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Corrêa-Velloso JC, Linardi AM, Glaser T, Velloso FJ, Rivas MP, Leite REP, Grinberg LT, Ulrich H, Akins MR, Chiavegatto S, Haddad LA. Fmr1 exon 14 skipping in late embryonic development of the rat forebrain. BMC Neurosci 2022; 23:32. [PMID: 35641906 PMCID: PMC9158170 DOI: 10.1186/s12868-022-00711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fragile X syndrome, the major cause of inherited intellectual disability among men, is due to deficiency of the synaptic functional regulator FMR1 protein (FMRP), encoded by the FMRP translational regulator 1 (FMR1) gene. FMR1 alternative splicing produces distinct transcripts that may consequently impact FMRP functional roles. In transcripts without exon 14 the translational reading frame is shifted. For deepening current knowledge of the differential expression of Fmr1 exon 14 along the rat nervous system development, we conducted a descriptive study employing quantitative RT-PCR and BLAST of RNA-Seq datasets. RESULTS We observed in the rat forebrain progressive decline of total Fmr1 mRNA from E11 to P112 albeit an elevation on P3; and exon-14 skipping in E17-E20 with downregulation of the resulting mRNA. We tested if the reduced detection of messages without exon 14 could be explained by nonsense-mediated mRNA decay (NMD) vulnerability, but knocking down UPF1, a major component of this pathway, did not increase their quantities. Conversely, it significantly decreased FMR1 mRNA having exon 13 joined with either exon 14 or exon 15 site A. CONCLUSIONS The forebrain in the third embryonic week of the rat development is a period with significant skipping of Fmr1 exon 14. This alternative splicing event chronologically precedes a reduction of total Fmr1 mRNA, suggesting that it may be part of combinatorial mechanisms downregulating the gene's expression in the late embryonic period. The decay of FMR1 mRNA without exon 14 should be mediated by a pathway different from NMD. Finally, we provide evidence of FMR1 mRNA stabilization by UPF1, likely depending on FMRP.
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Affiliation(s)
- Juliana C Corrêa-Velloso
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Alessandra M Linardi
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Talita Glaser
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fernando J Velloso
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Maria P Rivas
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Renata E P Leite
- Department of Pathology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Lea T Grinberg
- Department of Pathology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Henning Ulrich
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Michael R Akins
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Silvana Chiavegatto
- Department of Pharmacology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil.,Department of Psychiatry, Instituto de Psiquiatria, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luciana A Haddad
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil.
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Zafarullah M, Tang HT, Durbin-Johnson B, Fourie E, Hessl D, Rivera SM, Tassone F. FMR1 locus isoforms: potential biomarker candidates in fragile X-associated tremor/ataxia syndrome (FXTAS). Sci Rep 2020; 10:11099. [PMID: 32632326 PMCID: PMC7338407 DOI: 10.1038/s41598-020-67946-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Fragile X associated tremor/ataxia syndrome (FXTAS) is a late adult-onset neurodegenerative disorder that affects movement and cognition in male and female carriers of a premutation allele of 55-200 CGG repeats in the Fragile X mental retardation (FMR1) gene. It is currently unknown if and when an individual carrier of a premutation allele will develop FXTAS, as clinical assessment fails to identify carriers at risk before significant neurological symptoms are evident. The primary objective of this study was to investigate the alternative splicing landscape at the FMR1 locus in conjunction with brain measures in male individuals with a premutation allele enrolled in a very first longitudinal study, compared to age-matched healthy male controls, with the purpose of identifying biomarkers for early diagnosis, disease prediction and, a progression of FXTAS. Our findings indicate that increased expression of FMR1 mRNA isoforms, including Iso4/4b, Iso10/10b, as well as of the ASFMR1 mRNAs Iso131bp, are present in premutation carriers as compared to non-carrier healthy controls. More specifically, we observed a higher expression of Iso4/4b and Iso10/10b, which encode for truncated proteins, only in those premutation carriers who developed symptoms of FXTAS over time as compared to non-carrier healthy controls, suggesting a potential role in the development of the disorder. In addition, we found a significant association of these molecular changes with various measurements of brain morphology, including the middle cerebellar peduncle (MCP), superior cerebellar peduncle (SCP), pons, and midbrain, indicating their potential contribution to the pathogenesis of FXTAS. Interestingly, the high expression levels of Iso4/4b observed both at visit 1 and visit 2 and found to be associated with a decrease in mean MCP width only in those individuals who developed FXTAS over time, suggests their role as potential biomarkers for early diagnosis of FXTAS.
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Affiliation(s)
- Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, 95817 CA, USA
| | - Hiu-Tung Tang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, 95817 CA, USA
| | - Blythe Durbin-Johnson
- Division of Biostatistics, School of Medicine, University of California Davis, Davis, CA, USA
| | - Emily Fourie
- Center for Mind and Brain, University of California Davis, Davis, CA, USA
- Department of Psychology, University of California, Davis, Davis, CA, USA
| | - David Hessl
- MIND Institute, University of California Davis Medical Center, Sacramento, 95817 CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California Davis Medical Center, Sacramento, 95817 CA, USA
| | - Susan M Rivera
- Center for Mind and Brain, University of California Davis, Davis, CA, USA
- Department of Psychology, University of California, Davis, Davis, CA, USA
- MIND Institute, University of California Davis Medical Center, Sacramento, 95817 CA, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, 95817 CA, USA.
