysis showed that 31.66 % of the FMR1 gene SNPs were disease related and that 50 % of SNPs had a pathogenic effect. The results of the structural and functional analysis revealed that although the R138Q mutation did not seem to have a damaging effect on the protein, the G266E and I304N SNPs appeared to disturb the interaction between the domains and affect the function of the protein. This is the first study to analyze all missense SNPs of the FMR1 gene. The results indicate the applicability of a bioinformatics approach to FXS and other FMR1-related diseases. I think that the analysis of FMR1 gene missense SNPs using bioinformatics methods would help diagnosis of FXS and other FMR1-related diseases.
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Affiliation(s)
- Akin Tekcan
- School of Health, Ahi Evran University, Kirsehir, Turkey.
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382
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Proteostasis and RNA Binding Proteins in Synaptic Plasticity and in the Pathogenesis of Neuropsychiatric Disorders. Neural Plast 2016; 2016:3857934. [PMID: 26904297 PMCID: PMC4745388 DOI: 10.1155/2016/3857934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 12/30/2022] Open
Abstract
Decades of research have demonstrated that rapid alterations in protein abundance are required for synaptic plasticity, a cellular correlate for learning and memory. Control of protein abundance, known as proteostasis, is achieved across a complex neuronal morphology that includes a tortuous axon as well as an extensive dendritic arbor supporting thousands of individual synaptic compartments. To regulate the spatiotemporal synthesis of proteins, neurons must efficiently coordinate the transport and metabolism of mRNAs. Among multiple levels of regulation, transacting RNA binding proteins (RBPs) control proteostasis by binding to mRNAs and mediating their transport and translation in response to synaptic activity. In addition to synthesis, protein degradation must be carefully balanced for optimal proteostasis, as deviations resulting in excess or insufficient abundance of key synaptic factors produce pathologies. As such, mutations in components of the proteasomal or translational machinery, including RBPs, have been linked to the pathogenesis of neurological disorders such as Fragile X Syndrome (FXS), Fragile X Tremor Ataxia Syndrome (FXTAS), and Autism Spectrum Disorders (ASD). In this review, we summarize recent scientific findings, highlight ongoing questions, and link basic molecular mechanisms to the pathogenesis of common neuropsychiatric disorders.
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383
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Controlling the Editor: The Many Roles of RNA-Binding Proteins in Regulating A-to-I RNA Editing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:189-213. [PMID: 27256387 DOI: 10.1007/978-3-319-29073-7_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA editing is a cellular process used to expand and diversify the RNA transcripts produced from a generally immutable genome. In animals, the most prevalent type of RNA editing is adenosine (A) to inosine (I) deamination catalyzed by the ADAR family. Throughout development, A-to-I editing levels increase while ADAR expression is constant, suggesting cellular mechanisms to regulate A-to-I editing exist. Furthermore, in several disease states, ADAR expression levels are similar to the normal state, but A-to-I editing levels are altered. Therefore, understanding how these enzymes are regulated in normal tissues and misregulated in disease states is of profound importance. This chapter will both discuss how to identify A-to-I editing sites across the transcriptome and explore the mechanisms that regulate ADAR editing activity, with particular focus on the diverse types of RNA-binding proteins implicated in regulating A-to-I editing in vivo.
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384
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Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:1-28. [PMID: 27256380 DOI: 10.1007/978-3-319-29073-7_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. The recent explosion in genomics techniques has enabled transcriptome-wide profiling of RNA processing in an unbiased manner. However, it has also brought with it both experimental challenges in developing improved methods to probe distinct processing steps, as well as computational challenges in data storage, processing, and analysis tools to enable large-scale interpretation in the genomics era. In this chapter we review experimental techniques and challenges in profiling various aspects of RNA processing, as well as recent efforts to develop analyses integrating multiple data sources and techniques to infer RNA regulatory networks.
