Non‐coding RNAs in the nervous system

Increasing evidence suggests that the development and function of the nervous system is heavily dependent on RNA editing and the intricate spatiotemporal expression of a wide repertoire of non‐coding RNAs, including micro RNAs, small nucleolar RNAs and longer non‐coding RNAs. Non‐coding RNAs may provide the key to understanding the multi‐tiered links between neural development, nervous system function, and neurological diseases.

[1]  D. Abrous,et al.  Adult Neurogenesis : From Precursors to Network and Physiology , 2005 .

[2]  A. Hüttenhofer,et al.  A Novel Brain-specific Box C/D Small Nucleolar RNA Processed from Tandemly Repeated Introns of a Noncoding RNA Gene in Rats* , 2001, The Journal of Biological Chemistry.

[3]  D. Turnbull,et al.  Motor neuron disease in a patient with a mitochondrial tRNAIle mutation , 2006, Annals of neurology.

[4]  S. Stamm,et al.  The snoRNA HBII-52 Regulates Alternative Splicing of the Serotonin Receptor 2C , 2006, Science.

[5]  A. Omori,et al.  The Single‐Stranded DNA‐ and RNA‐Binding Proteins Pur α and Pur β Link BC1 RNA to Microtubules Through Binding to the Dendrite‐Targeting RNA Motifs , 2000 .

[6]  J. Brosius,et al.  Activity-dependent Regulation of Dendritic BC1 RNA in Hippocampal Neurons in Culture , 1998, The Journal of cell biology.

[7]  Zipora Y. Fligelman,et al.  Systematic identification of abundant A-to-I editing sites in the human transcriptome , 2004, Nature Biotechnology.

[8]  Phillip D. Zamore,et al.  Ribo-gnome: The Big World of Small RNAs , 2005, Science.

[9]  Murat Gunel,et al.  Sequence Variants in SLITRK1 Are Associated with Tourette's Syndrome , 2005, Science.

[10]  J. Mattick Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[11]  A. Represa,et al.  Q/R editing of the rat GluR5 and GluR6 kainate receptors in vivo and in vitro: evidence for independent developmental, pathological and cellular regulation , 1999, The European journal of neuroscience.

[12]  K. Giese,et al.  Expression and Function of Brain Specific Small RNAs , 2004, Reviews in the neurosciences.

[13]  Richard Wooster,et al.  A survey of RNA editing in human brain. , 2004, Genome research.

[14]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[15]  M. Paupard,et al.  Patterns of developmental expression of the RNA editing enzyme rADAR2 , 1999, Neuroscience.

[16]  S. Naylor,et al.  Myotonic Dystrophy Type 2 Caused by a CCTG Expansion in Intron 1 of ZNF9 , 2001, Science.

[17]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[18]  Anton J. Enright,et al.  RNA editing of human microRNAs , 2006, Genome Biology.

[19]  V. Ambros,et al.  Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation , 2004, Genome Biology.

[20]  Nobutaka Hirokawa,et al.  Kinesin Transports RNA Isolation and Characterization of an RNA-Transporting Granule , 2004, Neuron.

[21]  J. Cavaille,et al.  A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. , 2004, Genome research.

[22]  Michael Q. Zhang,et al.  Regulating Gene Expression through RNA Nuclear Retention , 2005, Cell.

[23]  Takanori Yamagata,et al.  Large expansion of the ATTCT pentanucleotide repeat in spinocerebellar ataxia type 10 , 2000, Nature Genetics.

[24]  C. Amemiya,et al.  Myotonic dystrophy mutation: an unstable CTG repeat in the 3' untranslated region of the gene. , 1992, Science.

[25]  A. Hüttenhofer,et al.  Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[26]  K. Mikoshiba,et al.  Identification and characterization of Slitrk, a novel neuronal transmembrane protein family controlling neurite outgrowth , 2003, Molecular and Cellular Neuroscience.

[27]  J. Brosius,et al.  BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[28]  R. Goodman,et al.  Role reversal: the regulation of neuronal gene expression by microRNAs , 2005, Current Opinion in Neurobiology.

[29]  K. Nishikura,et al.  Dramatic Increase of the RNA Editing for Glutamate Receptor Subunits During Terminal Differentiation of Clonal Human Neurons , 1997, Journal of neurochemistry.

[30]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[31]  Konstantin Khrapko,et al.  A microRNA array reveals extensive regulation of microRNAs during brain development. , 2003, RNA.

[32]  N. Hecht,et al.  Mouse Testis Brain Ribonucleic Acid-Binding Protein/Translin Colocalizes with Microtubules and Is Immunoprecipitated with Messenger Ribonucleic Acids Encoding Myelin Basic Protein, α Calmodulin Kinase II, and Protamines 1 and 21 , 2000, Biology of reproduction.