- MIND Institute, University of California Davis Medical Center, Sacramento, 95817 CA, USA.
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Yang WJ, Yan AZ, Xu YJ, Guo XY, Fu XG, Li D, Liao J, Zhang D, Lan FH. Further identification of a 140bp sequence from amid intron 9 of human FMR1 gene as a new exon. BMC Genet 2020; 21:63. [PMID: 32552710 PMCID: PMC7301526 DOI: 10.1186/s12863-020-00870-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
Background The disease gene of fragile X syndrome, FMR1 gene, encodes fragile X mental retardation protein (FMRP). The alternative splicing (AS) of FMR1 can affect the structure and function of FMRP. However, the biological functions of alternatively spliced isoforms remain elusive. In a previous study, we identified a new 140bp exon from the intron 9 of human FMR1 gene. In this study, we further examined the biological functions of this new exon and its underlying signaling pathways. Results qRT-PCR results showed that this novel exon is commonly expressed in the peripheral blood of normal individuals. Comparative genomics showed that sequences paralogous to the 140 bp sequence only exist in the genomes of primates. To explore the biological functions of the new transcript, we constructed recombinant eukaryotic expression vectors and lentiviral overexpression vectors. Results showed that the spliced transcript encoded a truncated protein which was expressed mainly in the cell nucleus. Additionally, several genes, including the BEX1 gene involved in mGluR-LTP or mGluR-LTD signaling pathways were significantly influenced when the truncated FMRP was overexpressed. Conclusions our work identified a new exon from amid intron 9 of human FMR1 gene with wide expression in normal healthy individuals, which emphasizes the notion that the AS of FMR1 gene is complex and may in a large part account for the multiple functions of FMRP.
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Affiliation(s)
- Wen-Jing Yang
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ai-Zhen Yan
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Yong-Jun Xu
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Xiao-Yan Guo
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Fuzhou No. 2 Hospital Affiliated Xiamen University, Fuzhou, Fujian, 350007, People's Republic of China
| | - Xian-Guo Fu
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Ningde Municipal Hospital, Fujian Medical University, Ningde City, 352100, Fujian Province, China
| | - Dan Li
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Juan Liao
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Fujian University of Traditional Chinese Medicine Affiliated People's Hospital, Fuzhou, 350001, Fujian, China
| | - Duo Zhang
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Feng-Hua Lan
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.
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Fu XG, Yan AZ, Xu YJ, Liao J, Guo XY, Zhang D, Yang WJ, Zheng DZ, Lan FH. Splicing of exon 9a in FMR1 transcripts results in a truncated FMRP with altered subcellular distribution. Gene 2020; 731:144359. [PMID: 31935509 DOI: 10.1016/j.gene.2020.144359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
FMRP is an RNA-binding protein, loss of which causes fragile X syndrome (FXS). FMRP has several isoforms resulted from alternative splicing (AS) of fragile X mental retardation 1 (FMR1) gene, but their biological functions are still poorly understood. In the analysis of alternatively spliced FMR1 transcripts in the blood cells from a patient with FXS-like phenotypes (normal CGG repeats and no mutation in coding sequence of FMR1), we identified three novel FMR1 transcripts that include a previously unidentified microexon (46 bp), terming the exon 9a. This microexon exists widely in unaffected individuals, inclusion of which introduces an in-frame termination codon. To address whether these exon 9a-containing transcripts could produce protein by evading nonsense-mediated decay (NMD), Western blot was used to analysis blood cell lysate from unaffected individuals and a 34 kDa protein that consistent in size with the molecular weight of the predicted truncated protein produced from mRNA with this microexon was found. Meanwhile, treatment of peripheral blood mononuclear cells with an inhibitor of NMD (Cycloheximide) did not result in significant increase in exon 9a-containing transcripts. Using confocal immunofluorescence, we found the truncated protein displayed both nuclear and cytoplasmic localization in HEK293T and HeLa cells due to lacking C-terminal domains including KH2, NES, and RGG, while the full-length FMRP protein mainly localized in the cytoplasm. Therefore, we hypothesize that the inclusion of this microexon to generate exon 9a-containing transcripts may regulate the normal functionality of FMRP, and the dysregulation of normal FMRP due to increased exon 9a-containing alternatively spliced transcripts in that patient may be associated with the manifestation of FXS phenotype.
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Affiliation(s)
- Xian-Guo Fu
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Ai-Zhen Yan
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Yong-Jun Xu
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Juan Liao
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Xiao-Yan Guo
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Duo Zhang
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Wen-Jing Yang
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - De-Zhu Zheng
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Feng-Hua Lan
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Fujian Medical University, Fuzhou, Fujian 350025, China.