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385
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Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism 2015; 6:66. [PMID: 26697163 PMCID: PMC4687343 DOI: 10.1186/s13229-015-0061-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/10/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Fragile X syndrome (FXS) is a neurodevelopmental disorder whose biochemical manifestations involve dysregulation of mGluR5-dependent pathways, which are widely modeled using cultured neurons. In vitro phenotypes in cultured neurons using standard morphological, functional, and chemical approaches have demonstrated considerable variability. Here, we study transcriptomes obtained in situ in the intact brain tissues of a murine model of FXS to see how they reflect the in vitro state. METHODS We used genome-wide mRNA expression profiling as a robust characterization tool for studying differentially expressed pathways in fragile X mental retardation 1 (Fmr1) knockout (KO) and wild-type (WT) murine primary neuronal cultures and in embryonic hippocampal and cortical murine tissue. To study the developmental trajectory and to relate mouse model data to human data, we used an expression map of human development to plot murine differentially expressed genes in KO/WT cultures and brain. RESULTS We found that transcriptomes from cell cultures showed a stronger signature of Fmr1KO than whole tissue transcriptomes. We observed an over-representation of immunological signaling pathways in embryonic Fmr1KO cortical and hippocampal tissues and over-represented mGluR5-downstream signaling pathways in Fmr1KO cortical and hippocampal primary cultures. Genes whose expression was up-regulated in Fmr1KO murine cultures tended to peak early in human development, whereas differentially expressed genes in embryonic cortical and hippocampal tissues clustered with genes expressed later in human development. CONCLUSIONS The transcriptional profile in brain tissues primarily centered on immunological mechanisms, whereas the profiles from cell cultures showed defects in neuronal activity. We speculate that the isolation and culturing of neurons caused a shift in neurological transcriptome towards a "juvenile" or "de-differentiated" state. Moreover, cultured neurons lack the close coupling with glia that might be responsible for the immunological phenotype in the intact brain. Our results suggest that cultured cells may recapitulate an early phase of the disease, which is also less obscured with a consequent "immunological" phenotype and in vivo compensatory mechanisms observed in the embryonic brain. Together, these results suggest that the transcriptome of cultured primary neuronal cells, in comparison to whole brain tissue, more robustly demonstrated the difference between Fmr1KO and WT mice and might reveal a molecular phenotype, which is typically hidden by compensatory mechanisms present in vivo. Moreover, cultures might be useful for investigating the perturbed pathways in early human brain development and genes previously implicated in autism.
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386
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Shamay-Ramot A, Khermesh K, Porath HT, Barak M, Pinto Y, Wachtel C, Zilberberg A, Lerer-Goldshtein T, Efroni S, Levanon EY, Appelbaum L. Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish. PLoS Genet 2015; 11:e1005702. [PMID: 26637167 PMCID: PMC4670233 DOI: 10.1371/journal.pgen.1005702] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/04/2015] [Indexed: 01/03/2023] Open
Abstract
Fragile X syndrome (FXS) is the most frequent inherited form of mental retardation. The cause for this X-linked disorder is the silencing of the fragile X mental retardation 1 (fmr1) gene and the absence of the fragile X mental retardation protein (Fmrp). The RNA-binding protein Fmrp represses protein translation, particularly in synapses. In Drosophila, Fmrp interacts with the adenosine deaminase acting on RNA (Adar) enzymes. Adar enzymes convert adenosine to inosine (A-to-I) and modify the sequence of RNA transcripts. Utilizing the fmr1 zebrafish mutant (fmr1-/-), we studied Fmrp-dependent neuronal circuit formation, behavior, and Adar-mediated RNA editing. By combining behavior analyses and live imaging of single axons and synapses, we showed hyperlocomotor activity, as well as increased axonal branching and synaptic density, in fmr1-/- larvae. We identified thousands of clustered RNA editing sites in the zebrafish transcriptome and showed that Fmrp biochemically interacts with the Adar2a protein. The expression levels of the adar genes and Adar2 protein increased in fmr1-/- zebrafish. Microfluidic-based multiplex PCR coupled with deep sequencing showed a mild increase in A-to-I RNA editing levels in evolutionarily conserved neuronal and synaptic Adar-targets in fmr1-/- larvae. These findings suggest that loss of Fmrp results in increased Adar-mediated RNA editing activity on target-specific RNAs, which, in turn, might alter neuronal circuit formation and behavior in FXS. The most frequent inherited mental retardation disorder is fragile X syndrome, which is characterized by learning disabilities, cognitive impairment, anxiety, and