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Skene NG, Bryois J, Bakken TE, Breen G, Crowley JJ, Gaspar HA, Giusti-Rodriguez P, Hodge RD, Miller JA, Muñoz-Manchado AB, O'Donovan MC, Owen MJ, Pardiñas AF, Ryge J, Walters JTR, Linnarsson S, Lein ES, Sullivan PF, Hjerling-Leffler J. Genetic identification of brain cell types underlying schizophrenia. Nat Genet 2018; 50:825-833. [PMID: 29785013 PMCID: PMC6477180 DOI: 10.1038/s41588-018-0129-5] [Citation(s) in RCA: 344] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 04/03/2018] [Indexed: 12/17/2022]
Abstract
With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying knowledge of the cellular taxonomy of the brain from single-cell RNA sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. We found that the common-variant genomic results consistently mapped to pyramidal cells, medium spiny neurons (MSNs) and certain interneurons, but far less consistently to embryonic, progenitor or glial cells. These enrichments were due to sets of genes that were specifically expressed in each of these cell types. We also found that many of the diverse gene sets previously associated with schizophrenia (genes involved in synaptic function, those encoding mRNAs that interact with FMRP, antipsychotic targets, etc.) generally implicated the same brain cell types. Our results suggest a parsimonious explanation: the common-variant genetic results for schizophrenia point at a limited set of neurons, and the gene sets point to the same cells. The genetic risk associated with MSNs did not overlap with that of glutamatergic pyramidal cells and interneurons, suggesting that different cell types have biologically distinct roles in schizophrenia.
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Affiliation(s)
- Nathan G Skene
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- UCL Institute of Neurology, Queen Square, London, UK
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Gerome Breen
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
- National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Héléna A Gaspar
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
- National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK
| | | | | | | | - Ana B Muñoz-Manchado
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jesper Ryge
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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Zhou Y, Dong F, Mao Y. Control of CNS functions by RNA-binding proteins in neurological diseases. ACTA ACUST UNITED AC 2018; 4:301-313. [PMID: 30410853 DOI: 10.1007/s40495-018-0140-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarizes recent studies on the molecular mechanisms of RNA binding proteins (RBPs) that control neurological functions and pathogenesis in various neurodevelopmental and neurodegenerative diseases, including autism spectrum disorders, schizophrenia, Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and spinocerebellar ataxia. Recent Findings RBPs are critical players in gene expression that regulate every step of posttranscriptional modifications. Recent genome-wide approaches revealed that many proteins associate with RNA, but do not contain any known RNA binding motifs. Additionally, many causal and risk genes of neurodevelopmental and neurodegenerative diseases are RBPs. Development of high-throughput sequencing methods has mapped out the fingerprints of RBPs on transcripts and provides unprecedented potential to discover new mechanisms of neurological diseases. Insights into how RBPs modulate neural development are important for designing effective therapies for numerous neurodevelopmental and neurodegenerative diseases. Summary RBPs have diverse mechanisms for modulating RNA processing and, thereby, controlling neurogenesis. Understanding the role of disease-associated RBPs in neurogenesis is vital for developing novel treatments for neurological diseases.
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Affiliation(s)
- Yijing Zhou
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Fengping Dong
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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53
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Weighted Burden Analysis of Exome-Sequenced Case-Control Sample Implicates Synaptic Genes in Schizophrenia Aetiology. Behav Genet 2018; 48:198-208. [PMID: 29564678 PMCID: PMC5934462 DOI: 10.1007/s10519-018-9893-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/13/2018] [Indexed: 11/04/2022]
Abstract
A previous study of exome-sequenced schizophrenia cases and controls reported an excess of singleton, gene-disruptive variants among cases, concentrated in particular gene sets. The dataset included a number of subjects with a substantial Finnish contribution to ancestry. We have reanalysed the same dataset after removal of these subjects and we have also included non-singleton variants of all types using a weighted burden test which assigns higher weights to variants predicted to have a greater effect on protein function. We investigated the same 31 gene sets as previously and also 1454 GO gene sets. The reduced dataset consisted of 4225 cases and 5834 controls. No individual variants or genes were significantly enriched in cases but 13 out of the 31 gene sets were significant after Bonferroni correction and the “FMRP targets” set produced a signed log p value (SLP) of 7.1. The gene within this set with the highest SLP, equal to 3.4, was FYN, which codes for a tyrosine kinase which phosphorylates glutamate metabotropic receptors and ionotropic NMDA receptors, thus modulating their trafficking, subcellular distribution and function. In the most recent GWAS of schizophrenia it was identified as a “prioritized candidate gene”. Two of the subunits of the NMDA receptor which are substrates of FYN are coded for by GRIN1 (SLP = 1.7) and GRIN2B (SLP = 2.1). Of note, for some sets there was a substantial enrichment of non-singleton variants. Of 1454 GO gene sets, three were significant after Bonferroni correction. Identifying specific genes and variants will depend on genotyping them in larger samples and/or demonstrating that they cosegregate with illness within pedigrees.
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54
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hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons. Proc Natl Acad Sci U S A 2018; 115:E2859-E2868. [PMID: 29507242 PMCID: PMC5866599 DOI: 10.1073/pnas.1721670115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Neurons are highly polarized cells. RNA-binding proteins contribute to this polarization by generating diverse subcellular transcriptomes. The RNA-binding protein hnRNP R is essential for axon growth in motoneurons. This study reports the RNA interactome for hnRNP R. The main interacting RNA of hnRNP R was the noncoding RNA 7SK. Depletion of 7SK from primary motoneurons disturbed axon growth. This effect was dependent on the interaction of 7SK with hnRNP R. Both hnRNP R and 7SK localize to axons. Loss of 7SK led to a similar depletion of axonal transcripts as loss of hnRNP R. Our data suggest that 7SK, in addition to its role in transcriptional regulation, acts in concert with hnRNP R to sort specific transcripts into axons. Disturbed RNA processing and subcellular transport contribute to the pathomechanisms of motoneuron diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. RNA-binding proteins are involved in these processes, but the mechanisms by which they regulate the subcellular diversity of transcriptomes, particularly in axons, are not understood. Heterogeneous nuclear ribonucleoprotein R (hnRNP R) interacts with several proteins involved in motoneuron diseases. It is located in axons of developing motoneurons, and its depletion causes defects in axon growth. Here, we used individual nucleotide-resolution cross-linking and immunoprecipitation (iCLIP) to determine the RNA interactome of hnRNP R in motoneurons. We identified ∼3,500 RNA targets, predominantly with functions in synaptic transmission and axon guidance. Among the RNA targets identified by iCLIP, the noncoding RNA 7SK was the top interactor of hnRNP R. We detected 7SK in the nucleus and also in the cytosol of motoneurons. In axons, 7SK localized in close proximity to hnRNP R, and depletion of hnRNP R reduced axonal 7SK. Furthermore, suppression of 7SK led to defective axon growth that was accompanied by axonal transcriptome alterations similar to those caused by hnRNP R depletion. Using a series of 7SK-deletion mutants, we show that the function of 7SK in axon elongation depends on its interaction with hnRNP R but not with the PTEF-B complex involved in transcriptional regulation. These results propose a role for 7SK as an essential interactor of hnRNP R to regulate its function in axon maintenance.