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Tseng E, Tang HT, AlOlaby RR, Hickey L, Tassone F. Altered expression of the FMR1 splicing variants landscape in premutation carriers. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1117-1126. [PMID: 28888471 DOI: 10.1016/j.bbagrm.2017.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/17/2023]
Abstract
FMR1 premutation carriers (55-200 CGG repeats) are at risk for developing Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), an adult onset neurodegenerative disorder. Approximately 20% of female carriers will develop Fragile X-associated Primary Ovarian Insufficiency (FXPOI), in addition to a number of clinical problems affecting premutation carriers throughout their life span. Marked elevation in FMR1 mRNA levels have been observed with premutation alleles resulting in RNA toxicity, the leading molecular mechanism proposed for the FMR1 associated disorders observed in premutation carriers. The FMR1 gene undergoes alternative splicing and we have recently reported that the relative abundance of all FMR1 mRNA isoforms is significantly increased in premutation carriers. In this study, we characterized the transcriptional FMR1 isoforms distribution pattern in different tissues and identified a total of 49 isoforms, some of which observed only in premutation carriers and which might play a role in the pathogenesis of FXTAS. Further, we investigated the distribution pattern and expression levels of the FMR1 isoforms in asymptomatic premutation carriers and in those with FXTAS and found no significant differences between the two groups. Our findings suggest that the characterization of the expression levels of the different FMR1 isoforms is fundamental for understanding the regulation of the FMR1 gene as imbalance in their expression could lead to an altered functional diversity with neurotoxic consequences. Their characterization will also help to elucidating the mechanism(s) by which "toxic gain of function" of the FMR1 mRNA may play a role in FXTAS and/or in the other FMR1-associated conditions.
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Affiliation(s)
| | - Hiu-Tung Tang
- Biochemistry and Molecular Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Reem Rafik AlOlaby
- Biochemistry and Molecular Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Luke Hickey
- Pacific Biosciences, Inc., Menlo Park, CA 94025, USA
| | - Flora Tassone
- Biochemistry and Molecular Medicine, UC Davis, Sacramento, CA 95817, USA; MIND Institute, UC Davis, Sacramento, CA 95817, USA.
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Khalfallah O, Jarjat M, Davidovic L, Nottet N, Cestèle S, Mantegazza M, Bardoni B. Depletion of the Fragile X Mental Retardation Protein in Embryonic Stem Cells Alters the Kinetics of Neurogenesis. Stem Cells 2016; 35:374-385. [PMID: 27664080 DOI: 10.1002/stem.2505] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 08/07/2016] [Accepted: 08/30/2016] [Indexed: 01/14/2023]
Abstract
Fragile X syndrome (FXS) is the most common form of inherited intellectual disability and a leading cause of autism. FXS is due to the silencing of the Fragile X Mental Retardation Protein (FMRP), an RNA binding protein mainly involved in translational control, dendritic spine morphology and synaptic plasticity. Despite extensive studies, there is currently no cure for FXS. With the purpose to decipher the initial molecular events leading to this pathology, we developed a stem-cell-based disease model by knocking-down the expression of Fmr1 in mouse embryonic stem cells (ESCs). Repressing FMRP in ESCs increased the expression of amyloid precursor protein (APP) and Ascl1. When inducing neuronal differentiation, βIII-tubulin, p27kip1 , NeuN, and NeuroD1 were upregulated, leading to an accelerated neuronal differentiation that was partially compensated at later stages. Interestingly, we observed that neurogenesis is also accelerated in the embryonic brain of Fmr1-knockout mice, indicating that our cellular model recapitulates the molecular alterations present in vivo. Importantly, we rescued the main phenotype of the Fmr1 knockdown cell line, not only by reintroducing FMRP but also by pharmacologically targeting APP processing, showing the role of this protein in the pathophysiology of FXS during the earliest steps of neurogenesis. Our work allows to define an early therapeutic window but also to identify more effective molecules for treating this disorder. Stem Cells 2017;35:374-385.
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Affiliation(s)
- Olfa Khalfallah
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France.,CNRS, LIA « NEOGENEX », Valbonne Sophia-Antipolis, France
| | - Marielle Jarjat
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France.,CNRS, LIA « NEOGENEX », Valbonne Sophia-Antipolis, France
| | - Laetitia Davidovic
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France
| | - Nicolas Nottet
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France
| | - Sandrine Cestèle
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France
| | - Massimo Mantegazza
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France
| | - Barbara Bardoni
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne Sophia-Antipolis, France.,CNRS, LIA « NEOGENEX », Valbonne Sophia-Antipolis, France
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Zimmer SE, Doll SG, Garcia ADR, Akins MR. Splice form-dependent regulation of axonal arbor complexity by FMRP. Dev Neurobiol 2016; 77:738-752. [PMID: 27643955 DOI: 10.1002/dneu.22453] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 01/01/2023]
Abstract
The autism-related protein Fragile X mental retardation protein (FMRP) is an RNA binding protein that plays important roles during both nervous system development and experience dependent plasticity. Alternative splicing of the Fmr1 locus gives rise to 12 different FMRP splice forms that differ in the functional and regulatory domains they contain as well as in their expression profile among brain regions and across development. Complete loss of FMRP leads to morphological and functional changes in neurons, including an increase in the size and complexity of the axonal arbor. To investigate the relative contribution of the FMRP splice forms to the regulation of axon morphology, we overexpressed individual splice forms in cultured wild type rat cortical neurons. FMRP overexpression led to a decrease in axonal arbor complexity that suggests that FMRP regulates axon branching. This reduction in complexity was specific to three splice forms-the full-length splice form 1, the most highly expressed splice form 7, and splice form 9. A focused analysis of splice form 7 revealed that this regulation is independent of RNA binding. Instead this regulation is disrupted by mutations affecting phosphorylation of a conserved serine as well as by mutating the nuclear export sequence. Surprisingly, this mutation in the nuclear export sequence also led to increased localization to the distal axonal arbor. Together, these findings reveal domain-specific functions of FMRP in the regulation of axonal complexity that may be controlled by differential expression of FMRP splice forms. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 738-752, 2017.