hyperactive behavior. The genetic cause of this disorder is the silencing of the fmr1 gene, which encodes the RNA-binding protein Fmrp. This protein inhibits the production of various proteins in the brain and interacts with the Adar enzyme, which converts the nucleotide A into I in RNAs. However, it is unclear by which mechanism the loss of Fmrp affects the sequence of neuronal genes and, ultimately, brain function. Here, we used the fmr1 mutant zebrafish (fmr1-/-), which enables high-throughput genetics and live imaging experiments in a transparent and evolutionarily conserved brain. We found that loss of Fmrp altered neuronal circuit formation. Furthermore, similar to human patients, the fmr1-/- larvae were hyperactive. Biochemical assays showed that Fmrp interacts with the Adar2a protein, which is increased in fmr1-/- larvae. Thus, we characterized global RNA editing in the zebrafish transcriptome and used a microfluidic-based high-throughput technique to accurately quantify RNA editing levels. Loss of Fmrp resulted in a mild increase in RNA editing in the coding sequences of conserved synaptic genes. These findings propose that altered RNA editing levels may affect neuronal and behavioral deficiencies in FXS.
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Affiliation(s)
- Adi Shamay-Ramot
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Khen Khermesh
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hagit T. Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michal Barak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Chaim Wachtel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tali Lerer-Goldshtein
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Erez Y. Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Lior Appelbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail:
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387
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Zhang P, Abdelmohsen K, Liu Y, Tominaga-Yamanaka K, Yoon JH, Ioannis G, Martindale JL, Zhang Y, Becker KG, Yang IH, Gorospe M, Mattson MP. Novel RNA- and FMRP-binding protein TRF2-S regulates axonal mRNA transport and presynaptic plasticity. Nat Commun 2015; 6:8888. [PMID: 26586091 PMCID: PMC4673492 DOI: 10.1038/ncomms9888] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 10/06/2015] [Indexed: 02/07/2023] Open
Abstract
Despite considerable evidence that RNA-binding proteins (RBPs) regulate mRNA transport and local translation in dendrites, roles for axonal RBPs are poorly understood. Here we demonstrate that a non-telomeric isoform of telomere repeat-binding factor 2 (TRF2-S) is a novel RBP that regulates axonal plasticity. TRF2-S interacts directly with target mRNAs to facilitate their axonal delivery. The process is antagonized by fragile X mental retardation protein (FMRP). Distinct from the current RNA-binding model of FMRP, we show that FMRP occupies the GAR domain of TRF2-S protein to block the assembly of TRF2-S–mRNA complexes. Overexpressing TRF2-S and silencing FMRP promotes mRNA entry to axons and enhances axonal outgrowth and neurotransmitter release from presynaptic terminals. Our findings suggest a pivotal role for TRF2-S in an axonal mRNA localization pathway that enhances axon outgrowth and neurotransmitter release. The molecular mechanisms regulating axonal mRNA transport are only partially understood. Here, Zhang et al. show a nontelomeric TRF2 splice variant interacts with FMRP to regulate the transport of several axonal mRNAs involved in axonal elongation and neurotransmitter release.
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Affiliation(s)
- Peisu Zhang
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Yong Liu
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Kumiko Tominaga-Yamanaka
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Grammatikakis Ioannis
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Kevin G Becker
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - In Hong Yang
- Department of Biomedical Engineering, National University of Singapore, Singapore 117465, Singapore.,SINAPSE, National University of Singapore, Singapore 117465, Singapore
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA
| | - Mark P Mattson
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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388
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Nelson SB, Valakh V. Excitatory/Inhibitory Balance and Circuit Homeostasis in Autism Spectrum Disorders. Neuron 2015; 87:684-98. [PMID: 26291155 DOI: 10.1016/j.neuron.2015.07.033] [Citation(s) in RCA: 670] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autism spectrum disorders (ASDs) and related neurological disorders are associated with mutations in many genes affecting the ratio between neuronal excitation and inhibition. However, understanding the impact of these mutations on network activity is complicated by the plasticity of these networks, making it difficult in many cases to separate initial deficits from homeostatic compensation. Here we explore the contrasting evidence for primary defects in inhibition or excitation in ASDs and attempt to integrate the findings in terms of the brain's ability to maintain functional homeostasis.