[33]  C. Thornton,et al.  The Role of RNA and RNA Processing in Neurodegeneration , 2005, Journal of Neuroscience.

[34]  F. Doetsch,et al.  Stem Cells From Epigeneticsto microRNAs , 2005, Neuron.

[35]  T. Ashizawa,et al.  An unstable triplet repeat in a gene related to myotonic muscular dystrophy. , 1992, Science.

[36]  A. Hüttenhofer,et al.  The expanding snoRNA world. , 2002, Biochimie.

[37]  Michael O'Shea,et al.  Natural Antisense RNAs in the Nervous System , 2005, Reviews in the neurosciences.

[38]  Sin Lam Tan,et al.  Complex Loci in Human and Mouse Genomes , 2006, PLoS genetics.

[39]  Alexander Rich,et al.  A-to-I RNA Editing: Recent News and Residual Mysteries* , 2003, The Journal of Biological Chemistry.

[40]  K. Nishikura,et al.  ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. , 2005, Progress in nucleic acid research and molecular biology.

[41]  Huda Y. Zoghbi,et al.  Diseases of Unstable Repeat Expansion: Mechanisms and Common Principles , 2005, Nature Reviews Genetics.

[42]  K. Taira,et al.  Functional analysis of microRNAs during the retinoic acid-induced neuronal differentiation of human NT2 cells. , 2003, Nucleic acids research. Supplement.

[43]  L. Ranum,et al.  Genetic mapping of a second myotonic dystrophy locus , 1998, Nature Genetics.

[44]  F. Costa,et al.  Non-coding RNAs: new players in eukaryotic biology. , 2005, Gene.

[45]  Henry Mirsky,et al.  RNA editing of a miRNA precursor. , 2004, RNA.

[46]  Melvin G McInnis,et al.  Expansion of a novel CAG trinucleotide repeat in the 5′ region of PPP2R2B is associated with SCA12 , 1999, Nature Genetics.

[47]  T. Tuschl,et al.  The Human DiGeorge Syndrome Critical Region Gene 8 and Its D. melanogaster Homolog Are Required for miRNA Biogenesis , 2004, Current Biology.

[48]  M. Swanson,et al.  Myotonic dystrophy type 1 is associated with nuclear foci of mutant RNA, sequestration of muscleblind proteins and deregulated alternative splicing in neurons. , 2004, Human molecular genetics.

[49]  J. Mattick,et al.  Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. , 2005, Genome research.

[50]  Lena Smirnova,et al.  Regulation of miRNA expression during neural cell specification , 2005, The European journal of neuroscience.

[51]  Anton J. Enright,et al.  Materials and Methods Figs. S1 to S4 Tables S1 to S5 References and Notes Micrornas Regulate Brain Morphogenesis in Zebrafish , 2022 .

[52]  N. Brandon,et al.  DISC1 and DISC2: discovering and dissecting molecular mechanisms underlying psychiatric illness , 2004, Annals of medicine.

[53]  T. Bird,et al.  An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8) , 1999, Nature Genetics.

[54]  R. Reenan,et al.  Nervous System Targets of RNA Editing Identified by Comparative Genomics , 2003, Science.

[55]  David E. Housman,et al.  Molecular basis of myotonic dystrophy: Expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member , 1992, Cell.

[56]  M. Mehler Regional forebrain patterning and neural subtype specification: implications for cerebral cortical functional connectivity and the pathogenesis of neurodegenerative diseases. , 2002, Results and problems in cell differentiation.

[57]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[58]  R. Artero,et al.  The Muscleblind family of proteins: an emerging class of regulators of developmentally programmed alternative splicing. , 2006, Differentiation; research in biological diversity.

[59]  S. Batalov,et al.  A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT , 2005, Science.

[60]  K. Khalili,et al.  Role of Pur alpha in targeting mRNA to sites of translation in hippocampal neuronal dendrites. , 2006, Journal of neuroscience research.

[61]  E. I. Rogaev,et al.  Small RNAs in Human Brain Development and Disorders , 2005, Biochemistry (Moscow).

[62]  J. Mattick,et al.  Small regulatory RNAs in mammals. , 2005, Human molecular genetics.

[63]  M. Weiss,et al.  Stress-induced Apoptosis Associated with Null Mutation of ADAR1 RNA Editing Deaminase Gene* , 2004, Journal of Biological Chemistry.

[64]  Alexander Rich,et al.  Widespread A-to-I RNA Editing of Alu-Containing mRNAs in the Human Transcriptome , 2004, PLoS biology.

[65]  P. Seeburg,et al.  Candidate editases for GluR channels in single neurons of rat hippocampus and cerebellum , 1998, Neuropharmacology.

[66]  U. Meier,et al.  The many facets of H/ACA ribonucleoproteins , 2005, Chromosoma.

[67]  J. Birchler,et al.  Heterochromatin: On the ADAR Radar? , 2005, Current Biology.