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Affiliation(s)
| | - Steven G Doll
- Department of Biology, Drexel University, Philadelphia, Pennsylvania
| | - A Denise R Garcia
- Department of Biology, Drexel University, Philadelphia, Pennsylvania.,Department of Neurobiology and Anatomy, Drexel University, Philadelphia, Pennsylvania
| | - Michael R Akins
- Department of Biology, Drexel University, Philadelphia, Pennsylvania.,Department of Neurobiology and Anatomy, Drexel University, Philadelphia, Pennsylvania
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Brasa S, Mueller A, Jacquemont S, Hahne F, Rozenberg I, Peters T, He Y, McCormack C, Gasparini F, Chibout SD, Grenet O, Moggs J, Gomez-Mancilla B, Terranova R. Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome. Clin Epigenetics 2016; 8:15. [PMID: 26855684 PMCID: PMC4743126 DOI: 10.1186/s13148-016-0181-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/24/2016] [Indexed: 01/22/2023] Open
Abstract
Background Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, resulting from the loss of function of the fragile X mental retardation 1 (FMR1) gene. The molecular pathways associated with FMR1 epigenetic silencing are still elusive, and their characterization may enhance the discovery of novel therapeutic targets as well as the development of novel clinical biomarkers for disease status. Results We have deployed customized epigenomic profiling assays to comprehensively map the FMR1 locus chromatin landscape in peripheral mononuclear blood cells (PBMCs) from eight FXS patients and in fibroblast cell lines derived from three FXS patient. Deoxyribonucleic acid (DNA) methylation (5-methylcytosine (5mC)) and hydroxymethylation (5-hydroxymethylcytosine (5hmC)) profiling using methylated DNA immunoprecipitation (MeDIP) combined with a custom FMR1 microarray identifies novel regions of DNA (hydroxy)methylation changes within the FMR1 gene body as well as in proximal flanking regions. At the region surrounding the FMR1 transcriptional start sites, increased levels of 5mC were associated to reciprocal changes in 5hmC, representing a novel molecular feature of FXS disease. Locus-specific validation of FMR1 5mC and 5hmC changes highlighted inter-individual differences that may account for the expected DNA methylation mosaicism observed at the FMR1 locus in FXS patients. Chromatin immunoprecipitation (ChIP) profiling of FMR1 histone modifications, together with 5mC/5hmC and gene expression analyses, support a functional relationship between 5hmC levels and FMR1 transcriptional activation and reveal cell-type specific differences in FMR1 epigenetic regulation. Furthermore, whilst 5mC FMR1 levels positively correlated with FXS disease severity (clinical scores of aberrant behavior), our data reveal for the first time an inverse correlation between 5hmC FMR1 levels and FXS disease severity. Conclusions We identify novel, cell-type specific, regions of FMR1 epigenetic changes in FXS patient cells, providing new insights into the molecular mechanisms of FXS. We propose that the combined measurement of 5mC and 5hmC at selected regions of the FMR1 locus may significantly enhance FXS clinical diagnostics and patient stratification. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0181-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Brasa
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Arne Mueller
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Sébastien Jacquemont
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, CH-1011 Lausanne, Switzerland
| | - Florian Hahne
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Izabela Rozenberg
- Neuroscience Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Thomas Peters
- BioMarker Development, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA USA
| | - Yunsheng He
- BioMarker Development, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA USA
| | - Christine McCormack
- Clinical Diagnostics, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA USA
| | - Fabrizio Gasparini
- Neuroscience, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Salah-Dine Chibout
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Olivier Grenet
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Jonathan Moggs
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
| | - Baltazar Gomez-Mancilla
- Neuroscience Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Rémi Terranova
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland
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FU XIANGUO, ZHENG DEZHU, LIAO JUAN, LI QINGQIN, LIN YUXIANG, ZHANG DUO, YAN AIZHEN, LAN FENGHUA. Alternatively spliced products lacking exon 12 dominate the expression of fragile X mental retardation 1 gene in human tissues. Mol Med Rep 2015; 12:1957-62. [DOI: 10.3892/mmr.2015.3574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 02/17/2015] [Indexed: 11/06/2022] Open
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10