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Affiliation(s)
- Sacha B Nelson
- Department of Biology and Center for Behavioral Genomics, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| | - Vera Valakh
- Department of Biology and Center for Behavioral Genomics, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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389
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Abstract
Fragile X syndrome (FXS) results from a genetic mutation in a single gene yet produces a phenotypically complex disorder with a range of neurological and psychiatric problems. Efforts to decipher how perturbations in signaling pathways lead to the myriad alterations in synaptic and cellular functions have provided insights into the molecular underpinnings of this disorder. From this large body of data, the theme of circuit hyperexcitability has emerged as a potential explanation for many of the neurological and psychiatric symptoms in FXS. The mechanisms for hyperexcitability range from alterations in the expression or activity of ion channels to changes in neurotransmitters and receptors. Contributions of these processes are often brain region and cell type specific, resulting in complex effects on circuit function that manifest as altered excitability. Here, we review the current state of knowledge of the molecular, synaptic, and circuit-level mechanisms underlying hyperexcitability and their contributions to the FXS phenotypes.
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390
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Drosophila Homolog of FMRP Maintains Genome Integrity by Interacting with Piwi. J Genet Genomics 2015; 43:11-24. [PMID: 26842990 DOI: 10.1016/j.jgg.2015.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022]
Abstract
Fragile X syndrome (FraX), the most common form of inherited mental retardation, is caused by the absence of the evolutionally conserved fragile X mental retardation protein (FMRP). While neuronal functions of FMRP have been intensively studied for the last two decades, its role in non-neuronal cells remains poorly understood. Piwi, a key component of the Piwi-interacting RNA (piRNA) pathway, plays an essential role in germline development. In the present study, we report that similar to piwi, dfmr1, the Drosophila homolog of human FMR1, is required for transposon suppression in the germlines. Genetic analyses showed that dfmr1 and piwi act synergistically in heterochromatic silencing, and in inhibiting the differentiation of primordial germline cells and transposon expression. Northern analyses showed that roo piRNA expression levels are reduced in dfmr1 mutant ovaries, suggesting a role of dfmr1 in piRNA biogenesis. Biochemical analysis demonstrated a physical interaction between dFMRP and Piwi via their N-termini. Taken together, we propose that dFMRP cooperates with Piwi in maintaining genome integrity by regulating heterochromatic silencing in somatic cells and suppressing transposon activity via the piRNA pathway in germlines.
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391
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Sanders SJ. First glimpses of the neurobiology of autism spectrum disorder. Curr Opin Genet Dev 2015; 33:80-92. [PMID: 26547130 DOI: 10.1016/j.gde.2015.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 12/22/2022]
Abstract
Rapid progress in identifying the genes underlying autism spectrum disorder (ASD) has provided the substrate for a first wave of analyses into the underlying neurobiology. This review describes the consensus across these diverse analyses, highlighting two distinct sets of genes: 1) Genes that regulate chromatin and transcription, especially in cortical projection neurons and striatal medium spiny neurons during mid-fetal development; and 2) Genes involved in synapse development and function, especially during infancy and early childhood, and differentially expressed in the post mortem ASD brain. Both gene sets are also regulatory targets of the ASD genes CHD8 and FMRP. It remains to be seen whether these represent two independent paths to the ASD phenotype or two components of a common path.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA.