[68]  A. Omori,et al.  The single-stranded DNA- and RNA-binding proteins pur alpha and pur beta link BC1 RNA to microtubules through binding to the dendrite-targeting RNA motifs. , 2000, Journal of neurochemistry.

[69]  K. Martin,et al.  Synaptic tagging — who's it? , 2002, Nature Reviews Neuroscience.

[70]  Martin S. Taylor,et al.  Disruption of two novel genes by a translocation co-segregating with schizophrenia. , 2000, Human molecular genetics.

[71]  P. Hagerman,et al.  Recent advances in fragile X: a model for autism and neurodegeneration , 2005, Current opinion in psychiatry.

[72]  L. Wilkinson,et al.  X‐linked imprinting: effects on brain and behaviour , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[73]  K. Nishikura,et al.  A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains. , 2000, RNA.

[74]  S. Kobayashi,et al.  The dendritic translocation of translin protein in the form of BC1 RNA protein particles in developing rat hippocampal neurons in primary culture. , 1998, Biochemical and biophysical research communications.

[75]  S. Ceman,et al.  Identification of mouse YB1/p50 as a component of the FMRP-associated mRNP particle. , 2000, Biochemical and biophysical research communications.

[76]  K. Mikoshiba,et al.  Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. , 2003, Gene.

[77]  S. Ceman,et al.  Isolation of an FMRP-Associated Messenger Ribonucleoprotein Particle and Identification of Nucleolin and the Fragile X-Related Proteins as Components of the Complex , 1999, Molecular and Cellular Biology.

[78]  Kazunari Taira,et al.  A Small Modulatory dsRNA Specifies the Fate of Adult Neural Stem Cells , 2004, Cell.

[79]  Guido Davidzon,et al.  Mitochondrial DNA and disease , 2005, Annals of medicine.

[80]  P. Seeburg,et al.  Modulation of microRNA processing and expression through RNA editing by ADAR deaminases , 2006, Nature Structural &Molecular Biology.

[81]  J. Mattick,et al.  Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. , 2006, Trends in genetics : TIG.

[82]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[83]  J. Cavaille,et al.  Small non-coding RNAs and genomic imprinting , 2006, Cytogenetic and Genome Research.

[84]  Masaru Tomita,et al.  Identification and expression analysis of putative mRNA‐like non‐coding RNA in Drosophila , 2005, Genes to cells : devoted to molecular & cellular mechanisms.

[85]  J. Brosius,et al.  Neuronal BC1 RNA: intracellular transport and activity-dependent modulation. , 2001, Results and problems in cell differentiation.

[86]  John S Mattick,et al.  The hidden genetic program of complex organisms. , 2004, Scientific American.

[87]  A. Hüttenhofer,et al.  RNomics: identification and function of small, non-messenger RNAs. , 2002, Current opinion in chemical biology.

[88]  Gene W. Yeo,et al.  Noncoding RNAs in the mammalian central nervous system. , 2006, Annual review of neuroscience.

[89]  Martin C Frith,et al.  The amazing complexity of the human transcriptome. , 2005, European Journal of Human Genetics.

[90]  L. Wilkinson,et al.  Imprinted gene expression in the brain , 2005, Neuroscience & Biobehavioral Reviews.

[91]  S. Kunes,et al.  Synaptic Protein Synthesis Associated with Memory Is Regulated by the RISC Pathway in Drosophila , 2006, Cell.

[92]  Marie Öhman,et al.  RNA editing and alternative splicing: the importance of co‐transcriptional coordination , 2006, EMBO reports.

[93]  F. Gage,et al.  Epigenetic control of neural stem cell fate. , 2004, Current opinion in genetics & development.

[94]  O. Fattal,et al.  Review of the literature on major mental disorders in adult patients with mitochondrial diseases. , 2006, Psychosomatics.

[95]  W. Reik,et al.  How imprinting centres work , 2006, Cytogenetic and Genome Research.

[96]  J. Mattick,et al.  The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. , 2001, Molecular biology and evolution.

[97]  G. Dreyfuss,et al.  Numerous microRNPs in neuronal cells containing novel microRNAs. , 2003, RNA.

[98]  R. Reenan The RNA world meets behavior: A-->I pre-mRNA editing in animals. , 2001, Trends in genetics : TIG.

[99]  Oliver Hobert,et al.  MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode , 2004, Nature.

[100]  Brenda L Bass,et al.  RNA editing by adenosine deaminases that act on RNA. , 2002, Annual review of biochemistry.

[101]  H. Gelbard Synapses and Sisyphus: life without paraplegin. , 2004, The Journal of clinical investigation.

[102]  A. Hüttenhofer,et al.  RNomics: an experimental approach that identifies 201 candidates for novel, small, non‐messenger RNAs in mouse , 2001, The EMBO journal.