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Pretto DI, Eid JS, Yrigollen CM, Tang HT, Loomis EW, Raske C, Durbin-Johnson B, Hagerman PJ, Tassone F. Differential increases of specific FMR1 mRNA isoforms in premutation carriers. J Med Genet 2014; 52:42-52. [PMID: 25358671 DOI: 10.1136/jmedgenet-2014-102593] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Over 40% of male and ∼16% of female carriers of a premutation FMR1 allele (55-200 CGG repeats) will develop fragile X-associated tremor/ataxia syndrome, an adult onset neurodegenerative disorder, while about 20% of female carriers will develop fragile X-associated primary ovarian insufficiency. Marked elevation in FMR1 mRNA transcript levels has been observed with premutation alleles, and RNA toxicity due to increased mRNA levels is the leading molecular mechanism proposed for these disorders. However, although the FMR1 gene undergoes alternative splicing, it is unknown whether all or only some of the isoforms are overexpressed in premutation carriers and which isoforms may contribute to the premutation pathology. METHODS To address this question, we have applied a long-read sequencing approach using single-molecule real-time (SMRT) sequencing and qRT-PCR. RESULTS Our SMRT sequencing analysis performed on peripheral blood mononuclear cells, fibroblasts and brain tissue samples derived from premutation carriers and controls revealed the existence of 16 isoforms of 24 predicted variants. Although the relative abundance of all mRNA isoforms was significantly increased in the premutation group, as expected based on the bulk increase in mRNA levels, there was a disproportionate (fourfold to sixfold) increase, relative to the overall increase in mRNA, in the abundance of isoforms spliced at both exons 12 and 14, specifically Iso10 and Iso10b, containing the complete exon 15 and differing only in splicing in exon 17. CONCLUSIONS These findings suggest that RNA toxicity may arise from a relative increase of all FMR1 mRNA isoforms. Interestingly, the Iso10 and Iso10b mRNA isoforms, lacking the C-terminal functional sites for fragile X mental retardation protein function, are the most increased in premutation carriers relative to normal, suggesting a functional relevance in the pathology of FMR1-associated disorders.
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Affiliation(s)
- Dalyir I Pretto
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - John S Eid
- Pacific Biosciences, Menlo Park, California, USA
| | - Carolyn M Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Hiu-Tung Tang
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Erick W Loomis
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Chris Raske
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California Davis, School of Medicine, Davis, California, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
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11
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Denman RB, Xie W, Merz G, Sung YJ. GABAAergic stimulation modulates intracellular protein arginine methylation. Neurosci Lett 2014; 572:38-43. [PMID: 24793772 DOI: 10.1016/j.neulet.2014.04.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/26/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
Changes in cytoplasmic pH are known to regulate diverse cellular processes and influence neuronal activities. In neurons, the intracellular alkalization is shown to occur after stimulating several channels and receptors. For example, it has previously demonstrated in P19 neurons that a sustained intracellular alkalinization can be mediated by the Na(+)/H(+) antiporter. In addition, the benzodiazepine binding subtypes of the γ-amino butyric acid type A (GABAA) receptor mediate a transient intracellular alkalinization when they are stimulated. Because the activities of many enzymes are sensitive to pH shift, here we investigate the effects of intracellular pH modulation resulted from stimulating GABAA receptor on the protein arginine methyltransferases (PRMT) activities. We show that the major benzodiazepine subtype (2α1, 2β2, 1γ2) is constitutively expressed in both undifferentiated P19 cells and retinoic acid (RA) differentiated P19 neurons. Furthermore stimulation with diazepam and, diazepam plus muscimol produce an intracellular alkalinization that can be detected ex vivo with the fluorescence dye. The alkalinization results in significant perturbation in protein arginine methylation activity as measured in methylation assays with specific protein substrates. Altered protein arginine methylation is also observed when cells are treated with the GABAA agonist muscimol but not an antagonist, bicuculline. These data suggest that pH-dependent and pH-independent methylation pathways can be activated by GABAAergic stimulation, which we verified using hippocampal slice preparations from a mouse model of fragile X syndrome.
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Affiliation(s)
- Robert B Denman
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York, NY 10314, USA
| | - Wen Xie
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY 1065, USA
| | - George Merz
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York, NY 10314, USA
| | - Ying-Ju Sung
- Department of Basic Sciences, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, USA.