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392
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Buijsen RAM, Visser JA, Kramer P, Severijnen EAWFM, Gearing M, Charlet-Berguerand N, Sherman SL, Berman RF, Willemsen R, Hukema RK. Presence of inclusions positive for polyglycine containing protein, FMRpolyG, indicates that repeat-associated non-AUG translation plays a role in fragile X-associated primary ovarian insufficiency. Hum Reprod 2015; 31:158-68. [PMID: 26537920 DOI: 10.1093/humrep/dev280] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/15/2015] [Indexed: 12/11/2022] Open
Abstract
STUDY QUESTION Does repeat-associated non-AUG (RAN) translation play a role in fragile X-associated primary ovarian insufficiency (FXPOI), leading to the presence of polyglycine containing protein (FMRpolyG)-positive inclusions in ovarian tissue? SUMMARY ANSWER Ovaries of a woman with FXPOI and of an Fmr1 premutation (PM) mouse model (exCGG-KI) contain intranuclear inclusions that stain positive for both FMRpolyG and ubiquitin. WHAT IS KNOWN ALREADY Women who carry the FMR1 PM are at 20-fold increased risk to develop primary ovarian insufficiency (FXPOI). A toxic RNA gain-of-function has been suggested as the underlying mechanism since the PM results in increased levels of mRNA containing an expanded repeat, but reduced protein levels of fragile X mental retardation protein (FMRP). Recently, RAN translation has been shown to occur from FMR1 mRNA that contains PM repeat expansions, leading to FMRpolyG inclusions in brain and non-CNS tissues of fragile X-associated tremor/ataxia syndrome (FXTAS) patients. STUDY DESIGN, SIZE, DURATION Ovaries of a woman with FXPOI and women without PM (controls), and ovaries from wild-type and exCGG-KI mice were analyzed by immunohistochemistry for the presence of inclusions that stained for ubiquitin and FMRpolyG . The ovaries from wild-type and exCGG-KI mice were further characterized for the number of follicles, Fmr1 mRNA levels and FMRP protein expression. The presence of inclusions was also analyzed in pituitaries of a man with FXTAS and the exCGG-KI mice. PARTICIPANTS/MATERIALS, SETTING, METHODS Human ovaries from a woman with FXPOI and two control subjects and pituitaries from a man with FXTAS and a control subjects were fixed in 4% formalin. Ovaries and pituitaries of wild-type and exCGG mice were fixed in Bouin's fluid or 4% paraformaldehyde. Immunohistochemistry was performed on the human and mouse samples using FMRpolyG, ubiquitin and Fmrp antibodies. Fmr1 mRNA and protein expression were determined in mouse ovaries by quantitative RT-PCR and Western blot analysis. Follicle numbers in mouse ovaries were determined in serial sections by microscopy. MAIN RESULTS AND THE ROLE OF CHANCE FMRpolyG-positive inclusions were present in ovarian stromal cells of a woman with FXPOI but not in the ovaries of control subjects. The FMRpolyG-positive inclusions colocalized with ubiquitin-positive inclusions. Similar inclusions were also observed in the pituitary of a man with FXTAS but not in control subjects. Similarly, ovaries of 40-week-old exCGG-KI mice, but not wild-type mice, contained numerous inclusions in the stromal cells that stained for both FMRpolyG- and ubiquitin, while the ovaries of 20-week-old exCGG-KI contained fewer inclusions. At 40 weeks ovarian Fmr1 mRNA expression was increased by 5-fold in exCGG-KI mice compared with wild-type mice, while Fmrp expression was reduced by 2-fold. With respect to ovarian function in exCGG-KI mice: (i) although the number of healthy growing follicles did not differ between wild-type and exCGG-KI mice, the number of atretic large antral follicles was increased by nearly 9-fold in 40-week old exCGG-KI mice (P < 0.001); (ii) at 40 weeks of age only 50% of exCGG-KI mice had recent ovulations compared with 89% in wild-type mice (P = 0.07) and (iii) those exCGG-KI mice with recent ovulations tended to have a reduced number of fresh corpora lutea (4.8 ± 1.74 versus 8.50 ± 0.98, exCGG-KI versus wild-type mice, respectively, P = 0.07). LIMITATIONS, REASONS FOR CAUTION Although FMRpolyG-positive inclusions were detected in ovaries of both a woman with FXPOI and a mouse model of the FMR1 PM, we only analyzed one ovary from a FXPOI subject. Caution is needed to extrapolate these results to all women with the FMR1 PM. Furthermore, the functional consequence of FMRpolyG-positive inclusions in the ovaries for reproduction remains to be determined. WIDER IMPLICATIONS OF THE FINDINGS Our results suggest that a dysfunctional hypothalamic-pituitary-gonadal-axis may contribute to FXPOI in FMR1 PM carriers. STUDY FUNDING/COMPETING INTERESTS This study was supported by grants from NFXF, ZonMW, the Netherlands Brain Foundation and NIH. The authors have no conflict of interest to declare.
