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Abstract
microRNAs (miRNA) are small, noncoding RNAs that bind to messenger RNAs (mRNAs) and regulate their activity. They are, therefore, important posttranscriptional regulators. In recent years it has become clear that miRNAs regulate large genetic networks, rather than single genes, and that one gene can be targeted by several miRNAs. To understand the role of miRNAs in cells or tissues, it is therefore important to analyze the targetome of miRNAs. Here, we present a technique called Argonaute-RNA Immunoprecipitation (AGO-RIP) which takes advantages of the fact that miRNAs and their targets are directly bound by the Argonaute protein family. With this approach quantitative, genome-wide analysis of miRNA targets is possible. In this chapter we describe the RIP-methodology and provide advice for RNA sequencing and bioinformatic analyses.
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102
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Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Molecular and cellular reorganization of neural circuits in the human lineage. Science 2017; 358:1027-1032. [PMID: 29170230 PMCID: PMC5776074 DOI: 10.1126/science.aan3456] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/17/2017] [Indexed: 01/06/2023]
Abstract
To better understand the molecular and cellular differences in brain organization between human and nonhuman primates, we performed transcriptome sequencing of 16 regions of adult human, chimpanzee, and macaque brains. Integration with human single-cell transcriptomic data revealed global, regional, and cell-type-specific species expression differences in genes representing distinct functional categories. We validated and further characterized the human specificity of genes enriched in distinct cell types through histological and functional analyses, including rare subpallial-derived interneurons expressing dopamine biosynthesis genes enriched in the human striatum and absent in the nonhuman African ape neocortex. Our integrated analysis of the generated data revealed diverse molecular and cellular features of the phylogenetic reorganization of the human brain across multiple levels, with relevance for brain function and disease.
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Affiliation(s)
- André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Ying Zhu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Robert R Kitchen
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Marco Onorati
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Biology, Unit of Cell and Developmental Biology, University of Pisa, Pisa, Italy
| | - Andrew T N Tebbenkamp
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Bernardo Stutz
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Kyle A Meyer
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Yuka Imamura Kawasawa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Departments of Pharmacology and Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Raquel Garcia Perez
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Marta Mele
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Tiago Carvalho
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Mario Skarica
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mihovil Pletikos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Akemi Shibata
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Alexa R Stephenson
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Melissa K Edler
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, NM, USA
| | - John D Elsworth
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Tamas L Horvath
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Mark Reimers
- Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Matthew W State
- Department of Psychiatry and Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - James A Knowles
- Department of Psychiatry and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- Centro Nacional de Analisis Genomico, Barcelona, Catalonia, Spain
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
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103
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Zhang Z, Xing Y. CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome. Nucleic Acids Res 2017; 45:9260-9271. [PMID: 28934506 PMCID: PMC5766199 DOI: 10.1093/nar/gkx646] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 07/19/2017] [Indexed: 01/09/2023] Open
Abstract
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation–maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein–RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome.
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Affiliation(s)
- Zijun Zhang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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104
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Cabana-Domínguez J, Roncero C, Pineda-Cirera L, Palma-Álvarez RF, Ros-Cucurull E, Grau-López L, Esojo A, Casas M, Arenas C, Ramos-Quiroga JA, Ribasés M, Fernàndez-Castillo N, Cormand B. Association of the PLCB1 gene with drug dependence. Sci Rep 2017; 7:10110. [PMID: 28860459 PMCID: PMC5579249 DOI: 10.1038/s41598-017-10207-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/04/2017] [Indexed: 12/27/2022] Open
Abstract
Genetic factors involved in the susceptibility to drug addiction still remain largely unknown. MiRNAs seem to play key roles in the drug-induced plasticity of the brain that likely drives the emergence of addiction. In this work we explored the role of miRNAs in drug addiction. With this aim, we selected 62 SNPs located in the 3'UTR of target genes that are predicted to alter the binding of miRNA molecules and performed a case-control association study in a Spanish sample of 735 cases (mainly cocaine-dependent subjects with multiple drug dependencies) and 739 controls. We found an association between rs1047383 in the PLCB1 gene and drug dependence that was replicated in an independent sample (663 cases and 667 controls). Then we selected 9 miRNAs predicted to bind the rs1047383 region, but none of them showed any effect on PLCB1 expression. We also assessed two miRNAs binding a region that contains a SNP in linkage disequilibrium with rs1047383, but although one of them, hsa-miR-582, was found to downregulate PLCB1, no differences were observed between alleles. Finally, we explored the possibility that PLCB1 expression is altered by cocaine and we observed a significant upregulation of the gene in the nucleus accumbens of cocaine abusers and in human dopaminergic-like neurons after cocaine treatment. Our results, together with previous studies, suggest that PLCB1 participates in the susceptibility to drug dependence.
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Affiliation(s)
- Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Carlos Roncero
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Addiction and Dual Diagnosis Unit Vall Hebron, Psychiatric Services, Hospital Universitari Vall d'Hebron-ASPB, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Laura Pineda-Cirera
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - R Felipe Palma-Álvarez
- Addiction and Dual Diagnosis Unit Vall Hebron, Psychiatric Services, Hospital Universitari Vall d'Hebron-ASPB, Barcelona, Catalonia, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Elena Ros-Cucurull
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Addiction and Dual Diagnosis Unit Vall Hebron, Psychiatric Services, Hospital Universitari Vall d'Hebron-ASPB, Barcelona, Catalonia, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Lara Grau-López
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Addiction and Dual Diagnosis Unit Vall Hebron, Psychiatric Services, Hospital Universitari Vall d'Hebron-ASPB, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Abderaman Esojo
- Addiction and Dual Diagnosis Unit Vall Hebron, Psychiatric Services, Hospital Universitari Vall d'Hebron-ASPB, Barcelona, Catalonia, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Miquel Casas
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Antoni Ramos-Quiroga
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Ribasés
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain.
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain.
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
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105
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Piwecka M, Glažar P, Hernandez-Miranda LR, Memczak S, Wolf SA, Rybak-Wolf A, Filipchyk A, Klironomos F, Cerda Jara CA, Fenske P, Trimbuch T, Zywitza V, Plass M, Schreyer L, Ayoub S, Kocks C, Kühn R, Rosenmund C, Birchmeier C, Rajewsky N. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 2017; 357:science.aam8526. [DOI: 10.1126/science.aam8526] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/26/2017] [Indexed: 12/29/2022]
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106
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Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain. Transl Psychiatry 2017; 7:e1199. [PMID: 28786976 PMCID: PMC5611730 DOI: 10.1038/tp.2017.163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs orchestrate brain functioning via interaction with microRNA recognition elements (MRE) on target transcripts. However, the global impact of potential competition on the microRNA pool between coding and non-coding brain transcripts that share MREs with them remains unexplored. Here we report that non-coding pseudogene transcripts carrying MREs (PSG+MRE) often show duplicated origin, evolutionary conservation and higher expression in human temporal lobe neurons than comparable duplicated MRE-deficient pseudogenes (PSG-MRE). PSG+MRE participate in neuronal RNA-induced silencing complexes (RISC), indicating functional involvement. Furthermore, downregulation cell culture experiments validated bidirectional co-regulation of PSG+MRE with MRE-sharing coding transcripts, frequently not their mother genes, and with targeted microRNAs; also, PSG+MRE single-nucleotide polymorphisms associated with schizophrenia, bipolar disorder and autism, suggesting interaction with mental diseases. Our findings indicate functional roles of duplicated PSG+MRE in brain development and cognition, supporting physiological impact of the reciprocal co-regulation of PSG+MRE with MRE-sharing coding transcripts in human brain neurons.
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107
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Structural Foundations of RNA Silencing by Argonaute. J Mol Biol 2017; 429:2619-2639. [PMID: 28757069 DOI: 10.1016/j.jmb.2017.07.018] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Nearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse physiological process, such as stem cell maintenance, fertilization, and heart development. Over the last decade, remarkable progress has been made toward understanding Argonaute proteins, small RNAs, and their roles in eukaryotic biology. Here, we review current understanding of Argonaute proteins from a structural prospective and discuss unanswered questions surrounding this fascinating class of enzymes.
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108
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Skariah G, Seimetz J, Norsworthy M, Lannom MC, Kenny PJ, Elrakhawy M, Forsthoefel C, Drnevich J, Kalsotra A, Ceman S. Mov10 suppresses retroelements and regulates neuronal development and function in the developing brain. BMC Biol 2017; 15:54. [PMID: 28662698 PMCID: PMC5492891 DOI: 10.1186/s12915-017-0387-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 05/26/2017] [Indexed: 12/20/2022] Open
Abstract
Background Moloney leukemia virus 10 (Mov10) is an RNA helicase that mediates access of the RNA-induced silencing complex to messenger RNAs (mRNAs). Until now, its role as an RNA helicase and as a regulator of retrotransposons has been characterized exclusively in cell lines. We investigated the role of Mov10 in the mouse brain by examining its expression over development and attempting to create a Mov10 knockout mouse. Loss of both Mov10 copies led to early embryonic lethality. Results Mov10 was significantly elevated in postnatal murine brain, where it bound retroelement RNAs and mRNAs. Mov10 suppressed retroelements in the nucleus by directly inhibiting complementary DNA synthesis, while cytosolic Mov10 regulated cytoskeletal mRNAs to influence neurite outgrowth. We verified this important function by observing reduced dendritic arborization in hippocampal neurons from the Mov10 heterozygote mouse and shortened neurites in the Mov10 knockout Neuro2A cells. Knockdown of Fmrp also resulted in shortened neurites. Mov10, Fmrp, and Ago2 bound a common set of mRNAs in the brain. Reduced Mov10 in murine brain resulted in anxiety and increased activity in a novel environment, supporting its important role in the development of normal brain circuitry. Conclusions Mov10 is essential for normal neuronal development and brain function. Mov10 preferentially binds RNAs involved in actin binding, neuronal projection, and cytoskeleton. This is a completely new and critically important function for Mov10 in neuronal development and establishes a precedent for Mov10 being an important candidate in neurological disorders that have underlying cytoarchitectural causes like autism and Alzheimer’s disease. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0387-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Geena Skariah
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Joseph Seimetz
- Biochemistry, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Miles Norsworthy
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Monica C Lannom
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Phillip J Kenny
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Mohamed Elrakhawy
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Craig Forsthoefel
- College of Medicine, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Jenny Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Auinash Kalsotra
- Biochemistry, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA.,College of Medicine, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Stephanie Ceman
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA. .,Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA. .,College of Medicine, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA.