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55
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Nguyen HT, Bryois J, Kim A, Dobbyn A, Huckins LM, Munoz-Manchado AB, Ruderfer DM, Genovese G, Fromer M, Xu X, Pinto D, Linnarsson S, Verhage M, Smit AB, Hjerling-Leffler J, Buxbaum JD, Hultman C, Sklar P, Purcell SM, Lage K, He X, Sullivan PF, Stahl EA. Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. Genome Med 2017; 9:114. [PMID: 29262854 PMCID: PMC5738153 DOI: 10.1186/s13073-017-0497-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Integrating rare variation from trio family and case-control studies has successfully implicated specific genes contributing to risk of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), intellectual disability (ID), developmental disorders (DDs), and epilepsy (EPI). For schizophrenia (SCZ), however, while sets of genes have been implicated through the study of rare variation, only two risk genes have been identified. METHODS We used hierarchical Bayesian modeling of rare-variant genetic architecture to estimate mean effect sizes and risk-gene proportions, analyzing the largest available collection of whole exome sequence data for SCZ (1,077 trios, 6,699 cases, and 13,028 controls), and data for four NDDs (ASD, ID, DD, and EPI; total 10,792 trios, and 4,058 cases and controls). RESULTS For SCZ, we estimate there are 1,551 risk genes. There are more risk genes and they have weaker effects than for NDDs. We provide power analyses to predict the number of risk-gene discoveries as more data become available. We confirm and augment prior risk gene and gene set enrichment results for SCZ and NDDs. In particular, we detected 98 new DD risk genes at FDR < 0.05. Correlations of risk-gene posterior probabilities are high across four NDDs (ρ>0.55), but low between SCZ and the NDDs (ρ<0.3). An in-depth analysis of 288 NDD genes shows there is highly significant protein-protein interaction (PPI) network connectivity, and functionally distinct PPI subnetworks based on pathway enrichment, single-cell RNA-seq cell types, and multi-region developmental brain RNA-seq. CONCLUSIONS We have extended a pipeline used in ASD studies and applied it to infer rare genetic parameters for SCZ and four NDDs ( https://github.com/hoangtn/extTADA ). We find many new DD risk genes, supported by gene set enrichment and PPI network connectivity analyses. We find greater similarity among NDDs than between NDDs and SCZ. NDD gene subnetworks are implicated in postnatally expressed presynaptic and postsynaptic genes, and for transcriptional and post-transcriptional gene regulation in prenatal neural progenitor and stem cells.
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Affiliation(s)
- Hoang T. Nguyen
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Surgery, Massachusetts General Hospital, Boston, 02114 MA USA
| | - Amanda Dobbyn
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Laura M. Huckins
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Ana B. Munoz-Manchado
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Douglas M. Ruderfer
- Division of Genetic Medicine, Departments of Medicine, Psychiatry and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, 37235 TN USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Genetics, Harvard Medical School, Cambridge, Massachusetts USA
| | - Menachem Fromer
- Verily Life Sciences, 269 E Grand Ave, South San Francisco, 94080 CA USA
| | - Xinyi Xu
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Dalila Pinto
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Matthijs Verhage
- Department of Functional Genomics, The Center for Neurogenomics and Cognitive Research, VU University and VU Medical Center, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, The Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Joseph D. Buxbaum
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Shaun M. Purcell
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Sleep Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Surgery, Massachusetts General Hospital, Boston, 02114 MA USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, 60637 IL USA
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, 27599-7264 North Carolina USA
| | - Eli A. Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
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56
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Smidak R, Sialana FJ, Kristofova M, Stojanovic T, Rajcic D, Malikovic J, Feyissa DD, Korz V, Hoeger H, Wackerlig J, Mechtcheriakova D, Lubec G. Reduced Levels of the Synaptic Functional Regulator FMRP in Dentate Gyrus of the Aging Sprague-Dawley Rat. Front Aging Neurosci 2017; 9:384. [PMID: 29218006 PMCID: PMC5703695 DOI: 10.3389/fnagi.2017.00384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/09/2017] [Indexed: 11/15/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) encoded by Fragile X mental retardation 1 (FMR1) gene is a RNA-binding regulator of mRNA translation, transport and stability with multiple targets responsible for proper synaptic function. Epigenetic silencing of FMR1 gene expression leads to the development of Fragile X syndrome (FXS) that is characterized by intellectual disability and other behavioral problems including autism. In the rat FXS model, the lack of FMRP caused a deficit in hippocampal-dependent memory. However, the hippocampal changes of FMRP in aging rats are not fully elucidated. The current study addresses the changes in FMRP levels in dentate gyrus (DG) from young (17 weeks) and aging (22 months) Sprague – Dawley rats. The aging animal group showed significant decline in spatial reference memory. Protein samples from five rats per each group were analyzed by quantitative proteomic analysis resulting in 153 significantly changed proteins. FMRP showed significant reduction in aging animals which was confirmed by immunoblotting and immunofluorescence microscopy. Furthermore, bioinformatic analysis of the differential protein dataset revealed several functionally related protein groups with individual interactions with FMRP. These include high representation of the RNA translation and processing machinery connected to FMRP and other RNA-binding regulators including CAPRIN1, the members of Pumilio (PUM) and CUG-BP, Elav-like (CELF) family, and YTH N(6)-methyladenosine RNA-binding proteins (YTHDF). The results of the current study point to the important role of FMRP and regulation of RNA processing in the rat DG and memory decline during the aging process.
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Affiliation(s)
- Roman Smidak
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Fernando J Sialana
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Martina Kristofova
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Tamara Stojanovic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Dragana Rajcic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Jovana Malikovic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Daniel D Feyissa
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Volker Korz
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Harald Hoeger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Judit Wackerlig
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
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Sun Q, Xie N, Tang B, Li R, Shen Y. Alzheimer's Disease: From Genetic Variants to the Distinct Pathological Mechanisms. Front Mol Neurosci 2017; 10:319. [PMID: 29056900 PMCID: PMC5635057 DOI: 10.3389/fnmol.2017.00319] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Being the most common cause of dementia, AD is a polygenic and neurodegenerative disease. Complex and multiple factors have been shown to be involved in its pathogenesis, of which the genetics play an indispensable role. It is widely accepted that discovery of potential genes related to the pathogenesis of AD would be of great help for the understanding of neurodegeneration and thus further promote molecular diagnosis in clinic settings. Generally, AD could be clarified into two types according to the onset age, the early-onset AD (EOAD) and the late-onset AD (LOAD). Progresses made by genetic studies on both EOAD and LOAD are believed to be essential not only for the revolution of conventional ideas but also for the revelation of new pathological mechanisms underlying AD pathogenesis. Currently, albeit the genetics of LOAD is much less well-understood compared to EOAD due to its complicated and multifactorial essence, Genome-wide association studies (GWASs) and next generation sequencing (NGS) approaches have identified dozens of novel genes that may provide insight mechanism of LOAD. In this review, we analyze functions of the genes and summarize the distinct pathological mechanisms of how these genes would be involved in the pathogenesis of AD.