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Affiliation(s)
- R A M Buijsen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CE Rotterdam, The Netherlands
| | - J A Visser
- Department of Internal Medicine, Erasmus Medical Center, 3015 CE Rotterdam, The Netherlands
| | - P Kramer
- Department of Internal Medicine, Erasmus Medical Center, 3015 CE Rotterdam, The Netherlands
| | - E A W F M Severijnen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CE Rotterdam, The Netherlands
| | - M Gearing
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - N Charlet-Berguerand
- Department of Neurobiology and Genetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - S L Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - R F Berman
- Department of Neurological Surgery, UC Davis, Davis 95618, CA, USA
| | - R Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CE Rotterdam, The Netherlands
| | - R K Hukema
- Department of Clinical Genetics, Erasmus Medical Center, 3015 CE Rotterdam, The Netherlands
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393
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Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M. Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders. Cell Syst 2015; 1:361-374. [PMID: 26949739 DOI: 10.1016/j.cels.2015.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The prevalence of autism spectrum disorders (ASDs) is rapidly growing, yet its molecular basis is poorly understood. We used a systems approach in which ASD candidate genes were mapped onto the ubiquitous human protein complexes and the resulting complexes were characterized. The studies revealed the role of histone deacetylases (HDAC1/2) in regulating the expression of ASD orthologs in the embryonic mouse brain. Proteome-wide screens for the co-complexed subunits with HDAC1 and six other key ASD proteins in neuronal cells revealed a protein interaction network, which displayed preferential expression in fetal brain development, exhibited increased deleterious mutations in ASD cases, and were strongly regulated by FMRP and MECP2 causal for Fragile X and Rett syndromes, respectively. Overall, our study reveals molecular components in ASD, suggests a shared mechanism between the syndromic and idiopathic forms of ASDs, and provides a systems framework for analyzing complex human diseases.
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Affiliation(s)
- Jingjing Li
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, California, 94305 USA
| | - Zhihai Ma
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, California, 94305 USA
| | - Minyi Shi
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, California, 94305 USA
| | - Ramy H Malty
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Zoran Minic
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ke Jin
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada; Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Dennis P Wall
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305 USA; Department of Pediatrics, Stanford, California, 94305 USA
| | - Zhaolei Zhang
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Alexander E Urban
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, California, 94305 USA; Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305 USA
| | - Joachim Hallmayer
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305 USA
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Michael Snyder
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, California, 94305 USA
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394
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Livi CM, Klus P, Delli Ponti R, Tartaglia GG. catRAPID signature: identification of ribonucleoproteins and RNA-binding regions. Bioinformatics 2015; 32:773-5. [PMID: 26520853 PMCID: PMC4795616 DOI: 10.1093/bioinformatics/btv629] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets. AVAILABILITY AND IMPLEMENTATION catRAPID signature can be accessed at http://s.tartaglialab.com/new_submission/signature CONTACT gian.tartaglia@crg.es or gian@tartaglialab.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carmen Maria Livi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and
| | - Petr Klus
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and
| | - Riccardo Delli Ponti
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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395
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Yang Y, Wen L, Zhu H. Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein. Cell Biosci 2015; 5:59. [PMID: 26500759 PMCID: PMC4618879 DOI: 10.1186/s13578-015-0050-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/08/2015] [Indexed: 12/13/2022] Open
Abstract
Tens of thousands of long non-coding RNAs (lncRNAs) have been discovered in eukarya, but their functions are largely unknown. Fortunately, lncRNA-protein interactions may offer details of how lncRNAs play important roles in various biological processes, thus identifying proteins associated with lncRNA is critical. Here we review progress of molecular archetypes that lncRNAs execute as guides, scaffolds, or decoys for protein, focusing on advantages, shortcomings and applications of various conventional and emerging technologies to probe lncRNAs and protein interactions, including protein-centric biochemistry approaches such as nRIP and CLIP, and RNA-centric biochemistry approaches such as ChIRP, CHART and RAP. Overall, this review provides strategies for probing interactions between lncRNAs and protein.