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109
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Li H, Li J, Shi B, Chen F. MicroRNA‑296 targets AKT2 in pancreatic cancer and functions as a potential tumor suppressor. Mol Med Rep 2017; 16:466-472. [PMID: 28534950 DOI: 10.3892/mmr.2017.6602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
Although microRNA-296 (miR-296) has been studied in various types of human cancer, its expression, biological role and mechanism of action in pancreatic cancer remains to be elucidated. The aim of the current study was to investigate the expression level, possible roles and underlying molecular mechanisms of miR‑296 in pancreatic cancer. The present study revealed that miR‑296 is significantly downregulated in tissue from patients with pancreatic cancer and in human pancreatic carcinoma cell lines, when compared with matched healthy tissue and normal human pancreatic cell lines, respectively. In addition, restoration of miR‑296 expression was revealed to inhibit the proliferation, migration and invasive activity of pancreatic cancer cells. Furthermore, bioinformatics analysis and a luciferase reporter assay validated the AKT2 gene as a direct target of miR‑296 in pancreatic cancer. Reverse transcription‑quantitative polymerase chain reaction and western blot analysis revealed that miR‑296 was able to decrease AKT2 expression at the post‑transcriptional level. Notably, the effects of AKT2 knockdown were similar to miR‑296 overexpression in pancreatic cancer. In conclusion, the present findings indicate a role for miR‑296 as a tumor suppressor in pancreatic cancer through directly targeting AKT2, thus suggesting that miR‑296 may serve as a potential therapeutic target for the treatment of pancreatic cancer.
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Affiliation(s)
- Hailing Li
- Department of Endocrinology, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Jilin Li
- Department of Medical Laboratory Medicine, Family Planning Guidance Center of Weifang, Weifang, Shandong 261061, P.R. China
| | - Baolin Shi
- Department of Neurology, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Feng Chen
- Department of Endocrine, Weifang Municipal Official Hospital, Weifang, Shandong 261041, P.R. China
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110
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Hamilton MP, Rajapakshe KI, Bader DA, Cerne JZ, Smith EA, Coarfa C, Hartig SM, McGuire SE. The Landscape of microRNA Targeting in Prostate Cancer Defined by AGO-PAR-CLIP. Neoplasia 2017; 18:356-70. [PMID: 27292025 PMCID: PMC4909715 DOI: 10.1016/j.neo.2016.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/08/2016] [Accepted: 04/23/2016] [Indexed: 01/13/2023] Open
Abstract
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
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Affiliation(s)
- Mark P Hamilton
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA
| | - Kimal I Rajapakshe
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - David A Bader
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA
| | - Jasmina Z Cerne
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA
| | - Eric A Smith
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Sean M Hartig
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA
| | - Sean E McGuire
- Department of Molecular and Cell Biology, Baylor College of Medicine Hospital, Houston, TX, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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111
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Identification of targets of tumor suppressor microRNA-34a using a reporter library system. Proc Natl Acad Sci U S A 2017; 114:3927-3932. [PMID: 28356515 DOI: 10.1073/pnas.1620019114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
miRNAs play critical roles in various biological processes by targeting specific mRNAs. Current approaches to identifying miRNA targets are insufficient for elucidation of a miRNA regulatory network. Here, we created a cell-based screening system using a luciferase reporter library composed of 4,891 full-length cDNAs, each of which was integrated into the 3' UTR of a luciferase gene. Using this reporter library system, we conducted a screening for targets of miR-34a, a tumor-suppressor miRNA. We identified both previously characterized and previously uncharacterized targets. miR-34a overexpression in MDA-MB-231 breast cancer cells repressed the expression of these previously unrecognized targets. Among these targets, GFRA3 is crucial for MDA-MB-231 cell growth, and its expression correlated with the overall survival of patients with breast cancer. Furthermore, GFRA3 was found to be directly regulated by miR-34a via its coding region. These data show that this system is useful for elucidating miRNA functions and networks.
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112
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Simchovitz A, Heneka MT, Soreq H. Personalized genetics of the cholinergic blockade of neuroinflammation. J Neurochem 2017; 142 Suppl 2:178-187. [PMID: 28326544 PMCID: PMC5600134 DOI: 10.1111/jnc.13928] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/27/2016] [Accepted: 12/05/2016] [Indexed: 01/09/2023]
Abstract
Acetylcholine signaling is essential for cognitive functioning and blocks inflammation. To maintain homeostasis, cholinergic signaling is subjected to multi‐leveled and bidirectional regulation by both proteins and non‐coding microRNAs (‘CholinomiRs’). CholinomiRs coordinate the cognitive and inflammatory aspects of cholinergic signaling by targeting major cholinergic transcripts including the acetylcholine hydrolyzing enzyme acetylcholinesterase (AChE). Notably, AChE inhibitors are the only currently approved line of treatment for Alzheimer's disease patients. Since cholinergic signaling blocks neuroinflammation which is inherent to Alzheimer's disease, genomic changes modifying AChE's properties and its susceptibility to inhibitors and/or to CholinomiRs regulation may affect the levels and properties of inflammasome components such as NLRP3. This calls for genomic‐based medicine approaches based on genotyping of both coding and non‐coding single nucleotide polymorphisms (SNPs) in the genes involved in cholinergic signaling. An example is a SNP in a recognition element for the primate‐specific microRNA‐608 within the 3′ untranslated region of the AChE transcript. Carriers of the minor allele of that SNP present massively elevated brain AChE levels, increased trait anxiety and inflammation, accompanied by perturbed CholinomiR‐608 regulatory networks and elevated prefrontal activity under exposure to stressful insults. Several additional SNPs in the AChE and other cholinergic genes await further studies, and might likewise involve different CholinomiRs and pathways including those modulating the initiation and progression of neurodegenerative diseases. CholinomiRs regulation of the cholinergic system thus merits in‐depth interrogation and is likely to lead to personalized medicine approaches for achieving better homeostasis in health and disease. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms. ![]()
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Affiliation(s)
- Alon Simchovitz
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | | | - Hermona Soreq
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
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113
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Millan MJ. Linking deregulation of non-coding RNA to the core pathophysiology of Alzheimer's disease: An integrative review. Prog Neurobiol 2017; 156:1-68. [PMID: 28322921 DOI: 10.1016/j.pneurobio.2017.03.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 02/06/2023]
Abstract
The human genome encodes a vast repertoire of protein non-coding RNAs (ncRNA), some specific to the brain. MicroRNAs, which interfere with the translation of target mRNAs, are of particular interest since their deregulation has been implicated in neurodegenerative disorders like Alzheimer's disease (AD). However, it remains challenging to link the complex body of observations on miRNAs and AD into a coherent framework. Using extensive graphical support, this article discusses how a diverse panoply of miRNAs convergently and divergently impact (and are impacted by) core pathophysiological processes underlying AD: neuroinflammation and oxidative stress; aberrant generation of β-amyloid-42 (Aβ42); anomalies in the production, cleavage and post-translational marking of Tau; impaired clearance of Aβ42 and Tau; perturbation of axonal organisation; disruption of synaptic plasticity; endoplasmic reticulum stress and the unfolded protein response; mitochondrial dysfunction; aberrant induction of cell cycle re-entry; and apoptotic loss of neurons. Intriguingly, some classes of miRNA provoke these cellular anomalies, whereas others act in a counter-regulatory, protective mode. Moreover, changes in levels of certain species of miRNA are a consequence of the above-mentioned anomalies. In addition to miRNAs, circular RNAs, piRNAs, long non-coding RNAs and other types of ncRNA are being increasingly implicated in AD. Overall, a complex mesh of deregulated and multi-tasking ncRNAs reciprocally interacts with core pathophysiological mechanisms underlying AD. Alterations in ncRNAs can be detected in CSF and the circulation as well as the brain and are showing promise as biomarkers, with the ultimate goal clinical exploitation as targets for novel modes of symptomatic and course-altering therapy.
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Affiliation(s)
- Mark J Millan
- Centre for Therapeutic Innovation in Neuropsychiatry, institut de recherche Servier, 125 chemin de ronde, 78290 Croissy sur Seine, France.