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Affiliation(s)
- Qiying Sun
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Advanced Therapeutic Strategies for Brain Disorders and Center for Hormone Advanced Science and Education, Roskamp Institute, Sarasota, FL, United States
| | - Nina Xie
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Rena Li
- Center for Advanced Therapeutic Strategies for Brain Disorders and Center for Hormone Advanced Science and Education, Roskamp Institute, Sarasota, FL, United States.,National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.,Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| | - Yong Shen
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Advanced Therapeutic Strategies for Brain Disorders and Center for Hormone Advanced Science and Education, Roskamp Institute, Sarasota, FL, United States.,Neurodegenerative Disorder Research Center, University of Science and Technology of China School of Life Sciences, Hefei, China.,Hefei Material Science at Microscale National Laboratory, Hefei, China
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58
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Curtis D. Construction of an Exome-Wide Risk Score for Schizophrenia Based on a Weighted Burden Test. Ann Hum Genet 2017; 82:11-22. [PMID: 28895126 DOI: 10.1111/ahg.12212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/06/2017] [Accepted: 08/01/2017] [Indexed: 02/05/2023]
Abstract
Polygenic risk scores obtained as a weighted sum of associated variants can be used to explore association in additional data sets and to assign risk scores to individuals. The methods used to derive polygenic risk scores from common SNPs are not suitable for variants detected in whole exome sequencing studies. Rare variants, which may have major effects, are seen too infrequently to judge whether they are associated and may not be shared between training and test subjects. A method is proposed whereby variants are weighted according to their frequency, their annotations and the genes they affect. A weighted sum across all variants provides an individual risk score. Scores constructed in this way are used in a weighted burden test and are shown to be significantly different between schizophrenia cases and controls using a five-way cross-validation procedure. This approach represents a first attempt to summarise exome sequence variation into a summary risk score, which could be combined with risk scores from common variants and from environmental factors. It is hoped that the method could be developed further.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, UCL, Darwin Building, Gower Street, London, WC1E 6BT.,Centre for Psychiatry, Barts and the London School of Medicine and Dentistry
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59
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Cholinergic Regulation of hnRNPA2/B1 Translation by M1 Muscarinic Receptors. J Neurosci 2017; 36:6287-96. [PMID: 27277805 DOI: 10.1523/jneurosci.4614-15.2016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 05/02/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Cholinergic vulnerability, characterized by loss of acetylcholine (ACh), is one of the hallmarks of Alzheimer's disease (AD). Previous work has suggested that decreased ACh activity in AD may contribute to pathological changes through global alterations in alternative splicing. This occurs, at least partially, via the regulation of the expression of a critical protein family in RNA processing, heterogeneous nuclear ribonucleoprotein (hnRNP) A/B proteins. These proteins regulate several steps of RNA metabolism, including alternative splicing, RNA trafficking, miRNA export, and gene expression, providing multilevel surveillance in RNA functions. To investigate the mechanism by which cholinergic tone regulates hnRNPA2/B1 expression, we used a combination of genetic mouse models and in vivo and in vitro techniques. Decreasing cholinergic tone reduced levels of hnRNPA2/B1, whereas increasing cholinergic signaling in vivo increased expression of hnRNPA2/B1. This effect was not due to decreased hnRNPA2/B1 mRNA expression, increased aggregation, or degradation of the protein, but rather to decreased mRNA translation by nonsense-mediated decay regulation of translation. Cell culture and knock-out mice experiments demonstrated that M1 muscarinic signaling is critical for cholinergic control of hnRNPA2/B1 protein levels. Our experiments suggest an intricate regulation of hnRNPA2/B1 levels by cholinergic activity that interferes with alternative splicing in targeted neurons mimicking deficits found in AD. SIGNIFICANCE STATEMENT In Alzheimer's disease, degeneration of basal forebrain cholinergic neurons is an early event. These neurons communicate with target cells and regulate their long-term activity by poorly understood mechanisms. Recently, the splicing factor hnRNPA2/B, which is decreased in Alzheimer's disease, was implicated as a potential mediator of long-term cholinergic regulation. Here, we demonstrate a mechanism by which cholinergic signaling controls the translation of hnRNPA2/B1 mRNA by activation of M1 muscarinic type receptors. Loss of cholinergic activity can have profound effects in target cells by modulating hnRNPA2/B1 levels.
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60
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Ohi K, Shimada T, Yasuyama T, Kimura K, Uehara T, Kawasaki Y. Spatial and temporal expression patterns of genes around nine neuroticism-associated loci. Prog Neuropsychopharmacol Biol Psychiatry 2017; 77:164-171. [PMID: 28433457 DOI: 10.1016/j.pnpbp.2017.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Abstract
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci. Functional gene-network analysis for neuroticism-associated genes was performed. The spatial expression analysis revealed that the nearest genes (GRIK3, SRP9, KLHL2, PTPRD, ELAVL2, CRHR1 and CELF4) from index single-nucleotide polymorphisms (SNPs) at the nine loci were intensively enriched in the brain compared with their representation in non-brain tissues (p<1.56×10-3). The nearest genes associated with the glutamate receptor activity network consisted mainly of GRIK3 (FDR q=4.25×10-2). The temporal expression analysis revealed that the neuroticism-associated genes were divided into three expression patterns: KLHL2, CELF4 and CRHR1 were preferentially expressed during postnatal stages; PTPRD, ELAVL2 and MFHAS1 were expressed during prenatal stages; and the other three genes were not expressed during specific life stages. These findings suggest that the glutamate network might be a target for investigating the neurobiological mechanisms underlying susceptibilities to higher neuroticism and several psychiatric disorders and that neuroticism is mediated by genes specifically expressed in the brain during several developmental stages.
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Affiliation(s)
- Kazutaka Ohi
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan.
| | - Takamitsu Shimada
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Toshiki Yasuyama
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Kohei Kimura
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Takashi Uehara
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Yasuhiro Kawasaki
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
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61
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Gazzara MR, Mallory MJ, Roytenberg R, Lindberg JP, Jha A, Lynch KW, Barash Y. Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes. Genome Res 2017; 27:1360-1370. [PMID: 28512194 PMCID: PMC5538552 DOI: 10.1101/gr.220517.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/08/2017] [Indexed: 12/11/2022]
Abstract
Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic splicing code models, we find evidence of splicing antagonism between CELF2 and the RBFOX family of splicing factors. We validate this functional antagonism through knockdown and overexpression experiments in human cells and find CELF2 represses RBFOX2 mRNA and protein levels. Because both families of proteins have been implicated in the development and maintenance of neuronal, muscle, and heart tissues, we analyzed publicly available data in these systems. Our analysis suggests global, antagonistic coregulation of splicing by the CELF and RBFOX proteins in mouse muscle and heart in several physiologically relevant targets, including proteins involved in calcium signaling and members of the MEF2 family of transcription factors. Importantly, a number of these coregulated events are aberrantly spliced in mouse models and human patients with diseases that affect these tissues, including heart failure, diabetes, or myotonic dystrophy. Finally, analysis of exons regulated by ancient CELF family homologs in chicken, Drosophila, and Caenorhabditis elegans suggests this antagonism is conserved throughout evolution.
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Affiliation(s)
- Matthew R Gazzara
- Department of Genetics.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael J Mallory
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Renat Roytenberg
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John P Lindberg
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Anupama Jha
- Department of Computer and Information Science, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Department of Genetics.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yoseph Barash
- Department of Genetics.,Department of Computer and Information Science, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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62
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Barone R, Fichera M, De Grandi M, Battaglia M, Lo Faro V, Mattina T, Rizzo R. Familial 18q12.2 deletion supports the role of RNA-binding protein CELF4 in autism spectrum disorders. Am J Med Genet A 2017; 173:1649-1655. [DOI: 10.1002/ajmg.a.38205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 12/15/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Rita Barone
- Department of Clinical and Experimental Medicine, Child Neurology and Psychiatry; University of Catania; Catania Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics; University of Catania; Catania Italy
- Laboratory of Medical Genetics; I.R.C.C.S. Associazione Oasi Maria Santissima; Troina Italy
| | - Mariaclara De Grandi
- Department of Clinical and Experimental Medicine, Child Neurology and Psychiatry; University of Catania; Catania Italy
| | - Marta Battaglia
- Department of Clinical and Experimental Medicine, Child Neurology and Psychiatry; University of Catania; Catania Italy
| | - Valeria Lo Faro
- Department of Biomedical and Biotechnological Sciences, Medical Genetics; University of Catania; Catania Italy
| | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences, Medical Genetics; University of Catania; Catania Italy
| | - Renata Rizzo
- Department of Clinical and Experimental Medicine, Child Neurology and Psychiatry; University of Catania; Catania Italy
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63
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Namjoshi SV, Raab-Graham KF. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci 2017; 10:45. [PMID: 28286470 PMCID: PMC5323403 DOI: 10.3389/fnmol.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.