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12
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Fernández E, Rajan N, Bagni C. The FMRP regulon: from targets to disease convergence. Front Neurosci 2013; 7:191. [PMID: 24167470 PMCID: PMC3807044 DOI: 10.3389/fnins.2013.00191] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/04/2013] [Indexed: 01/08/2023] Open
Abstract
The fragile X mental retardation protein (FMRP) is an RNA-binding protein that regulates mRNA metabolism. FMRP has been largely studied in the brain, where the absence of this protein leads to fragile X syndrome, the most frequent form of inherited intellectual disability. Since the identification of the FMRP gene in 1991, many studies have primarily focused on understanding the function/s of this protein. Hundreds of potential FMRP mRNA targets and several interacting proteins have been identified. Here, we report the identification of FMRP mRNA targets in the mammalian brain that support the key role of this protein during brain development and in regulating synaptic plasticity. We compared the genes from databases and genome-wide association studies with the brain FMRP transcriptome, and identified several FMRP mRNA targets associated with autism spectrum disorders, mood disorders and schizophrenia, showing a potential common pathway/s for these apparently different disorders.
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Affiliation(s)
- Esperanza Fernández
- Center for the Biology of Disease, Vlaams Institut voor Biotechnologie Leuven, Belgium ; Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven Leuven, Belgium
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13
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Bagni C, Oostra BA. Fragile X syndrome: From protein function to therapy. Am J Med Genet A 2013; 161A:2809-21. [PMID: 24115651 DOI: 10.1002/ajmg.a.36241] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/28/2013] [Indexed: 12/23/2022]
Abstract
Fragile X syndrome (FXS) is the leading monogenic cause of intellectual disability and autism. The FMR1 gene contains a CGG repeat present in the 5'-untranslated region which can be unstable upon transmission to the next generation. The repeat is up to 55 CGGs long in the normal population. In patients with fragile X syndrome (FXS), a repeat length exceeding 200 CGGs generally leads to methylation of the repeat and the promoter region, which is accompanied by silencing of the FMR1 gene. The disease is a result of lack of expression of the fragile X mental retardation protein leading to severe symptoms, including intellectual disability, hyperactivity, and autistic-like behavior. The FMR1 protein (FMRP) has a number of functions. The translational dysregulation of a subset of mRNAs targeted by FMRP is probably the major contribution to FXS. FMRP is also involved in mRNA transport to synapses where protein synthesis occurs. For some FMRP-bound mRNAs, FMRP is a direct modulator of mRNA stability either by sustaining or preventing mRNA decay. Increased knowledge about the role of FMRP has led to the identification of potential treatments for fragile X syndrome that were often tested first in the different animal models. This review gives an overview about the present knowledge of the function of FMRP and the therapeutic strategies in mouse and man.
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Affiliation(s)
- Claudia Bagni
- VIB Center for the Biology of Disease, Catholic University of Leuven, Leuven, Belgium; Department of Biomedicine and Prevention, University of Rome, Tor Vergata, Italy
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14
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Brackett DM, Qing F, Amieux PS, Sellers DL, Horner PJ, Morris DR. FMR1 transcript isoforms: association with polyribosomes; regional and developmental expression in mouse brain. PLoS One 2013; 8:e58296. [PMID: 23505481 PMCID: PMC3591412 DOI: 10.1371/journal.pone.0058296] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/01/2013] [Indexed: 12/31/2022] Open
Abstract
The primary transcript of the mammalian Fragile X Mental Retardation-1 gene (Fmr1), like many transcripts in the central nervous system, is alternatively spliced to yield mRNAs encoding multiple proteins, which can possess quite different biochemical properties. Despite the fact that the relative levels of the 12 Fmr1 transcript isoforms examined here vary by as much as two orders of magnitude amongst themselves in both adult and embryonic mouse brain, all are associated with polyribosomes, consistent with translation into the corresponding isoforms of the protein product, FMRP (Fragile X Mental Retardation Protein). Employing the RiboTag methodology developed in our laboratory, the relative proportions of the 7 most abundant transcript isoforms were measured specifically in neurons and found to be similar to those identified in whole brain. Measurements of isoform profiles across 11 regions of adult brain yielded similar distributions, with the exceptions of the hippocampus and the olfactory bulb. These two regions differ from most of the brain in relative amounts of transcripts encoding an alternate form of one of the KH RNA binding domains. A possible relationship between patterns of expression in the hippocampus and olfactory bulb and the presence of neuroblasts in these two regions is suggested by the isoform patterns in early embryonic brain and in cultured neural progenitor cells. These results demonstrate that the relative levels of the Fmr1 isoforms are modulated according to developmental stage, highlighting the complex ramifications of losing all the protein isoforms in individuals with Fragile X Syndrome. It should also be noted that, of the eight most prominent FMRP isoforms (1–3, 6–9 and 12) in mouse, only two have the major site of phosphorylation at Ser-499, which is thought to be involved in some of the regulatory interactions of this protein.