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114
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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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115
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Carmona V, Cunha-Santos J, Onofre I, Simões AT, Vijayakumar U, Davidson BL, Pereira de Almeida L. Unravelling Endogenous MicroRNA System Dysfunction as a New Pathophysiological Mechanism in Machado-Joseph Disease. Mol Ther 2017; 25:1038-1055. [PMID: 28236575 DOI: 10.1016/j.ymthe.2017.01.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/28/2016] [Accepted: 01/24/2017] [Indexed: 01/07/2023] Open
Abstract
Machado-Joseph disease (MJD) is a genetic neurodegenerative disease caused by an expanded polyglutamine tract within the protein ataxin-3 (ATXN3). Despite current efforts, MJD's mechanism of pathogenesis remains unclear and no disease-modifying treatment is available. Therefore, in this study, we investigated (1) the role of the 3' UTR of ATXN3, a putative microRNA (miRNA) target, (2) whether miRNA biogenesis and machinery are dysfunctional in MJD, and (3) which specific miRNAs target ATXN3-3' UTR and whether they can alleviate MJD neuropathology in vivo. Our results demonstrate that endogenous miRNAs, by targeting sequences in the 3' UTR, robustly reduce ATXN3 expression and aggregation in vitro and neurodegeneration and neuroinflammation in vivo. Importantly, we found an abnormal MJD-associated downregulation of genes involved in miRNA biogenesis and silencing activity. Finally, we identified three miRNAs-mir-9, mir-181a, and mir-494-that interact with the ATXN3-3' UTR and whose expression is dysregulated in human MJD neurons and in other MJD cell and animal models. Furthermore, overexpression of these miRNAs in mice resulted in reduction of mutATXN3 levels, aggregate counts, and neuronal dysfunction. Altogether, these findings indicate that endogenous miRNAs and the 3' UTR of ATXN3 play a crucial role in MJD pathogenesis and provide a promising opportunity for MJD treatment.
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Affiliation(s)
- Vitor Carmona
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra 3000-548, Portugal
| | - Janete Cunha-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra 3000-548, Portugal
| | - Isabel Onofre
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra 3000-548, Portugal
| | - Ana Teresa Simões
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal
| | - Udaya Vijayakumar
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal
| | - Beverly L Davidson
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luís Pereira de Almeida
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra 3000-548, Portugal.
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116
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Abstract
RNA-binding proteins play important roles in the various stages of RNA maturation through binding to its target RNAs. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Several Hidden Markov model-based (HMM) approaches have been suggested to identify protein-RNA binding sites from CLIP-Seq datasets. In this chapter, we describe how HMM can be applied to analyze CLIP-Seq datasets, including the bioinformatics preprocessing steps to extract count information from the sequencing data before HMM and the downstream analysis steps following peak-calling.
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Affiliation(s)
- Tao Wang
- Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA
| | - Jonghyun Yun
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA
| | - Guanghua Xiao
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA.
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117
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Lippi G, Fernandes CC, Ewell LA, John D, Romoli B, Curia G, Taylor SR, Frady EP, Jensen AB, Liu JC, Chaabane MM, Belal C, Nathanson JL, Zoli M, Leutgeb JK, Biagini G, Yeo GW, Berg DK. MicroRNA-101 Regulates Multiple Developmental Programs to Constrain Excitation in Adult Neural Networks. Neuron 2016; 92:1337-1351. [PMID: 27939580 DOI: 10.1016/j.neuron.2016.11.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/07/2016] [Accepted: 11/03/2016] [Indexed: 11/15/2022]
Abstract
A critical feature of neural networks is that they balance excitation and inhibition to prevent pathological dysfunction. How this is achieved is largely unknown, although deficits in the balance contribute to many neurological disorders. We show here that a microRNA (miR-101) is a key orchestrator of this essential feature, shaping the developing network to constrain excitation in the adult. Transient early blockade of miR-101 induces long-lasting hyper-excitability and persistent memory deficits. Using target site blockers in vivo, we identify multiple developmental programs regulated in parallel by miR-101 to achieve balanced networks. Repression of one target, NKCC1, initiates the switch in γ-aminobutyric acid (GABA) signaling, limits early spontaneous activity, and constrains dendritic growth. Kif1a and Ank2 are targeted to prevent excessive synapse formation. Simultaneous de-repression of these three targets completely phenocopies major dysfunctions produced by miR-101 blockade. Our results provide new mechanistic insight into brain development and suggest novel candidates for therapeutic intervention.
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Affiliation(s)
- Giordano Lippi
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Catarina C Fernandes
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laura A Ewell
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Danielle John
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benedetto Romoli
- Department of Biomedical, Metabolic, and Neural Sciences, Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulia Curia
- Department of Biomedical, Metabolic, and Neural Sciences, Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Seth R Taylor
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - E Paxon Frady
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anne B Jensen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jerry C Liu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melanie M Chaabane
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cherine Belal
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason L Nathanson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michele Zoli
- Department of Biomedical, Metabolic, and Neural Sciences, Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Jill K Leutgeb
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Neural Circuits and Behavior, University of California, San Diego, La Jolla, CA 92093, USA
| | - Giuseppe Biagini
- Department of Biomedical, Metabolic, and Neural Sciences, Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gene W Yeo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Darwin K Berg
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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118
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O'Connor RM, Gururajan A, Dinan TG, Kenny PJ, Cryan JF. All Roads Lead to the miRNome: miRNAs Have a Central Role in the Molecular Pathophysiology of Psychiatric Disorders. Trends Pharmacol Sci 2016; 37:1029-1044. [PMID: 27832923 DOI: 10.1016/j.tips.2016.10.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 12/14/2022]
Abstract
Current treatment strategies for psychiatric disorders remain inadequate. Impeding development of novel therapeutics is our incomplete knowledge of the molecular pathophysiology underlying these disorders. Changes to miRNA function and expression are increasingly being associated with pathological behavioral states. Furthermore, the prospect of using of miRNA expression profiles (the miRNome) as objective psychiatric diagnosis tools is gaining traction. In this review, we focus on recent findings surrounding the link between miRNA function and psychiatric disorders, and outline some of the key challenges that will need to be overcome if the therapeutic potential of these molecular effectors is to be fully realized.
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Affiliation(s)
- Richard M O'Connor
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai Hospital, NY, USA.
| | - Anand Gururajan
- Department of Anatomy and Neuroscience, University College Cork, Ireland
| | - Timothy G Dinan
- Department of Psychiatry, University College Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Paul J Kenny
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai Hospital, NY, USA
| | - John F Cryan
- Department of Anatomy and Neuroscience, University College Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
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119
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Catalanotto C, Cogoni C, Zardo G. MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions. Int J Mol Sci 2016; 17:ijms17101712. [PMID: 27754357 PMCID: PMC5085744 DOI: 10.3390/ijms17101712] [Citation(s) in RCA: 769] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/04/2016] [Accepted: 10/07/2016] [Indexed: 12/14/2022] Open
Abstract
The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs. Among these, miRNAs appear as important cytoplasmic regulators of gene expression. miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA degradation and/or translational repression. However, it is becoming evident that miRNAs also have specific nuclear functions. Among these, the most studied and debated activity is the miRNA-guided transcriptional control of gene expression. Although available data detail quite precisely the effectors of this activity, the mechanisms by which miRNAs identify their gene targets to control transcription are still a matter of debate. Here, we focus on nuclear functions of miRNAs and on alternative mechanisms of target recognition, at the promoter lavel, by miRNAs in carrying out transcriptional gene silencing.
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Affiliation(s)
- Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
| | - Giuseppe Zardo
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
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120
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Wake C, Labadorf A, Dumitriu A, Hoss AG, Bregu J, Albrecht KH, DeStefano AL, Myers RH. Novel microRNA discovery using small RNA sequencing in post-mortem human brain. BMC Genomics 2016; 17:776. [PMID: 27716130 PMCID: PMC5050850 DOI: 10.1186/s12864-016-3114-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/23/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. METHODS We used high-throughput small RNA sequencing to discover novel miRNAs in 93 human post-mortem prefrontal cortex samples from individuals with Huntington's disease (n = 28) or Parkinson's disease (n = 29) and controls without neurological impairment (n = 36). A custom miRNA identification analysis pipeline was built, which utilizes miRDeep* miRNA identification and result filtering based on false positive rate estimates. RESULTS Ninety-nine novel miRNA candidates with a false positive rate of less than 5 % were identified. Thirty-four of the candidate miRNAs show sequence similarity with known mature miRNA sequences and may be novel members of known miRNA families, while the remaining 65 may constitute previously undiscovered families of miRNAs. Nineteen of the 99 candidate miRNAs were replicated using independent, publicly-available human brain RNA-sequencing samples, and seven were experimentally validated using qPCR. CONCLUSIONS We have used small RNA sequencing to identify 99 putative novel miRNAs that are present in human brain samples.
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Affiliation(s)
- Christian Wake
- Department of Neurology, Boston University School of Medicine, Boston, USA. .,Bioinformatics Program, Boston University, Boston, USA.