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Affiliation(s)
- Sanjeev V Namjoshi
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA
| | - Kimberly F Raab-Graham
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA; Department of Physiology and Pharmacology, Wake Forest Health Sciences, Medical Center Boulevard, Winston-SalemNC, USA
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64
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Makinson CD, Tanaka BS, Sorokin JM, Wong JC, Christian CA, Goldin AL, Escayg A, Huguenard JR. Regulation of Thalamic and Cortical Network Synchrony by Scn8a. Neuron 2017; 93:1165-1179.e6. [PMID: 28238546 DOI: 10.1016/j.neuron.2017.01.031] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/30/2016] [Accepted: 01/30/2017] [Indexed: 12/22/2022]
Abstract
Voltage-gated sodium channel (VGSC) mutations cause severe epilepsies marked by intermittent, pathological hypersynchronous brain states. Here we present two mechanisms that help to explain how mutations in one VGSC gene, Scn8a, contribute to two distinct seizure phenotypes: (1) hypoexcitation of cortical circuits leading to convulsive seizure resistance, and (2) hyperexcitation of thalamocortical circuits leading to non-convulsive absence epilepsy. We found that loss of Scn8a leads to altered RT cell intrinsic excitability and a failure in recurrent RT synaptic inhibition. We propose that these deficits cooperate to enhance thalamocortical network synchrony and generate pathological oscillations. To our knowledge, this finding is the first clear demonstration of a pathological state tied to disruption of the RT-RT synapse. Our observation that loss of a single gene in the thalamus of an adult wild-type animal is sufficient to cause spike-wave discharges is striking and represents an example of absence epilepsy of thalamic origin.
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Affiliation(s)
- Christopher D Makinson
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| | - Brian S Tanaka
- Departments of Microbiology and Molecular Genetics and Anatomy and Neurobiology, University of California, Irvine, CA 92697, USA
| | - Jordan M Sorokin
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| | - Jennifer C Wong
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Catherine A Christian
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| | - Alan L Goldin
- Departments of Microbiology and Molecular Genetics and Anatomy and Neurobiology, University of California, Irvine, CA 92697, USA
| | - Andrew Escayg
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA.
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA.
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65
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Dalal JS, Yang C, Sapkota D, Lake AM, O'Brien DR, Dougherty JD. Quantitative Nucleotide Level Analysis of Regulation of Translation in Response to Depolarization of Cultured Neural Cells. Front Mol Neurosci 2017; 10:9. [PMID: 28190998 PMCID: PMC5269599 DOI: 10.3389/fnmol.2017.00009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/06/2017] [Indexed: 01/12/2023] Open
Abstract
Studies on regulation of gene expression have contributed substantially to understanding mechanisms for the long-term activity-dependent alterations in neural connectivity that are thought to mediate learning and memory. Most of these studies, however, have focused on the regulation of mRNA transcription. Here, we utilized high-throughput sequencing coupled with ribosome footprinting to globally characterize the regulation of translation in primary mixed neuronal-glial cultures in response to sustained depolarization. We identified substantial and complex regulation of translation, with many transcripts demonstrating changes in ribosomal occupancy independent of transcriptional changes. We also examined sequence-based mechanisms that might regulate changes in translation in response to depolarization. We found that these are partially mediated by features in the mRNA sequence—notably upstream open reading frames and secondary structure in the 5′ untranslated region—both of which predict downregulation in response to depolarization. Translationally regulated transcripts are also more likely to be targets of FMRP and include genes implicated in autism in humans. Our findings support the idea that control of mRNA translation plays an important role in response to neural activity across the genome.
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Affiliation(s)
- Jasbir S Dalal
- Department of Genetics, Washington University School of MedicineSt. Louis, MO, USA; Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - Chengran Yang
- Department of Genetics, Washington University School of MedicineSt. Louis, MO, USA; Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - Darshan Sapkota
- Department of Genetics, Washington University School of MedicineSt. Louis, MO, USA; Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - Allison M Lake
- Department of Genetics, Washington University School of MedicineSt. Louis, MO, USA; Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - David R O'Brien
- Department of Genetics, Washington University School of MedicineSt. Louis, MO, USA; Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of MedicineSt. Louis, MO, USA; Department of Psychiatry, Washington University School of MedicineSt. Louis, MO, USA
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66
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Culver BP, DeClercq J, Dolgalev I, Yu MS, Ma B, Heguy A, Tanese N. Huntington's Disease Protein Huntingtin Associates with its own mRNA. J Huntingtons Dis 2016; 5:39-51. [PMID: 26891106 PMCID: PMC4927879 DOI: 10.3233/jhd-150177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background: The Huntington’s disease (HD) protein huntingtin (Htt) plays a role in multiple cellular pathways. Deregulation of one or more of these pathways by the mutant Htt protein has been suggested to contribute to the disease pathogenesis. Our recent discovery-based proteomics studies have uncovered RNA binding proteins and translation factors associated with the endogenous Htt protein purified from mouse brains, suggesting a potential new role for Htt in RNA transport and translation. Objective: To investigate how Htt might affect RNA metabolism we set out to purify and analyze RNA associated with Htt. Methods: RNA was extracted from immunopurified Htt-containing protein complexes and analyzed by microarrays and RNA-Seq. Results: Surprisingly, the most enriched mRNA that co-purified with Htt was Htt mRNA itself. The association of Htt protein and Htt mRNA was detected independent of intact ribosomes suggesting that it is not an RNA undergoing translation. Furthermore, we identified the recently reported mis-spliced Htt mRNA encoding a truncated protein comprised of exon 1 and a portion of the downstream intron in the immunoprecipitates containing mutant Htt protein. We show that Htt protein co-localizes with Htt mRNA and that wild-type Htt reduces expression of a reporter construct harboring the Htt 3’ UTR. Conclusions: HD protein is found in a complex with its own mRNA and RNA binding proteins and translation factors. Htt may be involved in modulating its expression through post-transcriptional pathways. It is possible that Htt shares mechanistic properties similar to RNA binding proteins such as TDP-43 and FUS implicated in other neurodegenerative diseases.
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Affiliation(s)
- Brady P Culver
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Josh DeClercq
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Igor Dolgalev
- Genome Technology Center, New York University School of Medicine, New York, NY, USA
| | - Man Shan Yu
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Bin Ma
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Adriana Heguy
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Genome Technology Center, New York University School of Medicine, New York, NY, USA
| | - Naoko Tanese
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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67
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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68
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Genovese G, Fromer M, Stahl EA, Ruderfer DM, Chambert K, Landén M, Moran JL, Purcell SM, Sklar P, Sullivan PF, Hultman CM, McCarroll SA. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat Neurosci 2016; 19:1433-1441. [PMID: 27694994 PMCID: PMC5104192 DOI: 10.1038/nn.4402] [Citation(s) in RCA: 314] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Abstract
By analyzing the exomes of 12,332 unrelated Swedish individuals – including 4,877 affected with schizophrenia – in ways informed by exome sequences from 45,376 other individuals, we identified 244,246 coding-sequence and splice-site ultra-rare variants (URVs) that were unique to individual Swedes. We found that gene-disruptive and putatively protein-damaging URVs (but not synonymous URVs) were more abundant in schizophrenia cases than controls (P = 1.3 × 10−10). This elevation of protein-compromising URVs was several times larger than an analogously elevated rate for de novo mutations, suggesting that most rare-variant effects on schizophrenia risk are inherited. Among individuals with schizophrenia, the elevated frequency of protein-compromising URVs was concentrated in brain-expressed genes, particularly in neuronally expressed genes; most of this genetic signal arose from large sets of genes whose RNAs have been found to interact with synaptically localized proteins. Our results suggest that synaptic dysfunction may mediate a large fraction of strong, individually rare genetic influences on schizophrenia risk.