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Affiliation(s)
- David M. Brackett
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Feng Qing
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Paul S. Amieux
- Department of Pharmacology; University of Washington, Seattle, Washington, United States of America
| | - Drew L. Sellers
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States of America
| | - Philip J. Horner
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States of America
| | - David R. Morris
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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15
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Evans TL, Blice-Baum AC, Mihailescu MR. Analysis of the Fragile X mental retardation protein isoforms 1, 2 and 3 interactions with the G-quadruplex forming semaphorin 3F mRNA. ACTA ACUST UNITED AC 2012; 8:642-9. [DOI: 10.1039/c1mb05322a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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Molecular and Cellular Aspects of Mental Retardation in the Fragile X Syndrome: From Gene Mutation/s to Spine Dysmorphogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 970:517-51. [DOI: 10.1007/978-3-7091-0932-8_23] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Blackwell E, Ceman S. A new regulatory function of the region proximal to the RGG box in the fragile X mental retardation protein. J Cell Sci 2011; 124:3060-5. [PMID: 21868366 DOI: 10.1242/jcs.086751] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is required for normal cognition. FMRP has two autosomal paralogs, which although similar to FMRP, cannot compensate for the loss of FMRP expression in brain. The arginine- and glycine-rich region of FMRP (the RGG box) is unique; it is the high-affinity RNA-binding motif in FMRP and is encoded by exon 15. Alternative splicing occurs in the 5' end of exon 15, which is predicted to affect the structure of the distally encoded RGG box. Here, we provide evidence that isoform 3, which removes 25 amino acids from the 5' end of exon 15, has an altered conformation that reduces binding of a specific antibody and renders the RGG box unable to efficiently associate with polyribosomes. Isoform 3 is also compromised in its ability to form granules and to associate with a key messenger ribonucleoprotein Yb1 (also known as p50, NSEP1 and YBX1). Significantly, these functions are similarly compromised when the RGG box is absent from FMRP, suggesting an important regulatory role of the N-terminal region encoded by exon 15.
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Affiliation(s)
- Ernest Blackwell
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
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18
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Yan X, Denman RB. Conformational-dependent and independent RNA binding to the fragile x mental retardation protein. J Nucleic Acids 2011; 2011:246127. [PMID: 21772992 PMCID: PMC3136132 DOI: 10.4061/2011/246127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 03/16/2011] [Indexed: 01/13/2023] Open
Abstract
The interaction between the fragile X mental retardation protein (FMRP) and BC1 RNA has been the subject of controversy. We probed the parameters of RNA binding to FMRP in several ways. Nondenaturing agarose gel analysis showed that BC1 RNA transcripts produced by in vitro transcription contain a population of conformers, which can be modulated by preannealing. Accordingly, FMRP differentially binds to the annealed and unannealed conformer populations. Using partial RNase digestion, we demonstrate that annealed BC1 RNA contains a unique conformer that FMRP likely binds. We further demonstrate that this interaction is 100-fold weaker than that the binding of eEF-1A mRNA and FMRP, and that preannealing is not a general requirement for FMRP's interaction with RNA. In addition, binding does not require the N-terminal 204 amino acids of FMRP, methylated arginine residues and can be recapitulated by both fragile X paralogs. Altogether, our data continue to support a model in which BC1 RNA functions independently of FMRP.
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Affiliation(s)
- Xin Yan
- CSI/IBR Center for Developmental Neuroscience, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | - Robert B. Denman
- Biochemical Molecular Neurobiology Laboratory, Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
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19
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Tassone F, De Rubeis S, Carosi C, La Fata G, Serpa G, Raske C, Willemsen R, Hagerman PJ, Bagni C. Differential usage of transcriptional start sites and polyadenylation sites in FMR1 premutation alleles. Nucleic Acids Res 2011; 39:6172-85. [PMID: 21478165 PMCID: PMC3152321 DOI: 10.1093/nar/gkr100] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
5′- and 3′-untranslated regions (UTRs) are important regulators of gene expression and play key roles in disease progression and susceptibility. The 5′-UTR of the fragile X mental retardation 1 (FMR1) gene contains a CGG repeat element that is expanded (>200 CGG repeats; full mutation) and methylated in fragile X syndrome (FXS), the most common form of inherited intellectual disability (ID) and known cause of autism. Significant phenotypic involvement has also emerged in some individuals with the premutation (55–200 CGG repeats), including fragile X-associated premature ovarian insufficiency (FXPOI) in females, and the neurodegenerative disorder, fragile X-associated tremor/ataxia syndrome (FXTAS), in older adult carriers. Here, we show that FMR1 mRNA in human and mouse brain is expressed as a combination of multiple isoforms that use alternative transcriptional start sites and different polyadenylation sites. Furthermore, we have identified a novel human transcription start site used in brain but not in lymphoblastoid cells, and have detected FMR1 isoforms generated through the use of both canonical and non-canonical polyadenylation signals. Importantly, in both human and mouse, a specific regulation of the UTRs is observed in brain of FMR1 premutation alleles, suggesting that the transcript variants may play a role in premutation-related pathologies.