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Affiliation(s)
- Yongfang Yang
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Liwei Wen
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Hongliang Zhu
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
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396
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Pacey LKK, Guan S, Tharmalingam S, Thomsen C, Hampson DR. Persistent astrocyte activation in the fragile X mouse cerebellum. Brain Behav 2015; 5:e00400. [PMID: 26516618 PMCID: PMC4614053 DOI: 10.1002/brb3.400] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/31/2015] [Accepted: 08/21/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Fragile X Syndrome, the most common single gene cause of autism, results from loss of the RNA-binding protein FMRP. Although FMRP is highly expressed in neurons, it has also recently been identified in glia. It has been postulated that in the absence of FMRP, abnormal function of non-neuronal cells may contribute to the pathogenesis of the disorder. We previously demonstrated reduced numbers of oligodendrocyte precursor cells and delayed myelination in the cerebellum of fragile X (Fmr1) knockout mice. METHODS We used quantitative western blotting and immunocytochemistry to examine the status of astrocytes and microglia in the cerebellum of Fmr1 mice during development and in adulthood. RESULTS We report increased expression of the astrocyte marker GFAP in the cerebellum of Fmr1 mice starting in the second postnatal week and persisting in to adulthood. At 2 weeks postnatal, expression of Tumor Necrosis Factor Receptor 2 (TNFR2) and Leukemia Inhibitory Factor (LIF) were elevated in the Fmr1 KO cerebellum. In adults, expression of TNFR2 and the glial marker S100β were also elevated in Fmr1 knockouts, but LIF expression was not different from wild-type mice. We found no evidence of microglial activation or neuroinflammation at any age examined. CONCLUSIONS These findings demonstrate an atypical pattern of astrogliosis in the absence of microglial activation in Fmr1 knockout mouse cerebellum. Enhanced TNFR2 and LIF expression in young mice suggests that changes in the expression of astrocytic proteins may be an attempt to compensate for delayed myelination in the developing cerebellum of Fmr1 mice.
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Affiliation(s)
- Laura K K Pacey
- Department of Pharmaceutical Sciences Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street Toronto Ontario Canada M5S 3M2
| | - Sihui Guan
- Department of Pharmaceutical Sciences Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street Toronto Ontario Canada M5S 3M2
| | - Sujeenthar Tharmalingam
- Department of Pharmaceutical Sciences Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street Toronto Ontario Canada M5S 3M2
| | - Christian Thomsen
- Department of Neuroinflammation Lundbeck Research USA 215 College Road Paramus New Jersey 07652
| | - David R Hampson
- Department of Pharmaceutical Sciences Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street Toronto Ontario Canada M5S 3M2 ; Department of Pharmacology Faculty of Medicine University of Toronto 144 College Street Toronto Ontario Canada M5S 3M2
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397
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Maeda M, Hasegawa H, Sugiyama M, Hyodo T, Ito S, Chen D, Asano E, Masuda A, Hasegawa Y, Hamaguchi M, Senga T. Arginine methylation of ubiquitin-associated protein 2-like is required for the accurate distribution of chromosomes. FASEB J 2015; 30:312-23. [PMID: 26381755 DOI: 10.1096/fj.14-268987] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 09/08/2015] [Indexed: 01/01/2023]
Abstract
Proper bioriented attachment of microtubules and kinetochores is essential for the precise distribution of duplicated chromosomes to each daughter cell. An aberrant kinetochore-microtubule attachment results in chromosome instability, which leads to cellular transformation or apoptosis. In this article, we show that ubiquitin-associated protein 2-like (UBAP2L) is necessary for correct kinetochore-microtubule attachment. Depletion of UBAP2L inhibited chromosome alignment in metaphase and delayed progression to anaphase by activating spindle assembly checkpoint signaling. In addition, UBAP2L knockdown increased side-on attachment of kinetochores along the microtubules and suppressed stable kinetochore fiber formation. A proteomics analysis identified protein arginine methyltransferase (PRMT)1 as a direct interaction partner of UBAP2L. UBAP2L has an arginine- and glycine-rich motif called the RGG/RG or GAR motif in the N terminus. Biochemical analysis confirmed that arginine residues in the RGG/RG motif of UBAP2L were directly methylated by PRMT1. Finally, we demonstrated that the RGG/RG motif of UBAP2L is essential for the proper alignment of chromosomes in metaphase for the accurate distribution of chromosomes. Our results show a possible role for arginine methylation in UBAP2L for the progression of mitosis.