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Affiliation(s)
- Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Menachem Fromer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mikael Landén
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience a Physiology at Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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69
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Chen L, Liu Z, Zhou B, Wei C, Zhou Y, Rosenfeld MG, Fu XD, Chisholm AD, Jin Y. CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins. eLife 2016; 5. [PMID: 27253061 PMCID: PMC4946901 DOI: 10.7554/elife.16072] [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: 03/15/2016] [Accepted: 06/01/2016] [Indexed: 01/08/2023] Open
Abstract
Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. In particular, we show that UNC-75 regulates alternative splicing of two mRNA isoforms of the SNARE Syntaxin/unc-64. In C. elegans mutants lacking unc-75 or its targets, regenerating axons form growth cones, yet are deficient in extension. Extending these findings to mammalian axon regeneration, we show that mouse Celf2 expression is upregulated after peripheral nerve injury and that Celf2 mutant mice are defective in axon regeneration. Further, mRNAs for several Syntaxins show CELF2 dependent regulation. Our data delineate a post-transcriptional regulatory pathway with a conserved role in regenerative axon extension. DOI:http://dx.doi.org/10.7554/eLife.16072.001 Nerve cells or neurons carry information around the body along projections known as axons. An injury or trauma, such as a stroke, can damage the axons and lead to permanent disability because the damaged axons fail to regenerate over long distances. Axon damage triggers large changes in the activity of many genes that promote regeneration. When a gene is active, its DNA is copied to make molecules of messenger RNA (mRNA), which are then used as templates to make proteins. Many mRNAs undergo a process called alternative splicing, in which different combinations of mRNA sections may be removed from the final molecule. This enables a single gene to produce more than one type of protein. Recent studies point to an important role for so-called RNA binding proteins in regulating the alternative splicing process. An RNA binding protein called UNC-75 in a worm known as Caenorhabditis elegans has previously been shown to be involved in axon regeneration, but it was not clear how UNC-75 acts on neurons. Here, Chen et al. combined a technique called CLIP-seq (Cross-linking ImmunoPrecipitation-deep sequencing) with genetic testing to identify the mRNAs that UNC-75 regulates during axon regeneration. The experiments found a set of C. elegans genes required for information to pass between neurons whose mRNAs are also targeted by UNC-75. Many of these genes are also required for axon regeneration. Chen et al. studied one of the mRNA targets – which encodes a protein called syntaxin – in more detail and found that the syntaxin mRNA is required for regenerating axons over long distances. UNC-75 alternatively splices this mRNA to produce a particular form of syntaxin that is mainly found in neurons. Mutant worms that lack either UNC-75 or syntaxin are unable to properly regenerate axons over long distances. Further experiments show that a mouse protein known as CELF2 that is equivalent to worm UNC-75 plays a similar role in regenerating axons. Moreover, mouse CELF2 restores the ability of worm neurons that lack UNC-75 to regenerate. Like worm UNC-75, the mouse protein is also involved in alternative splicing of syntaxin. The next step is to examine the other mRNA targets of UNC-75 to find out what role they play in axon regeneration and other processes in neurons. DOI:http://dx.doi.org/10.7554/eLife.16072.002
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Affiliation(s)
- Lizhen Chen
- Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, United States
| | - Zhijie Liu
- Department of Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Chaoliang Wei
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, University of California, San Diego, United States.,Department of Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Andrew D Chisholm
- Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States
| | - Yishi Jin
- Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
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70
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Genome-wide analysis of over 106 000 individuals identifies 9 neuroticism-associated loci. Mol Psychiatry 2016; 21:749-57. [PMID: 27067015 PMCID: PMC4879189 DOI: 10.1038/mp.2016.49] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/19/2016] [Accepted: 03/02/2016] [Indexed: 02/07/2023]
Abstract
Neuroticism is a personality trait of fundamental importance for psychological well-being and public health. It is strongly associated with major depressive disorder (MDD) and several other psychiatric conditions. Although neuroticism is heritable, attempts to identify the alleles involved in previous studies have been limited by relatively small sample sizes. Here we report a combined meta-analysis of genome-wide association study (GWAS) of neuroticism that includes 91 370 participants from the UK Biobank cohort, 6659 participants from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and 8687 participants from a QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute (QIMR) cohort. All participants were assessed using the same neuroticism instrument, the Eysenck Personality Questionnaire-Revised (EPQ-R-S) Short Form's Neuroticism scale. We found a single-nucleotide polymorphism-based heritability estimate for neuroticism of ∼15% (s.e.=0.7%). Meta-analysis identified nine novel loci associated with neuroticism. The strongest evidence for association was at a locus on chromosome 8 (P=1.5 × 10(-15)) spanning 4 Mb and containing at least 36 genes. Other associated loci included interesting candidate genes on chromosome 1 (GRIK3 (glutamate receptor ionotropic kainate 3)), chromosome 4 (KLHL2 (Kelch-like protein 2)), chromosome 17 (CRHR1 (corticotropin-releasing hormone receptor 1) and MAPT (microtubule-associated protein Tau)) and on chromosome 18 (CELF4 (CUGBP elav-like family member 4)). We found no evidence for genetic differences in the common allelic architecture of neuroticism by sex. By comparing our findings with those of the Psychiatric Genetics Consortia, we identified a strong genetic correlation between neuroticism and MDD and a less strong but significant genetic correlation with schizophrenia, although not with bipolar disorder. Polygenic risk scores derived from the primary UK Biobank sample captured ∼1% of the variance in neuroticism in the GS:SFHS and QIMR samples, although most of the genome-wide significant alleles identified within a UK Biobank-only GWAS of neuroticism were not independently replicated within these cohorts. The identification of nine novel neuroticism-associated loci will drive forward future work on the neurobiology of neuroticism and related phenotypes.
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Bubier JA, Phillips CA, Langston MA, Baker EJ, Chesler EJ. GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. Mamm Genome 2015; 26:556-66. [PMID: 26092690 PMCID: PMC4602068 DOI: 10.1007/s00335-015-9575-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/03/2015] [Indexed: 01/20/2023]
Abstract
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity.
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Affiliation(s)
| | - Charles A Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Erich J Baker
- Computer Science Department, Baylor University, Waco, TX, 76798, USA
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Moreira-Filho CA, Bando SY, Bertonha FB, Iamashita P, Silva FN, Costa LDF, Silva AV, Castro LHM, Wen HT. Community structure analysis of transcriptional networks reveals distinct molecular pathways for early- and late-onset temporal lobe epilepsy with childhood febrile seizures. PLoS One 2015; 10:e0128174. [PMID: 26011637 PMCID: PMC4444281 DOI: 10.1371/journal.pone.0128174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/24/2015] [Indexed: 12/21/2022] Open
Abstract
Age at epilepsy onset has a broad impact on brain plasticity and epilepsy pathomechanisms. Prolonged febrile seizures in early childhood (FS) constitute an initial precipitating insult (IPI) commonly associated with mesial temporal lobe epilepsy (MTLE). FS-MTLE patients may have early disease onset, i.e. just after the IPI, in early childhood, or late-onset, ranging from mid-adolescence to early adult life. The mechanisms governing early (E) or late (L) disease onset are largely unknown. In order to unveil the molecular pathways underlying E and L subtypes of FS-MTLE we investigated global gene expression in hippocampal CA3 explants of FS-MTLE patients submitted to hippocampectomy. Gene coexpression networks (GCNs) were obtained for the E and L patient groups. A network-based approach for GCN analysis was employed allowing: i) the visualization and analysis of differentially expressed (DE) and complete (CO) - all valid GO annotated transcripts - GCNs for the E and L groups; ii) the study of interactions between all the system's constituents based on community detection and coarse-grained community structure methods. We found that the E-DE communities with strongest connection weights harbor highly connected genes mainly related to neural excitability and febrile seizures, whereas in L-DE communities these genes are not only involved in network excitability but also playing roles in other epilepsy-related processes. Inversely, in E-CO the strongly connected communities are related to compensatory pathways (seizure inhibition, neuronal survival and responses to stress conditions) while in L-CO these communities harbor several genes related to pro-epileptic effects, seizure-related mechanisms and vulnerability to epilepsy. These results fit the concept, based on fMRI and behavioral studies, that early onset epilepsies, although impacting more severely the hippocampus, are associated to compensatory mechanisms, while in late MTLE development the brain is less able to generate adaptive mechanisms, what has implications for epilepsy management and drug discovery.