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Affiliation(s)
- Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
- *To whom correspondence should be addressed. Tel: +39 06 72596063/+32 16330944; Fax: +39 06 72596058/+39 16330939; ;
| | - Silvia De Rubeis
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Chiara Carosi
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Giorgio La Fata
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Gisele Serpa
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Christopher Raske
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Rob Willemsen
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Paul J. Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
| | - Claudia Bagni
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Davis, CA, USA M.I.N.D. Institute, University of California, Davis Medical Center, Sacramento, CA, USA, Center for Human Genetics, Katholieke Universiteit Leuven, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium, Fondazione Santa Lucia, IRCCS, Rome, Italy, Genomic Engineering Group, Chemical and Food Engineering Department, Federal University of Santa Catarina, Florianópolis, Brazil, CBG-Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands and Department of Experimental Medicine and Biochemical Sciences, University of Rome “Tor Vergata”, Rome, Italy
- *To whom correspondence should be addressed. Tel: +39 06 72596063/+32 16330944; Fax: +39 06 72596058/+39 16330939; ;
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20
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Beerman RW, Jongens TA. A non-canonical start codon in the Drosophila fragile X gene yields two functional isoforms. Neuroscience 2011; 181:48-66. [PMID: 21333716 DOI: 10.1016/j.neuroscience.2011.02.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 02/10/2011] [Accepted: 02/12/2011] [Indexed: 02/07/2023]
Abstract
Fragile X syndrome is caused by the loss of expression of the fragile X mental retardation protein (FMRP). As a RNA binding protein, FMRP functions in translational regulation, localization, and stability of its neuronal target transcripts. The Drosophila homologue, dFMR1, is well conserved in sequence and function with respect to human FMRP. Although dFMR1 is known to express two main isoforms, the mechanism behind production of the second, more slowly migrating isoform has remained elusive. Furthermore, it remains unknown whether the two isoforms may also contribute differentially to dFMR1 function. We have found that this second dFMR1 isoform is generated through an alternative translational start site in the dfmr1 5'UTR. This 5'UTR coding sequence is well conserved in the melanogaster group. Translation of the predominant, smaller form of dFMR1 (dFMR1-S(N)) begins at a canonical start codon (ATG), whereas translation of the minor, larger form (dFMR1-L(N)) begins upstream at a non-canonical start codon (CTG). To assess the contribution of the N-terminal extension toward dFMR1 activity, we generated transgenic flies that exclusively express either dFMR1-S(N) or dFMR1-L(N). Expression analyses throughout development revealed that dFMR1-S(N) is required for normal dFMR1-L(N) expression levels in adult brains. In situ expression analyses showed that either dFMR1-S(N) or dFMR1-L(N) is individually sufficient for proper dFMR1 localization in the nervous system. Functional studies demonstrated that both dFMR1-S(N) and dFMR1-L(N) can function independently to rescue dfmr1 null defects in synaptogenesis and axon guidance. Thus, dfmr1 encodes two functional isoforms with respect to expression and activity throughout neuronal development.
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Affiliation(s)
- R W Beerman
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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21
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Till SM, Li HL, Miniaci MC, Kandel ER, Choi YB. A presynaptic role for FMRP during protein synthesis-dependent long-term plasticity in Aplysia. Learn Mem 2010; 18:39-48. [PMID: 21177378 DOI: 10.1101/lm.1958811] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Loss of the Fragile X mental retardation protein (FMRP) is associated with presumed postsynaptic deficits in mouse models of Fragile X syndrome. However, the possible presynaptic roles of FMRP in learning-related plasticity have received little attention. As a result, the mechanisms whereby FMRP influences synaptic function remain poorly understood. To investigate the cellular locus of the effects of FMRP on synaptic plasticity, we cloned the Aplysia homolog of FMRP and find it to be highly expressed in neurons. By selectively down-regulating FMRP in individual Aplysia neurons at the sensory-to-motor neuron synapse reconstituted in co-cultures, we demonstrate that FMRP functions both pre- and postsynaptically to constrain the expression of long-term synaptic depression induced by repeated pulses of FMRF-amide. In contrast, FMRP has little to no effect on long-term synaptic facilitation induced by repeated pulses of serotonin. Since other components of signaling pathways involved in plasticity appear to be conserved between Aplysia and mammalian neurons, our findings suggest that FMRP can participate in both pre- and postsynaptic regulation of enduring synaptic plasticity that underlies the storage of certain types of long-term memory.
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Affiliation(s)
- Sally M Till
- Department of Neuroscience, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA
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22
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Short- and long-term memory are modulated by multiple isoforms of the fragile X mental retardation protein. J Neurosci 2010; 30:6782-92. [PMID: 20463240 DOI: 10.1523/jneurosci.6369-09.2010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The diversity of protein isoforms arising from alternative splicing is thought to modulate fine-tuning of synaptic plasticity. Fragile X mental retardation protein (FMRP), a neuronal RNA binding protein, exists in isoforms as a result of alternative splicing, but the contribution of these isoforms to neural plasticity are not well understood. We show that two isoforms of Drosophila melanogaster FMRP (dFMR1) have differential roles in mediating neural development and behavior functions conferred by the dfmr1 gene. These isoforms differ in the presence of a protein interaction module that is related to prion domains and is functionally conserved between FMRPs. Expression of both isoforms is necessary for optimal performance in tests of short- and long-term memory of courtship training. The presence or absence of the protein interaction domain may govern the types of ribonucleoprotein (RNP) complexes dFMR1 assembles into, with different RNPs regulating gene expression in a manner necessary for establishing distinct phases of memory formation.
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