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Affiliation(s)
- Masao Maeda
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitoki Hasegawa
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mai Sugiyama
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshinori Hyodo
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoko Ito
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Dan Chen
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Asano
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akio Masuda
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Hasegawa
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Michinari Hamaguchi
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takeshi Senga
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome. G3-GENES GENOMES GENETICS 2015; 5:2453-61. [PMID: 26384369 PMCID: PMC4632064 DOI: 10.1534/g3.115.021345] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromosome 22q11.2 microdeletions impart a high but incomplete risk for schizophrenia. Possible mechanisms include genome-wide effects of DGCR8 haploinsufficiency. In a proof-of-principle study to assess the power of this model, we used high-quality, whole-genome sequencing of nine individuals with 22q11.2 deletions and extreme phenotypes (schizophrenia, or no psychotic disorder at age >50 years). The schizophrenia group had a greater burden of rare, damaging variants impacting protein-coding neurofunctional genes, including genes involved in neuron projection (nominal P = 0.02, joint burden of three variant types). Variants in the intact 22q11.2 region were not major contributors. Restricting to genes affected by a DGCR8 mechanism tended to amplify between-group differences. Damaging variants in highly conserved long intergenic noncoding RNA genes also were enriched in the schizophrenia group (nominal P = 0.04). The findings support the 22q11.2 deletion model as a threshold-lowering first hit for schizophrenia risk. If applied to a larger and thus better-powered cohort, this appears to be a promising approach to identify genome-wide rare variants in coding and noncoding sequence that perturb gene networks relevant to idiopathic schizophrenia. Similarly designed studies exploiting genetic models may prove useful to help delineate the genetic architecture of other complex phenotypes.
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399
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Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. Proc Natl Acad Sci U S A 2015; 112:E5391-400. [PMID: 26374839 DOI: 10.1073/pnas.1515737112] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K(+)-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.
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400
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Richter JD, Bassell GJ, Klann E. Dysregulation and restoration of translational homeostasis in fragile X syndrome. Nat Rev Neurosci 2015; 16:595-605. [PMID: 26350240 DOI: 10.1038/nrn4001] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragile X syndrome (FXS), the most-frequently inherited form of intellectual disability and the most-prevalent single-gene cause of autism, results from a lack of fragile X mental retardation protein (FMRP), an RNA-binding protein that acts, in most cases, to repress translation. Multiple pharmacological and genetic manipulations that target receptors, scaffolding proteins, kinases and translational control proteins can rescue neuronal morphology, synaptic function and behavioural phenotypes in FXS model mice, presumably by reducing excessive neuronal translation to normal levels. Such rescue strategies might also be explored in the future to identify the mRNAs that are critical for FXS pathophysiology.
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Affiliation(s)
- Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01545, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York City, New York 10003, USA
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