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Affiliation(s)
| | - Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Fernanda Bernardi Bertonha
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | | | | | | | - Luiz Henrique Martins Castro
- Department of Neurology, FMUSP, São Paulo, SP, Brazil
- Clinical Neurology Division, Hospital das Clínicas, FMUSP, São Paulo, SP, Brazil
| | - Hung-Tzu Wen
- Epilepsy Surgery Group, Hospital das Clínicas, FMUSP, São Paulo, SP, Brazil
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73
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Cohen JE, Lee PR, Fields RD. Systematic identification of 3'-UTR regulatory elements in activity-dependent mRNA stability in hippocampal neurons. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0509. [PMID: 25135970 PMCID: PMC4142030 DOI: 10.1098/rstb.2013.0509] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Ongoing neuronal activity during development and plasticity acts to refine synaptic connections and contributes to the induction of plasticity and ultimately long-term memory storage. Activity-dependent, post-transcriptional control of mRNAs occurs through transport to axonal and dendritic compartments, local translation and mRNA stability. We have identified a mechanism that contributes to activity-dependent regulation of mRNA stability during synaptic plasticity in rat hippocampal neurons. In this study, we demonstrate rapid, post-transcriptional control over process-enriched mRNAs by neuronal activity. Systematic analysis of the 3'-UTRs of destabilized transcripts, identifies enrichment in sequence motifs corresponding to microRNA (miRNA)-binding sites. The miRNAs that were identified, miR-326-3p/miR-330-5p, miR-485-5p, miR-666-3p and miR-761 are predicted to regulate networks of genes important in plasticity and development. We find that these miRNAs are developmentally regulated in the hippocampus, many increasing by postnatal day 14. We further find that miR-485-5p controls NGF-induced neurite outgrowth in PC12 cells, tau expression and axonal development in hippocampal neurons. miRNAs can function at the synapse to rapidly control and affect short- and long-term changes at the synapse. These processes likely occur during refinement of synaptic connections and contribute to the induction of plasticity and learning and memory.
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Affiliation(s)
- Jonathan E Cohen
- Section on Nervous System Development and Plasticity, The Eunice Kennedy Shriver National Institute of Child and Human Development, National Institute of Health, Building 35, Room 2A211, Bethesda, MD 20892-3714, USA
| | - Philip R Lee
- Section on Nervous System Development and Plasticity, The Eunice Kennedy Shriver National Institute of Child and Human Development, National Institute of Health, Building 35, Room 2A211, Bethesda, MD 20892-3714, USA
| | - R Douglas Fields
- Section on Nervous System Development and Plasticity, The Eunice Kennedy Shriver National Institute of Child and Human Development, National Institute of Health, Building 35, Room 2A211, Bethesda, MD 20892-3714, USA
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74
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Nussbacher JK, Batra R, Lagier-Tourenne C, Yeo GW. RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci 2015; 38:226-36. [PMID: 25765321 PMCID: PMC4403644 DOI: 10.1016/j.tins.2015.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/02/2015] [Accepted: 02/09/2015] [Indexed: 12/13/2022]
Abstract
As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, genome-wide manner. Development of high-throughput sequencing (Seq) methodologies provides unparalleled potential to discover new mechanisms of disease-associated perturbations of RNA homeostasis. Complementary to candidate single-gene studies, these innovative technologies may elicit the discovery of unexpected mechanisms, and enable us to determine the widespread influence of the multifunctional RBPs on their targets. Given that the disruption of RNA processing is increasingly implicated in neurological diseases, these approaches will continue to provide insights into the roles of RBPs in disease pathogenesis.
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Affiliation(s)
- Julia K Nussbacher
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Ranjan Batra
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
| | - Gene W Yeo
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Department of Physiology, National University of Singapore, Singapore.
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75
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Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev 2015; 29:501-12. [PMID: 25737280 PMCID: PMC4358403 DOI: 10.1101/gad.258483.115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/06/2015] [Indexed: 12/14/2022]
Abstract
Cellular morphology is an essential determinant of cellular function in all kingdoms of life, yet little is known about how cell shape is controlled. Here we describe a molecular program that controls the early morphology of neurons through a metazoan-specific zinc finger protein, Unkempt. Depletion of Unkempt in mouse embryos disrupts the shape of migrating neurons, while ectopic expression confers neuronal-like morphology to cells of different nonneuronal lineages. We found that Unkempt is a sequence-specific RNA-binding protein and identified its precise binding sites within coding regions of mRNAs linked to protein metabolism and trafficking. RNA binding is required for Unkempt-induced remodeling of cellular shape and is directly coupled to a reduced production of the encoded proteins. These findings link post-transcriptional regulation of gene expression with cellular shape and have general implications for the development and disease of multicellular organisms.
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Affiliation(s)
- Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yawei J Yang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA;
| | - Omer Durak
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Elisabeth A Murphy
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Sihem Cheloufi
- Cancer Center, Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Johannes Zuber
- The Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jernej Ule
- Department of Molecular Neuroscience, University College London Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; UCL Genetics Institute, Department of Genetics, Environment, and Evolution, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
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76
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Maloney SE, Khangura E, Dougherty JD. The RNA-binding protein Celf6 is highly expressed in diencephalic nuclei and neuromodulatory cell populations of the mouse brain. Brain Struct Funct 2015; 221:1809-31. [PMID: 25682262 DOI: 10.1007/s00429-015-1005-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/06/2015] [Indexed: 12/16/2022]
Abstract
The gene CUG-BP, Elav-like factor 6 (CELF6) appears to be important for proper functioning of neurocircuitry responsible for behavioral output. We previously discovered that polymorphisms in or near CELF6 may be associated with autism spectrum disorder (ASD) in humans and that the deletion of this gene in mice results in a partial ASD-like phenotype. Here, to begin to understand which circuits might mediate these behavioral disruptions, we sought to establish in what structures, with what abundance, and at which ages Celf6 protein is present in the mouse brain. Using both a knockout-validated antibody to Celf6 and a novel transgenic mouse line, we characterized Celf6 expression in the mouse brain across development. Celf6 gene products were present early in neurodevelopment and in adulthood. The greatest protein expression was observed in distinct nuclei of the diencephalon and neuromodulatory cell populations of the midbrain and hindbrain, with clear expression in dopaminergic, noradrenergic, histaminergic, serotonergic and cholinergic populations, and a variety of presumptive peptidergic cells of the hypothalamus. These results suggest that disruption of Celf6 expression in hypothalamic nuclei may impact a variety of behaviors downstream of neuropeptide activity, while disruption in neuromodulatory transmitter expressing areas such as the ventral tegmental area, substantia nigra, raphe nuclei and locus coeruleus may have far-reaching influences on overall brain activity.