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Bioinformatics Program, Boston University, Boston, USA
| | - Alexandra Dumitriu
- Department of Neurology, Boston University School of Medicine, Boston, USA
| | - Andrew G Hoss
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, USA
| | - Joli Bregu
- Department of Neurology, Boston University School of Medicine, Boston, USA
| | - Kenneth H Albrecht
- Genome Science Institute, Boston University School of Medicine, Boston, USA.,Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, USA
| | - Anita L DeStefano
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Genome Science Institute, Boston University School of Medicine, Boston, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Bioinformatics Program, Boston University, Boston, USA.,Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, USA.,Genome Science Institute, Boston University School of Medicine, Boston, USA.,Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, USA
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121
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Poon VY, Gu M, Ji F, VanDongen AM, Fivaz M. miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1. BMC Genomics 2016; 17:777. [PMID: 27716060 PMCID: PMC5050705 DOI: 10.1186/s12864-016-3139-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/28/2016] [Indexed: 12/02/2022] Open
Abstract
Background MicroRNAs (miRNAs) are short non-coding RNAs that are emerging as important post-transcriptional regulators of neuronal and synaptic development. The precise impact of miRNAs on presynaptic function and neurotransmission remains, however, poorly understood. Results Here, we identify miR-27b—an abundant neuronal miRNA implicated in neurological disorders—as a global regulator of the presynaptic transcriptome. miR-27b influences the expression of three quarters of genes associated with presynaptic function in cortical neurons. Contrary to expectation, a large majority of these genes are up-regulated by miR-27b. This stimulatory effect is mediated by miR-27b-directed silencing of several transcriptional repressors that cooperate to suppress the presynaptic transcriptome. The strongest repressive activity appears to be mediated by Bmi1, a component of the polycomb repressive complex implicated in self-renewal of neural stem cells. miR-27b knockdown leads to reduced synaptogenesis and to a marked decrease in neural network activity, which is fully restored by RNAi-mediated silencing of Bmi1. Conclusions We conclude that silencing of Bmi1 by miR-27b relieves repression of the presynaptic transcriptome and supports neurotransmission in cortical networks. These results expand the repressive activity of Bmi1 to genes involved in synaptic function and identify a unique post-transcriptional circuitry that stimulates expression of synaptic genes and promotes synapse differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3139-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vivian Y Poon
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Minxia Gu
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Fang Ji
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Antonius M VanDongen
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Marc Fivaz
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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122
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Spengler RM, Zhang X, Cheng C, McLendon JM, Skeie JM, Johnson FL, Davidson BL, Boudreau RL. Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP. Nucleic Acids Res 2016; 44:7120-31. [PMID: 27418678 PMCID: PMC5009757 DOI: 10.1093/nar/gkw640] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 07/07/2016] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
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Affiliation(s)
- Ryan M Spengler
- Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Xiaoming Zhang
- Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Congsheng Cheng
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jared M McLendon
- Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Jessica M Skeie
- Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Frances L Johnson
- Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Beverly L Davidson
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA Department of Pathology and Laboratory Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan L Boudreau
- Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA
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123
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Liu XS, Fan BY, Pan WL, Li C, Levin AM, Wang X, Zhang RL, Zervos TM, Hu J, Zhang XM, Chopp M, Zhang ZG. Identification of miRNomes associated with adult neurogenesis after stroke using Argonaute 2-based RNA sequencing. RNA Biol 2016; 14:488-499. [PMID: 27315491 DOI: 10.1080/15476286.2016.1196320] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurogenesis is associated with functional recovery after stroke. However, the underlying molecular mechanisms have not been fully investigated. Using an Ago2-based RNA immunoprecipitation to immunoprecipated Ago2-RNA complexes followed by RNA sequencing (Ago2 RIP-seq) approach, we profiled the miRNomes in neural progenitor cells (NPCs) harvested from the subventricular zone (SVZ) of the lateral ventricles of young adult rats. We identified more than 7 and 15 million reads in normal and ischemic NPC libraries, respectively. We found that stroke substantially changed Ago2-associated miRNA profiles in NPCs compared to those in non-ischemic NPCs. We also discovered a new complex repertoire of isomiRs and multiple miRNA-miRNA* pairs and numerous novel miRNAs in the non-ischemic and ischemic NPCs. Among them, pc-3p-17172 significantly regulated NPC proliferation and neuronal differentiation. Collectively, the present study reveals profiles of Ago2-associated miRNomes in non-ischemic and ischemic NPCs, which provide a molecular basis to further investigate the role of miRNAs in mediating adult neurogenesis under physiological and ischemic conditions.
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Affiliation(s)
- Xian Shuang Liu
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
| | - Bao Yan Fan
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
| | - Wan Long Pan
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA.,b Sichuan Key Laboratory of Medical Imaging and Department of Immunology , North Sichuan Medical University , Nanchong , Sichuan , China
| | - Chao Li
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
| | - Albert M Levin
- c Department of Public Health Sciences , Henry Ford Health System , Detroit , MI , USA.,d Center for Bioinformatics , Henry Ford Health System , Detroit , MI , USA
| | - Xinli Wang
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
| | - Rui Lan Zhang
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
| | - Thomas M Zervos
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
| | - Jiani Hu
- e Department of Radiology , Wayne State University , Detroit , MI , USA
| | - Xiao Ming Zhang
- f Sichuan Key Laboratory of Medical Imaging and Department of Radiology , Affiliated Hospital of North Sichuan Medical University , Nanchong , Sichuan , China
| | - Michael Chopp
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA.,g Department of Physics , Oakland University , Rochester , MI , USA
| | - Zheng Gang Zhang
- a Department of Neurology , Henry Ford Health System , Detroit , MI , USA
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124
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Liu H, Robinson GE, Jakobsson E. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PLoS Comput Biol 2016; 12:e1004921. [PMID: 27359102 PMCID: PMC4928799 DOI: 10.1371/journal.pcbi.1004921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 04/17/2016] [Indexed: 01/11/2023] Open
Abstract
The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for social organization.
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Affiliation(s)
- Hui Liu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eric Jakobsson
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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125
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Seok H, Ham J, Jang ES, Chi SW. MicroRNA Target Recognition: Insights from Transcriptome-Wide Non-Canonical Interactions. Mol Cells 2016; 39:375-81. [PMID: 27117456 PMCID: PMC4870184 DOI: 10.14348/molcells.2016.0013] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 11/27/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (∼22 nucleotides) regulating gene expression at the post-transcriptional level. By directing the RNA-induced silencing complex (RISC) to bind specific target mRNAs, miRNA can repress target genes and affect various biological phenotypes. Functional miRNA target recognition is known to majorly attribute specificity to consecutive pairing with seed region (position 2-8) of miRNA. Recent advances in a transcriptome-wide method of mapping miRNA binding sites (Ago HITS-CLIP) elucidated that a large portion of miRNA-target interactions in vivo are mediated not only through the canonical "seed sites" but also via non-canonical sites (∼15-80%), setting the stage to expand and determine their properties. Here we focus on recent findings from transcriptome-wide non-canonical miRNA-target interactions, specifically regarding "nucleation bulges" and "seed-like motifs". We also discuss insights from Ago HITS-CLIP data alongside structural and biochemical studies, which highlight putative mechanisms of miRNA target recognition, and the biological significance of these non-canonical sites mediating marginal repression.
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Affiliation(s)
- Heeyoung Seok
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841,
Korea
| | - Juyoung Ham
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351,
Korea
| | | | - Sung Wook Chi
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841,
Korea
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126
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Cai P, Liu S, Piao X, Hou N, Gobert GN, McManus DP, Chen Q. Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum. PLoS Negl Trop Dis 2016; 10:e0004684. [PMID: 27128440 PMCID: PMC4851400 DOI: 10.1371/journal.pntd.0004684] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/12/2016] [Indexed: 12/23/2022] Open
Abstract
Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes) of the genus Schistosoma. Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex biological processes. In the current study, a 41,982 features custom DNA microarray, which represents the most comprehensive probe coverage for any schistosome transcriptome study, was designed based on public domain and local databases to explore differential gene expression in S. japonicum. We found that approximately 1/10 of the total annotated genes in the S. japonicum genome are differentially expressed between adult males and females. In general, genes associated with the cytoskeleton, and motor and neuronal activities were readily expressed in male adult worms, whereas genes involved in amino acid metabolism, nucleotide biosynthesis, gluconeogenesis, glycosylation, cell cycle processes, DNA synthesis and genome fidelity and stability were enriched in females. Further, miRNAs target sites within these gene sets were predicted, which provides a scenario whereby the miRNAs potentially regulate these sex-biased expressed genes. The study significantly expands the expressional and regulatory characteristics of gender-biased expressed genes in schistosomes with high accuracy. The data provide a better appreciation of the biological and physiological features of male and female schistosome parasites, which may lead to novel vaccine targets and the development of new therapeutic interventions.
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Affiliation(s)
- Pengfei Cai
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Shuai Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Xianyu Piao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Nan Hou
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Geoffrey N. Gobert
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Qijun Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Key Laboratory of Zoonosis, Shenyang Agriculture University, Shenyang, P.R. China
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127
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Hauberg ME, Roussos P, Grove J, Børglum AD, Mattheisen M. Analyzing the Role of MicroRNAs in Schizophrenia in the Context of Common Genetic Risk Variants. JAMA Psychiatry 2016; 73:369-77. [PMID: 26963595 PMCID: PMC7005318 DOI: 10.1001/jamapsychiatry.2015.3018] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
IMPORTANCE The recent implication of 108 genomic loci in schizophrenia marked a great advancement in our understanding of the disease. Against the background of its polygenic nature there is a necessity to identify how schizophrenia risk genes interplay. As regulators of gene expression, microRNAs (miRNAs) have repeatedly been implicated in schizophrenia etiology. It is therefore of interest to establish their role in the regulation of schizophrenia risk genes in disease-relevant biological processes. OBJECTIVE To examine the role of miRNAs in schizophrenia in the context of disease-associated genetic variation. DESIGN, SETTING, AND PARTICIPANTS The basis of this study was summary statistics from the largest schizophrenia genome-wide association study meta-analysis to date (83 550 individuals in a meta-analysis of 52 genome-wide association studies) completed in 2014 along with publicly available data for predicted miRNA targets. We examined whether schizophrenia risk genes were more likely to be regulated by miRNA. Further, we used gene set analyses to identify miRNAs that are regulators of schizophrenia risk genes. MAIN OUTCOMES AND MEASURES Results from association tests for miRNA targetomes and related analyses. RESULTS In line with previous studies, we found that similar to other complex traits, schizophrenia risk genes were more likely to be regulated by miRNAs (P < 2 × 10-16). Further, the gene set analyses revealed several miRNAs regulating schizophrenia risk genes, with the strongest enrichment for targets of miR-9-5p (P = .0056 for enrichment among the top 1% most-associated single-nucleotide polymorphisms, corrected for multiple testing). It is further of note that MIR9-2 is located in a genomic region showing strong evidence for association with schizophrenia (P = 7.1 × 10-8). The second and third strongest gene set signals were seen for the targets of miR-485-5p and miR-137, respectively. CONCLUSIONS AND RELEVANCE This study provides evidence for a role of miR-9-5p in the etiology of schizophrenia. Its implication is of particular interest as the functions of this neurodevelopmental miRNA tie in with established disease biology: it has a regulatory loop with the fragile X mental retardation homologue FXR1 and regulates dopamine D2 receptor density.