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Affiliation(s)
- Susan E Maloney
- Department of Genetics, Washington University School of Medicine, Campus Box 8232, 4566 Scott Ave., St. Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Eakta Khangura
- Department of Genetics, Washington University School of Medicine, Campus Box 8232, 4566 Scott Ave., St. Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, Campus Box 8232, 4566 Scott Ave., St. Louis, MO, 63110, USA.
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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77
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Oliva MK, McGarr TC, Beyer BJ, Gazina E, Kaplan DI, Cordeiro L, Thomas E, Dib-Hajj SD, Waxman SG, Frankel WN, Petrou S. Physiological and genetic analysis of multiple sodium channel variants in a model of genetic absence epilepsy. Neurobiol Dis 2014; 67:180-90. [PMID: 24657915 DOI: 10.1016/j.nbd.2014.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022] Open
Abstract
In excitatory neurons, SCN2A (NaV1.2) and SCN8A (NaV1.6) sodium channels are enriched at the axon initial segment. NaV1.6 is implicated in several mouse models of absence epilepsy, including a missense mutation identified in a chemical mutagenesis screen (Scn8a(V929F)). Here, we confirmed the prior suggestion that Scn8a(V929F) exhibits a striking genetic background-dependent difference in phenotypic severity, observing that spike-wave discharge (SWD) incidence and severity are significantly diminished when Scn8a(V929F) is fully placed onto the C57BL/6J strain compared with C3H. Examination of sequence differences in NaV subunits between these two inbred strains suggested NaV1.2(V752F) as a potential source of this modifier effect. Recognising that the spatial co-localisation of the NaV channels at the axon initial segment (AIS) provides a plausible mechanism for functional interaction, we tested this idea by undertaking biophysical characterisation of the variant NaV channels and by computer modelling. NaV1.2(V752F) functional analysis revealed an overall gain-of-function and for NaV1.6(V929F) revealed an overall loss-of-function. A biophysically realistic computer model was used to test the idea that interaction between these variant channels at the AIS contributes to the strain background effect. Surprisingly this modelling showed that neuronal excitability is dominated by the properties of NaV1.2(V752F) due to "functional silencing" of NaV1.6(V929F) suggesting that these variants do not directly interact. Consequent genetic mapping of the major strain modifier to Chr 7, and not Chr 2 where Scn2a maps, supported this biophysical prediction. While a NaV1.6(V929F) loss of function clearly underlies absence seizures in this mouse model, the strain background effect is apparently not due to an otherwise tempting Scn2a variant, highlighting the value of combining physiology and genetics to inform and direct each other when interrogating genetic complex traits such as absence epilepsy.
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Affiliation(s)
- M K Oliva
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Australia
| | - T C McGarr
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - B J Beyer
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - E Gazina
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Australia
| | - D I Kaplan
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Australia
| | - L Cordeiro
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Australia
| | - E Thomas
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Australia
| | - S D Dib-Hajj
- Department for Neurology, Center for Neuroscience and Regeneration Research, Yale University, New Haven, USA
| | - S G Waxman
- Department for Neurology, Center for Neuroscience and Regeneration Research, Yale University, New Haven, USA
| | | | - S Petrou
- The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Australia; The Centre for Neural Engineering, The University of Melbourne, Australia.
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78
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Shargunov AV, Krasnov GS, Ponomarenko EA, Lisitsa AV, Shurdov MA, Zverev VV, Archakov AI, Blinov VM. Tissue-Specific Alternative Splicing Analysis Reveals the Diversity of Chromosome 18 Transcriptome. J Proteome Res 2013; 13:173-82. [DOI: 10.1021/pr400808u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander V. Shargunov
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
| | - George S. Krasnov
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
| | - Elena A. Ponomarenko
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
- LLC PostGenTech, 10, Pogodinskaya Street, 119121 Moscow, Russia
| | - Andrey V. Lisitsa
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
- LLC PostGenTech, 10, Pogodinskaya Street, 119121 Moscow, Russia
| | | | - Vitaliy V. Zverev
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
| | - Alexander I. Archakov
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
| | - Vladimir M. Blinov
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
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Bando SY, Silva FN, Costa LDF, Silva AV, Pimentel-Silva LR, Castro LHM, Wen HT, Amaro E, Moreira-Filho CA. Complex network analysis of CA3 transcriptome reveals pathogenic and compensatory pathways in refractory temporal lobe epilepsy. PLoS One 2013; 8:e79913. [PMID: 24278214 PMCID: PMC3836787 DOI: 10.1371/journal.pone.0079913] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/25/2013] [Indexed: 12/21/2022] Open
Abstract
We previously described - studying transcriptional signatures of hippocampal CA3 explants - that febrile (FS) and afebrile (NFS) forms of refractory mesial temporal lobe epilepsy constitute two distinct genomic phenotypes. That network analysis was based on a limited number (hundreds) of differentially expressed genes (DE networks) among a large set of valid transcripts (close to two tens of thousands). Here we developed a methodology for complex network visualization (3D) and analysis that allows the categorization of network nodes according to distinct hierarchical levels of gene-gene connections (node degree) and of interconnection between node neighbors (concentric node degree). Hubs are highly connected nodes, VIPs have low node degree but connect only with hubs, and high-hubs have VIP status and high overall number of connections. Studying the whole set of CA3 valid transcripts we: i) obtained complete transcriptional networks (CO) for FS and NFS phenotypic groups; ii) examined how CO and DE networks are related; iii) characterized genomic and molecular mechanisms underlying FS and NFS phenotypes, identifying potential novel targets for therapeutic interventions. We found that: i) DE hubs and VIPs are evenly distributed inside the CO networks; ii) most DE hubs and VIPs are related to synaptic transmission and neuronal excitability whereas most CO hubs, VIPs and high hubs are related to neuronal differentiation, homeostasis and neuroprotection, indicating compensatory mechanisms. Complex network visualization and analysis is a useful tool for systems biology approaches to multifactorial diseases. Network centrality observed for hubs, VIPs and high hubs of CO networks, is consistent with the network disease model, where a group of nodes whose perturbation leads to a disease phenotype occupies a central position in the network. Conceivably, the chance for exerting therapeutic effects through the modulation of particular genes will be higher if these genes are highly interconnected in transcriptional networks.
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Affiliation(s)
- Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, São Paulo, Brazil
| | | | | | - Alexandre V. Silva
- Department of Biosciences, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
| | | | - Luiz HM. Castro
- Clinical Neurology Division, Hospital das Clínicas da FMUSP, São Paulo, São Paulo, Brazil
| | - Hung-Tzu Wen
- Epilepsy Surgery Group, Hospital das Clínicas da FMUSP, São Paulo, São Paulo, Brazil
| | - Edson Amaro
- Department of Radiology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, São Paulo, Brazil
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, São Paulo, Brazil
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Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 2013; 65:274-87. [PMID: 24184352 PMCID: PMC3988997 DOI: 10.1016/j.ymeth.2013.10.011] [Citation(s) in RCA: 300] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 01/06/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression. Precise knowledge about their binding sites is therefore critical to unravel their molecular function and to understand their role in development and disease. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) identifies protein–RNA crosslink sites on a genome-wide scale. The high resolution and specificity of this method are achieved by an intramolecular cDNA circularization step that enables analysis of cDNAs that truncated at the protein–RNA crosslink sites. Here, we describe the improved iCLIP protocol and discuss critical optimization and control experiments that are required when applying the method to new RBPs.