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Affiliation(s)
- Mads Engel Hauberg
- Department of Biomedicine, Aarhus University, Aarhus, Denmark2Lundbeck Foundation Initiative of Integrative Psychiatric Research, Lundbeck, Denmark3Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York5Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York6Institute for Genomics and Multiscale Biology, Icahn School of M
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark2Lundbeck Foundation Initiative of Integrative Psychiatric Research, Lundbeck, Denmark3Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark9Bioinformatics Research Centre, Aarhu
| | - Anders Dupont Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark2Lundbeck Foundation Initiative of Integrative Psychiatric Research, Lundbeck, Denmark3Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark10Research Department P, Aarhus Univer
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark2Lundbeck Foundation Initiative of Integrative Psychiatric Research, Lundbeck, Denmark3Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
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128
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Kim S, Seo D, Kim D, Hong Y, Chang H, Baek D, Kim VN, Lee S, Ahn K. Temporal Landscape of MicroRNA-Mediated Host-Virus Crosstalk during Productive Human Cytomegalovirus Infection. Cell Host Microbe 2016; 17:838-51. [PMID: 26067606 DOI: 10.1016/j.chom.2015.05.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/16/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
Temporal profiles of miRNA activity during productive virus infection can provide fundamental insights into host-virus interactions. Most reported miRNA targetome analyses in the context of virus infection have been performed in latently infected cells and lack reliable models for quantifying the suppression efficacy at specific miRNA target sites. Here, we identified highly competent temporal miRNA targetomes during lytic HCMV infection by using AGO-CLIP-seq together with a bioinformatic method that quantifies miRNA functionality at a specific target site, called ACE-scoring. The repression efficiency at target sites correlates with the magnitude of the ACE-score, and temporal HCMV-encoded miRNA targetomes identified by ACE-scoring were significantly enriched in functional categories involved in pathways central for HCMV biology. Furthermore, comparative analysis between human and viral miRNA targetomes supports the existence of intimate cooperation and co-targeting between them. Our holistic survey provides a valuable resource for understanding host-virus interactions during lytic HCMV infection.
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Affiliation(s)
- Sungchul Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea
| | - Daekwan Seo
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea
| | - Dongwoo Kim
- School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea
| | - Yujin Hong
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea
| | - Daehyun Baek
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea; Bioinformatics Institute, Seoul National University, Seoul 151-747, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea
| | - Sungwook Lee
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Kwangseog Ahn
- Center for RNA Research, Institute for Basic Science (IBS), Seoul 151-742, Korea; School for Biological Sciences, Seoul National University (SNU), Seoul 151-742, Korea.
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129
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MicroRNA-222 regulates muscle alternative splicing through Rbm24 during differentiation of skeletal muscle cells. Cell Death Dis 2016; 7:e2086. [PMID: 26844700 PMCID: PMC4849150 DOI: 10.1038/cddis.2016.10] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/15/2015] [Accepted: 01/03/2016] [Indexed: 02/01/2023]
Abstract
A number of microRNAs have been shown to regulate skeletal muscle development and differentiation. MicroRNA-222 is downregulated during myogenic differentiation and its overexpression leads to alteration of muscle differentiation process and specialized structures. By using RNA-induced silencing complex (RISC) pulldown followed by RNA sequencing, combined with in silico microRNA target prediction, we have identified two new targets of microRNA-222 involved in the regulation of myogenic differentiation, Ahnak and Rbm24. Specifically, the RNA-binding protein Rbm24 is a major regulator of muscle-specific alternative splicing and its downregulation by microRNA-222 results in defective exon inclusion impairing the production of muscle-specific isoforms of Coro6, Fxr1 and NACA transcripts. Reconstitution of normal levels of Rbm24 in cells overexpressing microRNA-222 rescues muscle-specific splicing. In conclusion, we have identified a new function of microRNA-222 leading to alteration of myogenic differentiation at the level of alternative splicing, and we provide evidence that this effect is mediated by Rbm24 protein.
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130
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Stražar M, Žitnik M, Zupan B, Ule J, Curk T. Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. Bioinformatics 2016; 32:1527-35. [PMID: 26787667 PMCID: PMC4894278 DOI: 10.1093/bioinformatics/btw003] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/01/2016] [Indexed: 12/15/2022] Open
Abstract
Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control of gene expression, including splicing, transport, polyadenylation and RNA stability. To model protein–RNA interactions by considering all available sources of information, it is necessary to integrate the rapidly growing RBP experimental data with the latest genome annotation, gene function, RNA sequence and structure. Such integration is possible by matrix factorization, where current approaches have an undesired tendency to identify only a small number of the strongest patterns with overlapping features. Because protein–RNA interactions are orchestrated by multiple factors, methods that identify discriminative patterns of varying strengths are needed. Results: We have developed an integrative orthogonality-regularized nonnegative matrix factorization (iONMF) to integrate multiple data sources and discover non-overlapping, class-specific RNA binding patterns of varying strengths. The orthogonality constraint halves the effective size of the factor model and outperforms other NMF models in predicting RBP interaction sites on RNA. We have integrated the largest data compendium to date, which includes 31 CLIP experiments on 19 RBPs involved in splicing (such as hnRNPs, U2AF2, ELAVL1, TDP-43 and FUS) and processing of 3’UTR (Ago, IGF2BP). We show that the integration of multiple data sources improves the predictive accuracy of retrieval of RNA binding sites. In our study the key predictive factors of protein–RNA interactions were the position of RNA structure and sequence motifs, RBP co-binding and gene region type. We report on a number of protein-specific patterns, many of which are consistent with experimentally determined properties of RBPs. Availability and implementation: The iONMF implementation and example datasets are available at https://github.com/mstrazar/ionmf. Contact: tomaz.curk@fri.uni-lj.si Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin Stražar
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia
| | - Marinka Žitnik
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia
| | - Blaž Zupan
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Tomaž Curk
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia
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131
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Jönsson ME, Nelander Wahlestedt J, Åkerblom M, Kirkeby A, Malmevik J, Brattaas PL, Jakobsson J, Parmar M. Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor. Development 2016; 142:3166-77. [PMID: 26395143 PMCID: PMC4582174 DOI: 10.1242/dev.122747] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
MicroRNAs (miRNAs) have been implicated in regulating multiple processes during brain development in various species. However, the function of miRNAs in human brain development remains largely unexplored. Here, we provide a comprehensive analysis of miRNA expression of regionalized neural progenitor cells derived from human embryonic stem cells and human foetal brain. We found miR-92b-3p and miR-130b-5p to be specifically associated with neural progenitors and several miRNAs that display both age-specific and region-specific expression patterns. Among these miRNAs, we identified miR-10 to be specifically expressed in the human hindbrain and spinal cord, while being absent from rostral regions. We found that miR-10 regulates a large number of genes enriched for functions including transcription, actin cytoskeleton and ephrin receptor signalling. When overexpressed, miR-10 influences caudalization of human neural progenitor cells. Together, these data confirm a role for miRNAs in establishing different human neural progenitor populations. This dataset also provides a comprehensive resource for future studies investigating the functional role of different miRNAs in human brain development. Summary: The profiling of neural progenitors derived from human ESCs and foetal brain shows that miRNAs display region-specific expression patterns, suggesting that they contribute to establishing regional identity.
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Affiliation(s)
- Marie E Jönsson
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Jenny Nelander Wahlestedt
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Malin Åkerblom
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Agnete Kirkeby
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Josephine Malmevik
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Per Ludvik Brattaas
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Johan Jakobsson
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
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132
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Maragkakis M, Alexiou P, Nakaya T, Mourelatos Z. CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite. RNA (NEW YORK, N.Y.) 2016; 22:1-9. [PMID: 26577377 PMCID: PMC4691824 DOI: 10.1261/rna.052167.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/18/2015] [Indexed: 05/22/2023]
Abstract
Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
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Affiliation(s)
- Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tadashi Nakaya
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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133
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Lee HS, Seok H, Lee DH, Ham J, Lee W, Youm EM, Yoo JS, Lee YS, Jang ES, Chi SW. Abasic pivot substitution harnesses target specificity of RNA interference. Nat Commun 2015; 6:10154. [PMID: 26679372 PMCID: PMC4703836 DOI: 10.1038/ncomms10154] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/08/2015] [Indexed: 01/06/2023] Open
Abstract
Gene silencing via RNA interference inadvertently represses hundreds of off-target transcripts. Because small interfering RNAs (siRNAs) can function as microRNAs, avoiding miRNA-like off-target repression is a major challenge. Functional miRNA-target interactions are known to pre-require transitional nucleation, base pairs from position 2 to the pivot (position 6). Here, by substituting nucleotide in pivot with abasic spacers, which prevent base pairing and alleviate steric hindrance, we eliminate miRNA-like off-target repression while preserving on-target activity at ∼ 80-100%. Specifically, miR-124 containing dSpacer pivot substitution (6pi) loses seed-mediated transcriptome-wide target interactions, repression activity and biological function, whereas other conventional modifications are ineffective. Application of 6pi allows PCSK9 siRNA to efficiently lower plasma cholesterol concentration in vivo, and abolish potentially deleterious off-target phenotypes. The smallest spacer, C3, also shows the same improvement in target specificity. Abasic pivot substitution serves as a general means to harness the specificity of siRNA experiments and therapeutic applications.
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Affiliation(s)
- Hye-Sook Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Heeyoung Seok
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Dong Ha Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 135-710, Korea
| | - Juyoung Ham
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 135-710, Korea
| | - Wooje Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Emilia Moonkyung Youm
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 135-710, Korea
| | - Jin Seon Yoo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 135-710, Korea
| | | | - Eun-Sook Jang
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 135-710, Korea.,EncodeGEN Co. Ltd., Seoul 135-994, Korea
| | - Sung Wook Chi
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 135-710, Korea.,Samsung Research Institute for Future Medicine, Samsung Medical Center, Seoul 135-710, Korea
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134
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Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. Neuron 2015; 89:113-28. [PMID: 26687839 DOI: 10.1016/j.neuron.2015.11.025] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/03/2015] [Accepted: 11/06/2015] [Indexed: 12/31/2022]
Abstract
Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate the function of cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that Rbfox1 bound predominantly to introns in nascent RNA, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and Rbfox1 and miRNA binding sites overlapped significantly. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease.
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Affiliation(s)
- Ji-Ann Lee
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mariana Fontes
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neelroop N Parikshak
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Erik S Anderson
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kelsey C Martin
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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135
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Kabaria S, Choi DC, Chaudhuri AD, Jain MR, Li H, Junn E. MicroRNA-7 activates Nrf2 pathway by targeting Keap1 expression. Free Radic Biol Med 2015; 89:548-56. [PMID: 26453926 PMCID: PMC4684759 DOI: 10.1016/j.freeradbiomed.2015.09.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/30/2022]
Abstract
Nuclear factor E2-related factor 2 (Nrf2) is a key transcription factor that regulates the expression of a number of antioxidant and detoxifying genes that provide cellular protection against various stressors including reactive oxygen species (ROS). Nrf2 activity is tightly regulated by a cytoplasmic inhibitory protein called Kelch-like ECH-associated protein 1 (Keap1). The mechanism that controls Keap1 expression, however, remains poorly understood. In the present study, we demonstrate that microRNA-7 (miR-7), which is highly expressed in the brain, represses Keap1 expression by targeting the 3'-untranslated region (UTR) of its mRNA in human neuroblastoma cells, SH-SY5Y. Subsequently, this event results in an increased Nrf2 activity, as evidenced by an increase in the expression of its transcriptional targets, heme oxygenase 1 (HO-1) and glutamate-cysteine ligase modifier subunit (GCLM), and an enhanced nuclear localization of Nrf2. In addition, miR-7 decreases the intracellular hydroperoxides level and increases the level of reduced form of glutathione, indicative of oxidative stress relief. We also demonstrate that targeted repression of Keap1 and activation of Nrf2 pathway, in part, underlies the protective effects of miR-7 against 1-methyl-4-phenylpyridinium (MPP+)-induced toxicity in SH-SY5Y and differentiated human neural progenitor cells, ReNcell VM. These findings point to a new mechanism by which miR-7 exerts cytoprotective effects by regulating the Nrf2 pathway.
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Affiliation(s)
- Savan Kabaria
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ., 08854, USA
| | - Doo Chul Choi
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ., 08854, USA
| | - Amrita Datta Chaudhuri
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ., 08854, USA
| | - Mohit Raja Jain
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, NJ., 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, NJ., 07103, USA
| | - Eunsung Junn
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ., 08854, USA.
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136
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Identification of microRNAs and microRNA targets in Xenopus gastrulae: The role of miR-26 in the regulation of Smad1. Dev Biol 2015; 409:26-38. [PMID: 26548531 DOI: 10.1016/j.ydbio.2015.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 10/20/2015] [Accepted: 11/04/2015] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are known to play diverse roles in the regulation of vertebrate development. To investigate miRNA-target mRNA relationships in embryonic development, we have carried out small-RNA sequencing to identify miRNAs expressed in the early gastrula of Xenopus laevis. We identify a total of 180 miRNAs, and we have identified the locations of the miRNA precursor sequences in the X. laevis genome. Of these miRNAs, 141 represent miRs previously identified in Xenopus tropicalis. Alignment to human miRNAs led to the identification of 39 miRNAs that have not previously been described for Xenopus. We have also used a biochemical approach to isolate mRNAs that are associated with the RNA-Induced Silencing Complex (RISC) in early gastrulae and thus candidate targets of miRNA-dependent regulation. Interrogation of this RISC-associated mRNA pool by RT-PCR indicates that a number of genes essential for early patterning and specification may be under regulation by miRNAs. Smad1 transcripts are associated with the RISC; target prediction algorithms identify a single miRNA-binding site for miR-26, which is common to the 3'UTRs of Smad1a and Smad1b. Disruption of the interaction between miR-26 and the Smad1 3'UTR via a Target Protector Morpholino Oligonucleotide (TPMO) leads to a 2-fold increase in Smad1 protein accumulation, moderate increases in the expression of BMP4/Smad1 target genes, and a reduction in organizer gene expression, as well as a partially ventralized phenotype in approximately 25% of embryos. Overexpression of miR-26 resulted in moderately decreased expression of Smad1-dependent genes and an expansion of the region expressing the Organizer gene not1. Our findings indicate that interactions between miR-26 and the Smad1 3'UTR modulate Smad1 function in the establishment of axial patterning; they also establish a foundation for the functional analysis of miRNAs and their regulatory interactions during gastrulation.
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137
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Dysregulated RNA-Induced Silencing Complex (RISC) Assembly within CNS Corresponds with Abnormal miRNA Expression during Autoimmune Demyelination. J Neurosci 2015; 35:7521-37. [PMID: 25972178 DOI: 10.1523/jneurosci.4794-14.2015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) associate with Argonaute (Ago), GW182, and FXR1 proteins to form RNA-induced silencing complexes (RISCs). RISCs represent a critical checkpoint in the regulation and bioavailability of miRNAs. Recent studies have revealed dysregulation of miRNAs in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE); however, the function of RISCs in EAE and MS is largely unknown. Here, we examined the expression of Ago, GW182, and FXR1 in CNS tissue, oligodendrocytes (OLs), brain-infiltrating T lymphocytes, and CD3(+)splenocytes (SCs) of EAE mic, and found that global RISC protein levels were significantly dysregulated. Specifically, Ago2 and FXR1 levels were decreased in OLs and brain-infiltrating T cells in EAE mice. Accordingly, assembly of Ago2/GW182/FXR1 complexes in EAE brain tissues was disrupted, as confirmed by immunoprecipitation experiments. In parallel with alterations in RISC complex content in OLs, we found downregulation of miRNAs essential for differentiation and survival of OLs and myelin synthesis. In brain-infiltrating T lymphocytes, aberrant RISC formation contributed to miRNA-dependent proinflammatory helper T-cell polarization. In CD3(+) SCs, we found increased expression of both Ago2 and FXR1 in EAE compared with nonimmunized mice. Therefore, our results demonstrate a gradient in expression of miRNA between primary activated T cells in the periphery and polarized CNS-infiltrating T cells. These results suggest that, in polarized autoreactive effector T cells, miRNA synthesis is inhibited in response to dysregulated RISC assembly, allowing these cells to maintain a highly specific proinflammatory program. Therefore, our findings may provide a mechanism that leads to miRNA dysregulation in EAE/MS.
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138
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Pathophysiological role of microRNA-29 in pancreatic cancer stroma. Sci Rep 2015; 5:11450. [PMID: 26095125 PMCID: PMC4476113 DOI: 10.1038/srep11450] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/26/2015] [Indexed: 12/24/2022] Open
Abstract
Dense fibrotic stroma associated with pancreatic ductal adenocarcinoma (PDAC) is a major obstacle for drug delivery to the tumor bed and plays a crucial role in pancreatic cancer progression. Current, anti-stromal therapies have failed to improve tumor response to chemotherapy and patient survival. Furthermore, recent studies show that stroma impedes tumor progression, and its complete ablation accelerates PDAC progression. In an effort to understand the molecular mechanisms associated with tumor-stromal interactions, using in vitro and in vivo models and PDAC patient biopsies, we show that the loss of miR-29 is a common phenomenon of activated pancreatic stellate cells (PSCs)/fibroblasts, the major stromal cells responsible for fibrotic stromal reaction. Loss of miR-29 is correlated with a significant increase in extracellular matrix (ECM) deposition, a major component in PDAC stroma. Our in vitro miR-29 gain/loss-of-function studies document the role of miR-29 in PSC-mediated ECM stromal protein accumulation. Overexpression of miR-29 in activated stellate cells reduced stromal deposition, cancer cell viability, and cancer growth in co-culture. Furthermore, the loss of miR-29 in TGF-β1 activated PSCs is SMAD3 dependent. These results provide insights into the mechanistic role of miR-29 in PDAC stroma and its potential use as a therapeutic agent to target PDAC.