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Affiliation(s)
- Ina Huppertz
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrea D'Ambrogio
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mojca Tajnik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Julian König
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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81
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Karunakaran DKP, Congdon S, Guerrette T, Banday AR, Lemoine C, Chhaya N, Kanadia R. The expression analysis of Sfrs10 and Celf4 during mouse retinal development. Gene Expr Patterns 2013; 13:425-36. [PMID: 23932931 DOI: 10.1016/j.gep.2013.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
Abstract
Processing of mRNAs including, alternative splicing (AS), mRNA transport and translation regulation are crucial to eukaryotic gene expression. For example, >90% of the genes in the human genome are known to undergo alternative splicing thereby expanding the proteome production capacity of a limited number of genes. Similarly, mRNA export and translation regulation plays a vital role in regulating protein production. Thus, it is important to understand how these RNA binding proteins including alternative splicing factors (ASFs) and mRNA transport and translation factors regulate these processes. Here we report the expression of an ASF, serine-arginine rich splicing factor 10 (Sfrs10) and a mRNA translation regulation factor, CUGBP, elav like family member 4 (Celf4) in the developing mouse retina. Sfrs10 was expressed throughout postnatal (P) retinal development and was observed progressively in newly differentiating neurons. Immunofluorescence (IF) showed Sfrs10 in retinal ganglion cells (RGCs) at P0, followed by amacrine and bipolar cells, and at P8 it was enriched in red/green cone photoreceptor cells. By P22, Sfrs10 was observed in rod photoreceptors in a peri-nuclear pattern. Like Sfrs10, Celf4 expression was also observed in the developing retina, but with two distinct retinal isoforms. In situ hybridization (ISH) showed progressive expression of Celf4 in differentiating neurons, which was confirmed by IF that showed a dynamic shift in Celf4 localization. Early in development Celf4 expression was restricted to the nuclei of newly differentiating RGCs and later (E16 onwards) it was observed in the initial segments of RGC axons. Later, during postnatal development, Celf4 was observed in amacrine and bipolar cells, but here it was predominantly cytoplasmic and enriched in the two synaptic layers. Specifically, at P14, Celf4 was observed in the synaptic boutons of rod bipolar cells marked by Pkc-α. Thus, Celf4 might be regulating AS early in development besides its known role of regulating mRNA localization/translation. In all, our data suggests an important role for AS and mRNA localization/translation in retinal neuron differentiation.
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82
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Oliva M, Petrou S. CELF expression in epilepsy linked to sodium channels. FUTURE NEUROLOGY 2013. [DOI: 10.2217/fnl.13.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evaluation of: Sun W, Wagnon JL, Mahaffey CL et al. Aberrant sodium channel activity in the complex seizure disorder of Celf4 mutant mice. J. Physiol. 591(1), 241–255 (2013). The choreographed expression of ion channels is critical for normal brain activity, as evidenced by the range of epilepsy syndromes associated with ion channel genetic variation. As large-scale sequencing efforts, such as Epi4K and EuroEPINOMICS, systematically deconstruct epilepsy genomes, it is likely that further progress will be made in our understanding of how ion channel dysfunction results in epilepsy. By contrast, our knowledge of non-ion channel genes in epilepsy is far less advanced, a problem frequently compounded by the lack of understanding of the basic neurobiology of these genes. Sun et al. address this shortcoming by providing an elegant account of how a key RNA metabolism gene, Celf4, gives rise to seizures by the regulation of axonal ion channels. This has implications for epilepsy genomics, where a priori knowledge of the gene networks that participate in seizure genesis is critical for bioinformatics filtering used to identify diagnostic and prognostic variants. The convergence on an ion channel target affirms their central role in seizure genesis but, more importantly, raises the idea that drugs that target key regulators such as CELF4 could be effective in epilepsy.
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Affiliation(s)
- Megan Oliva
- Florey Institute of Neuroscience & Mental Health, Centre for Neural Engineering, The University of Melbourne, Victoria 3010, Australia
| | - Steven Petrou
- Florey Institute of Neuroscience & Mental Health, Centre for Neural Engineering, The University of Melbourne, Victoria 3010, Australia.
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83
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Modic M, Ule J, Sibley CR. CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders. Mol Cell Neurosci 2013; 56:429-35. [PMID: 23583633 PMCID: PMC3793874 DOI: 10.1016/j.mcn.2013.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/31/2013] [Accepted: 04/03/2013] [Indexed: 02/07/2023] Open
Abstract
The fate of an mRNA is largely determined by its interactions with RNA binding proteins (RBPs). Post-transcriptional processing, RNA stability, localisation and translation are some of the events regulated by the plethora of RBPs present within cells. Mutations in various RBPs cause several diseases of the central nervous system, including frontotemporal lobar degeneration, amyotrophic lateral sclerosis and fragile X syndrome. Here we review the studies that integrated UV-induced cross-linked immunoprecipitation (CLIP) with other genome-wide methods to comprehensively characterise the function of diverse RBPs in the brain. We discuss the technical challenges of these studies and review the strategies that can be used to reliably identify the RNAs bound and regulated by an RBP. We conclude by highlighting how CLIP and related techniques have been instrumental in addressing the role of RBPs in neurologic diseases. This article is part of a Special Issue entitled: RNA and splicing regulation in neurodegeneration.
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Affiliation(s)
- Miha Modic
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- Corresponding authors at: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK. Fax: + 44 1223213556.
| | - Christopher R. Sibley
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- Corresponding authors at: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK. Fax: + 44 1223213556.
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84
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Vlasova-St Louis I, Dickson AM, Bohjanen PR, Wilusz CJ. CELFish ways to modulate mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:695-707. [PMID: 23328451 DOI: 10.1016/j.bbagrm.2013.01.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/03/2013] [Accepted: 01/05/2013] [Indexed: 12/14/2022]
Abstract
The CELF family of RNA-binding proteins regulates many steps of mRNA metabolism. Although their best characterized function is in pre-mRNA splice site choice, CELF family members are also powerful modulators of mRNA decay. In this review we focus on the different modes of regulation that CELF proteins employ to mediate mRNA decay by binding to GU-rich elements. After starting with an overview of the importance of CELF proteins during development and disease pathogenesis, we then review the mRNA networks and cellular pathways these proteins regulate and the mechanisms by which they influence mRNA decay. Finally, we discuss how CELF protein activity is modulated during development and in response to cellular signals. We conclude by highlighting the priorities for new experiments in this field. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Sun W, Wagnon JL, Mahaffey CL, Briese M, Ule J, Frankel WN. Aberrant sodium channel activity in the complex seizure disorder of Celf4 mutant mice. J Physiol 2012; 591:241-55. [PMID: 23090952 DOI: 10.1113/jphysiol.2012.240168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mice deficient for CELF4, a neuronal RNA-binding protein, have a complex seizure disorder that includes both convulsive and non-convulsive seizures, and is dependent upon Celf4 gene dosage and mouse strain background. It was previously shown that Celf4 is expressed predominantly in excitatory neurons, and that deficiency results in abnormal excitatory synaptic neurotransmission. To examine the physiological and molecular basis of this, we studied Celf4-deficient neurons in brain slices. Assessment of intrinsic properties of layer V cortical pyramidal neurons showed that neurons from mutant heterozygotes and homozygotes have a lower action potential (AP) initiation threshold and a larger AP gain when compared with wild-type neurons. Celf4 mutant neurons also demonstrate an increase in persistent sodium current (I(NaP)) and a hyperpolarizing shift in the voltage dependence of activation. As part of a related study, we find that CELF4 directly binds Scn8a mRNA, encoding sodium channel Na(v)1.6, the primary instigator of AP at the axon initial segment (AIS) and the main carrier of I(NaP). In the present study we find that CELF4 deficiency results in a dramatic elevation in the expression of Na(v)1.6 protein at the AIS in both null and heterozygous neurons. Together these results suggest that activation of Na(v)1.6 plays a crucial role in seizure generation in this complex model of neurological disease.
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Affiliation(s)
- Wenzhi Sun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609-1500, USA
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