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139
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Hommers L, Raab A, Bohl A, Weber H, Scholz CJ, Erhardt A, Binder E, Arolt V, Gerlach A, Gloster A, Kalisch R, Kircher T, Lonsdorf T, Ströhle A, Zwanzger P, Mattheisen M, Cichon S, Lesch KP, Domschke K, Reif A, Lohse MJ, Deckert J. MicroRNA hsa-miR-4717-5p regulates RGS2 and may be a risk factor for anxiety-related traits. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:296-306. [PMID: 25847876 DOI: 10.1002/ajmg.b.32312] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 03/17/2015] [Indexed: 12/30/2022]
Abstract
Regulator of G-protein Signaling 2 (RGS2) is a key regulator of G-protein-coupled signaling pathways involved in fear and anxiety. Data from rodent models and genetic analysis of anxiety-related traits and disorders in humans suggest down-regulation of RGS2 expression to be a risk factor for anxiety. Here we investigated, whether genetic variation in microRNAs mediating posttranscriptional down-regulation of RGS2 may be a risk factor for anxiety as well. 75 microRNAs predicted to regulate RGS2 were identified by four bioinformatic algorithms and validated experimentally by luciferase reporter gene assays. Specificity was confirmed for six microRNAs (hsa-miR-1271-5p, hsa-miR-22-3p, hsa-miR-3591-3p, hsa-miR-377-3p, hsa-miR-4717-5p, hsa-miR-96-5p) by disrupting their seed sequence at the 3' untranslated region of RGS2. Hsa-miR-4717-5p showed the most robust effect on RGS2 and regulated two other candidate genes of anxiety disorders (CNR1 and IKBKE) as well. Two SNPs (rs150925, rs161427) within and 1,000 bp upstream of the hostgene of hsa-miR-4717-5p (MIR4717) show a minor allele frequency greater than 0.05. Both were in high linkage disequilibrium (r(2) = 1, D' = 1) and both major (G) alleles showed a trend for association with panic disorder with comorbid agoraphobia in one of two patient/control samples (combined n(patients) = 497). Dimensional anxiety traits, as described by Anxiety Sensitivity Index (ASI) and Agoraphobic Cognitions Questionnaire (ACQ) were significantly higher among carriers of both major (G) alleles in a combined patient/control sample (n(combined) = 831). Taken together, data indicate that MIR4717 regulates human RGS2 and contributes to the genetic risk towards anxiety-related traits.
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Affiliation(s)
- Leif Hommers
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany.,Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Würzburg, Germany.,Comprehensive Heart Failure Center (CHFC), University Hospital of Würzburg, Würzburg, Germany
| | - Annette Raab
- Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Würzburg, Germany
| | - Alexandra Bohl
- Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Würzburg, Germany
| | - Heike Weber
- Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Würzburg, Germany
| | - Claus-Jürgen Scholz
- Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Würzburg, Germany
| | | | | | - Volker Arolt
- Department of Psychiatry, University of Muenster, Muenster, Germany
| | - Alexander Gerlach
- Department of Clinical Psychology and Psychotherapy, University of Cologne, Cologne, Germany
| | - Andrew Gloster
- Institute of Clinical Psychology and Psychotherapy, Technische Universität Dresden, Dresden, Germany
| | - Raffael Kalisch
- Neuroimaging Center Mainz, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, Philipps University Marburg, Marburg, Germany
| | - Tina Lonsdorf
- Institute for Systems Neuroscience, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Ströhle
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Zwanzger
- Department of Psychiatry, University of Muenster, Muenster, Germany
| | - Manuel Mattheisen
- Department of Biomedicine and Centre for integrative Sequencing (iSEQ), Aarhus University, Aarhus C, Denmark
| | - Sven Cichon
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Switzerland.,Institute of Human Genetics, Department of Genomics, Life & Brain Center, University of Bonn, Germany.,Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Germany
| | - Klaus-Peter Lesch
- Center of Mental Health, Division of Molecular Psychiatry, University Hospital of Würzburg, Würzburg, Germany
| | - Katharina Domschke
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Andreas Reif
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Martin J Lohse
- Department of Pharmacology, University of Würzburg, Würzburg, Germany
| | - Jürgen Deckert
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
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140
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Qureshi IA, Mehler MF. An evolving view of epigenetic complexity in the brain. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0506. [PMID: 25135967 DOI: 10.1098/rstb.2013.0506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Recent scientific advances have revolutionized our understanding of classical epigenetic mechanisms and the broader landscape of molecular interactions and cellular functions that are inextricably linked to these processes. Our current view of epigenetics includes an increasing appreciation for the dynamic nature of DNA methylation, active mechanisms for DNA demethylation, differential functions of 5-methylcytosine and its oxidized derivatives, the intricate regulatory logic of histone post-translational modifications, the incorporation of histone variants into chromatin, nucleosome occupancy and dynamics, and direct links between cellular signalling pathways and the actions of chromatin 'reader', 'writer' and 'eraser' molecules. We also have an increasing awareness of the seemingly ubiquitous roles played by diverse classes of selectively expressed non-coding RNAs in transcriptional, post-transcriptional, post-translational and local and higher order chromatin modulatory processes. These perspectives are still evolving with novel insights continuing to emerge rapidly (e.g. those related to epigenetic regulation of mobile genetic elements, epigenetic mechanisms in mitochondria, roles in nuclear architecture and 'RNA epigenetics'). The precise functions of these epigenetic factors/phenomena are largely unknown. However, it is unequivocal that they serve as key mediators of brain complexity and flexibility, including neural development and aging, cellular differentiation, homeostasis, stress responses, and synaptic and neural network connectivity and plasticity.
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Affiliation(s)
- Irfan A Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mark F Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA Ruth S. and David L. Gottesman Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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141
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Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res 2015; 43:5263-74. [PMID: 25958398 PMCID: PMC4477666 DOI: 10.1093/nar/gkv439] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/23/2015] [Indexed: 01/05/2023] Open
Abstract
The past decades have witnessed a surge of discoveries revealing RNA regulation as a central player in cellular processes. RNAs are regulated by RNA-binding proteins (RBPs) at all post-transcriptional stages, including splicing, transportation, stabilization and translation. Defects in the functions of these RBPs underlie a broad spectrum of human pathologies. Systematic identification of RBP functional targets is among the key biomedical research questions and provides a new direction for drug discovery. The advent of cross-linking immunoprecipitation coupled with high-throughput sequencing (genome-wide CLIP) technology has recently enabled the investigation of genome-wide RBP–RNA binding at single base-pair resolution. This technology has evolved through the development of three distinct versions: HITS-CLIP, PAR-CLIP and iCLIP. Meanwhile, numerous bioinformatics pipelines for handling the genome-wide CLIP data have also been developed. In this review, we discuss the genome-wide CLIP technology and focus on bioinformatics analysis. Specifically, we compare the strengths and weaknesses, as well as the scopes, of various bioinformatics tools. To assist readers in choosing optimal procedures for their analysis, we also review experimental design and procedures that affect bioinformatics analyses.
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Affiliation(s)
- Tao Wang
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yongjun Chu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA Bioinformatics Division, Center for Synthetic and System Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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142
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Wright C, Calhoun VD, Ehrlich S, Wang L, Turner JA, Bizzozero NIP. Meta gene set enrichment analyses link miR-137-regulated pathways with schizophrenia risk. Front Genet 2015; 6:147. [PMID: 25941532 PMCID: PMC4403556 DOI: 10.3389/fgene.2015.00147] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/27/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND A single nucleotide polymorphism (SNP) within MIR137, the host gene for miR-137, has been identified repeatedly as a risk factor for schizophrenia. Previous genetic pathway analyses suggest that potential targets of this microRNA (miRNA) are also highly enriched in schizophrenia-relevant biological pathways, including those involved in nervous system development and function. METHODS In this study, we evaluated the schizophrenia risk of miR-137 target genes within these pathways. Gene set enrichment analysis of pathway-specific miR-137 targets was performed using the stage 1 (21,856 subjects) schizophrenia genome wide association study data from the Psychiatric Genomics Consortium and a small independent replication cohort (244 subjects) from the Mind Clinical Imaging Consortium and Northwestern University. RESULTS Gene sets of potential miR-137 targets were enriched with variants associated with schizophrenia risk, including target sets involved in axonal guidance signaling, Ephrin receptor signaling, long-term potentiation, PKA signaling, and Sertoli cell junction signaling. The schizophrenia-risk association of SNPs in PKA signaling targets was replicated in the second independent cohort. CONCLUSIONS These results suggest that these biological pathways may be involved in the mechanisms by which this MIR137 variant enhances schizophrenia risk. SNPs in targets and the miRNA host gene may collectively lead to dysregulation of target expression and aberrant functioning of such implicated pathways. Pathway-guided gene set enrichment analyses should be useful in evaluating the impact of other miRNAs and target genes in different diseases.
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Affiliation(s)
- Carrie Wright
- The Mind Research NetworkAlbuquerque, NM, USA
- Department of Neurosciences, University of New MexicoAlbuquerque, NM, USA
| | - Vince D. Calhoun
- The Mind Research NetworkAlbuquerque, NM, USA
- Department of Neurosciences, University of New MexicoAlbuquerque, NM, USA
- Department of Electrical and Computer Engineering, University of New MexicoAlbuquerque, NM, USA
| | - Stefan Ehrlich
- Translational Developmental Neuroscience Section, Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität DresdenDresden, Germany
- Department of Psychiatry, Harvard Medical School, Massachusetts General HospitalBoston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Massachusetts Institute of Technology/Harvard Medical SchoolCharlestown, MA, USA
| | - Lei Wang
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of MedicineChicago, IL, USA
- Department of Radiology, Northwestern University Feinberg School of MedicineChicago, IL, USA
| | - Jessica A. Turner
- The Mind Research NetworkAlbuquerque, NM, USA
- Department of Psychology and Neuroscience Institute, Georgia State UniversityAtlanta, GA, USA
| | - Nora I. Perrone- Bizzozero
- Department of Neurosciences, University of New MexicoAlbuquerque, NM, USA
- Department of Psychiatry, University of New MexicoAlbuquerque, NM, USA
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143
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Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc Natl Acad Sci U S A 2015; 112:E1106-15. [PMID: 25713380 DOI: 10.1073/pnas.1420955112] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two decades after the discovery of the first animal microRNA (miRNA), the number of miRNAs in animal genomes remains a vexing question. Here, we report findings from analyzing 1,323 short RNA sequencing samples (RNA-seq) from 13 different human tissue types. Using stringent thresholding criteria, we identified 3,707 statistically significant novel mature miRNAs at a false discovery rate of ≤ 0.05 arising from 3,494 novel precursors; 91.5% of these novel miRNAs were identified independently in 10 or more of the processed samples. Analysis of these novel miRNAs revealed tissue-specific dependencies and a commensurate low Jaccard similarity index in intertissue comparisons. Of these novel miRNAs, 1,657 (45%) were identified in 43 datasets that were generated by cross-linking followed by Argonaute immunoprecipitation and sequencing (Ago CLIP-seq) and represented 3 of the 13 tissues, indicating that these miRNAs are active in the RNA interference pathway. Moreover, experimental investigation through stem-loop PCR of a random collection of newly discovered miRNAs in 12 cell lines representing 5 tissues confirmed their presence and tissue dependence. Among the newly identified miRNAs are many novel miRNA clusters, new members of known miRNA clusters, previously unreported products from uncharacterized arms of miRNA precursors, and previously unrecognized paralogues of functionally important miRNA families (e.g., miR-15/107). Examination of the sequence conservation across vertebrate and invertebrate organisms showed 56.7% of the newly discovered miRNAs to be human-specific whereas the majority (94.4%) are primate lineage-specific. Our findings suggest that the repertoire of human miRNAs is far more extensive than currently represented by public repositories and that there is a significant number of lineage- and/or tissue-specific miRNAs that are uncharacterized.
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Abstract
Over 100 loci are now associated with schizophrenia risk as identified by single nucleotide polymorphisms (SNPs) in genome-wide association studies. These findings mean that 'genes for schizophrenia' have unquestionably been found. However, many questions remain unanswered, including several which affect their therapeutic significance. The SNPs individually have minor effects, and even cumulatively explain only a modest fraction of the genetic predisposition. The remainder likely results from many more loci, from rare variants, and from gene-gene and gene-environment interactions. The risk SNPs are almost all non-coding, meaning that their biological significance is unclear; probably their effects are mediated via an influence on gene regulation, and emerging evidence suggests that some key molecular events occur during early brain development. The loci include novel genes of unknown function as well as genes and pathways previously implicated in the pathophysiology of schizophrenia, e.g. NMDA receptor signalling. Genes in the latter category have the clearer therapeutic potential, although even this will be a challenging process because of the many complexities concerning the genetic architecture and mediating mechanisms. This review summarises recent schizophrenia genetic findings and some key issues they raise, particularly with regard to their implications for identifying and validating novel drug targets.
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Affiliation(s)
- Paul J Harrison
- University Department of Psychiatry, Warneford Hospital, Oxford, UK
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145
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Abernathy DG, Yoo AS. MicroRNA-dependent genetic networks during neural development. Cell Tissue Res 2015; 359:179-85. [PMID: 24865244 PMCID: PMC4247364 DOI: 10.1007/s00441-014-1899-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/15/2014] [Indexed: 12/21/2022]
Abstract
The development of the structurally and functionally diverse mammalian nervous system requires the integration of numerous levels of gene regulation. Accumulating evidence suggests that microRNAs are key mediators of genetic networks during neural development. Importantly, microRNAs are found to regulate both feedback and feedforward loops during neural development leading to large changes in gene expression. These repressive interactions provide an additional mechanism that facilitates the establishment of complexity within the nervous system. Here, we review studies that have enabled the identification of microRNAs enriched in the brain and discuss the way that genetic networks in neural development depend on microRNAs.
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Affiliation(s)
- Daniel G Abernathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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146
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Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T. ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. Cell Rep 2014; 9:2330-43. [PMID: 25533351 DOI: 10.1016/j.celrep.2014.11.030] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 09/17/2014] [Accepted: 11/19/2014] [Indexed: 12/19/2022] Open
Abstract
Posttranscriptional gene regulation by miRNAs and RNA binding proteins (RBP) is important in development, physiology, and disease. To examine the interplay between miRNAs and the RBP ELAVL1 (HuR), we mapped miRNA binding sites at the transcriptome-wide scale in wild-type and Elavl1 knockout murine bone-marrow-derived macrophages. Proximity of ELAVL1 binding sites attenuated miRNA binding to transcripts and promoted gene expression. Transcripts that regulate angiogenesis and macrophage/endothelial crosstalk were preferentially targeted by miRNAs, suggesting that ELAVL1 promotes angiogenesis, at least in part by antagonism of miRNA function. We found that ELAVL1 antagonized binding of miR-27 to the 3' UTR of Zfp36 mRNA and alleviated miR-27-mediated suppression of the RBP ZFP36 (Tristetraprolin). Thus, the miR-27-regulated mechanism synchronizes the expression of ELAVL1 and ZFP36. This study provides a resource for systems-level interrogation of posttranscriptional gene regulation in macrophages, a key cell type in inflammation, angiogenesis, and tissue homeostasis.
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Affiliation(s)
- Yi-Chien Lu
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Sung-Hee Chang
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Xi Li
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Timothy Hla
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
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147
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Campbell K, Booth SA. MicroRNA in neurodegenerative drug discovery: the way forward? Expert Opin Drug Discov 2014; 10:9-16. [DOI: 10.1517/17460441.2015.981254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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148
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Hommers LG, Domschke K, Deckert J. Heterogeneity and individuality: microRNAs in mental disorders. J Neural Transm (Vienna) 2014; 122:79-97. [PMID: 25395183 DOI: 10.1007/s00702-014-1338-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/07/2014] [Indexed: 12/21/2022]
Abstract
MicroRNAs are about 22 nucleotide long single-stranded RNA molecules, negatively regulating gene expression of a single gene or a gene network. In neural tissues, they have been implicated in developmental and neuroplasticity-related processes, such as neurogenesis, differentiation, apoptosis and long-term potentiation. Their molecular mode of action is reminiscent of findings of genome-wide association studies in mental disorders, unable to attribute the risk of disease to a specific gene, but rather to multiple genes, gene-networks and gene-environment interaction. As such, microRNAs are an attractive target for research. Here, we review clinical studies conducted in humans on microRNAs in mental disorders with a particular focus on schizophrenia, bipolar disorder, major depressive disorder and anxiety disorders. The majority of clinical studies have focused on schizophrenia. The most robust finding has been reported for rs1625579 located in MIR137HG, which was associated with schizophrenia on a genome-wide level. Concerning bipolar disorder, major depression and anxiety disorders, promising results have been published, but only a considerably smaller number of clinical studies is available and genome-wide association studies did not suggest a direct link to microRNAs so far. Expression of microRNAs as biomarkers of mental disorders and treatment response is currently emerging with preliminary results. Larger-scaled genetic and functional studies along with translational research are needed to enhance our understanding of microRNAs in mental disorders. These studies will aid in disentangling the complex genetic nature of these disorders and possibly contribute to the development of novel, individualized diagnostic and therapeutic approaches.
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Affiliation(s)
- Leif G Hommers
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Füchsleinstrasse 15, 97080, Würzburg, Germany,
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MicroRNAs in Schizophrenia: Implications for Synaptic Plasticity and Dopamine-Glutamate Interaction at the Postsynaptic Density. New Avenues for Antipsychotic Treatment Under a Theranostic Perspective. Mol Neurobiol 2014; 52:1771-1790. [PMID: 25394379 DOI: 10.1007/s12035-014-8962-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/23/2014] [Indexed: 12/17/2022]
Abstract
Despite dopamine-glutamate aberrant interaction that has long been considered a relevant landmark of psychosis pathophysiology, several aspects of these two neurotransmitters reciprocal interaction remain to be defined. The emerging role of postsynaptic density (PSD) proteins at glutamate synapse as a molecular "lego" making a functional hub where different signals converge may add a new piece of information to understand how dopamine-glutamate interaction may work with regard to schizophrenia pathophysiology and treatment. More recently, compelling evidence suggests a relevant role for microRNA (miRNA) as a new class of dopamine and glutamate modulators with regulatory functions in the reciprocal interaction of these two neurotransmitters. Here, we aimed at addressing the following issues: (i) Do miRNAs have a role in schizophrenia pathophysiology in the context of dopamine-glutamate aberrant interaction? (ii) If miRNAs are relevant for dopamine-glutamate interaction, at what level this modulation takes place? (iii) Finally, will this knowledge open the door to innovative diagnostic and therapeutic tools? The biogenesis of miRNAs and their role in synaptic plasticity with relevance to schizophrenia will be considered in the context of dopamine-glutamate interaction, with special focus on miRNA interaction with PSD elements. From this framework, implications both for biomarkers identification and potential innovative interventions will be considered.
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150
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Abstract
There have been considerable advances in uncovering the complex genetic mechanisms that underlie nervous system disease pathogenesis, particularly with the advent of exome and whole genome sequencing techniques. The emerging field of epigenetics is also providing further insights into these mechanisms. Here, we discuss our understanding of the interplay that exists between genetic and epigenetic mechanisms in these disorders, highlighting the nascent field of epigenetic epidemiology-which focuses on analyzing relationships between the epigenome and environmental exposures, development and aging, other health-related phenotypes, and disease states-and next-generation research tools (i.e., those leveraging synthetic and chemical biology and optogenetics) for examining precisely how epigenetic modifications at specific genomic sites affect disease processes.
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Affiliation(s)
- Irfan A. Qureshi
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461 USA
| | - Mark F. Mehler
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461 USA
- />Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Ruth L. and David S. Gottesman Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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