[103]  J. Mattick RNA regulation: a new genetics? , 2004, Nature Reviews Genetics.

[104]  Maryann E Martone,et al.  Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain‐dependent manner , 2005, Journal of neurochemistry.

[105]  M. Mehler Mechanisms regulating lineage diversity during mammalian cerebral cortical neurogenesis and gliogenesis. , 2002, Results and problems in cell differentiation.

[106]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[107]  R. Margolis,et al.  Why is SCA12 different from other SCAs? , 2003, Cytogenetic and Genome Research.

[108]  C. Ehresmann,et al.  The RNA binding protein FMRP: new connections and missing links , 2003, Biology of the cell.

[109]  Chris M. Brown,et al.  Visualization of RNA–protein interactions in living cells: FMRP and IMP1 interact on mRNAs , 2004, The EMBO journal.

[110]  P. Jin,et al.  RNA and microRNAs in fragile X mental retardation , 2004, Nature Cell Biology.

[111]  N. Bresolin,et al.  Cognitive impairment in neuromuscular disorders , 2006, Muscle & nerve.

[112]  J. Brosius,et al.  RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. , 1999, Gene.

[113]  Gary Ruvkun,et al.  Identification of many microRNAs that copurify with polyribosomes in mammalian neurons , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[114]  L. Wilkinson,et al.  Expression patterns of the novel imprinted genes Nap1l5 and Peg13 and their non-imprinted host genes in the adult mouse brain. , 2004, Gene expression patterns : GEP.

[115]  Laurent Lestrade,et al.  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs , 2005, Nucleic Acids Res..

[116]  K. Khalili,et al.  Role of Purα in targeting mRNA to sites of translation in hippocampal neuronal dendrites , 2006 .

[117]  R. Bodmer,et al.  The bereft gene, a potential target of the neural selector gene cut, contributes to bristle morphogenesis. , 2002, Genetics.

[118]  Gail Mandel,et al.  Reciprocal actions of REST and a microRNA promote neuronal identity , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[119]  B. Bass,et al.  RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[120]  H. Van Esch The Fragile X premutation: new insights and clinical consequences. , 2006, European journal of medical genetics.

[121]  Mu-ming Poo,et al.  Coincidence Detection of Synaptic Inputs Is Facilitated at the Distal Dendrites after Long-Term Potentiation Induction , 2006, The Journal of Neuroscience.

[122]  T. Mukai,et al.  The Mouse Murr1 Gene Is Imprinted in the Adult Brain, Presumably Due to Transcriptional Interference by the Antisense-Oriented U2af1-rs1 Gene , 2004, Molecular and Cellular Biology.

[123]  Philipp Kapranov,et al.  Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. , 2005, Genome research.

[124]  M. O’Neill The influence of non-coding RNAs on allele-specific gene expression in mammals. , 2005, Human molecular genetics.

[125]  K. Kosik,et al.  MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. , 2005, Cancer research.

[126]  J. Nemes,et al.  The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). , 2000, Human molecular genetics.

[127]  Brian S. Roberts,et al.  The colorectal microRNAome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[128]  B. Bass,et al.  RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans , 2002, The EMBO journal.

[129]  Christopher A. Ross,et al.  A schizophrenia-associated mutation of DISC1 perturbs cerebral cortex development , 2005, Nature Cell Biology.

[130]  S. Minoshima,et al.  Molecular cloning and expression analysis of a novel gene DGCR8 located in the DiGeorge syndrome chromosomal region. , 2003, Biochemical and biophysical research communications.

[131]  Kenneth S. Kosik,et al.  The Elegance of the MicroRNAs: A Neuronal Perspective , 2005, Neuron.

[132]  M. Mutsuddi,et al.  The Spinocerebellar Ataxia 8 Noncoding RNA Causes Neurodegeneration and Associates with Staufen in Drosophila , 2004, Current Biology.

[133]  Oliver Hobert,et al.  A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans , 2003, Nature.

[134]  R. Shiekhattar,et al.  The Microprocessor complex mediates the genesis of microRNAs , 2004, Nature.

[135]  R. Lyle,et al.  The uniqueness of the imprinting mechanism. , 2000, Current opinion in genetics & development.

[136]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[137]  Jun Kawai,et al.  Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs , 2006, PLoS genetics.

[138]  J. Mattick,et al.  Non-coding RNA. , 2006, Human molecular genetics.

[139]  F. Doetsch,et al.  Stem cells: from epigenetics to microRNAs. , 2005, Neuron.

[140]  Michael E. Greenberg,et al.  A brain-specific microRNA regulates dendritic spine development , 2006, Nature.

[141]  K. Kosik,et al.  Specific MicroRNAs Modulate Embryonic Stem Cell–Derived Neurogenesis , 2006, Stem cells.

[142]  Edouard Bertrand,et al.  ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs , 2005, The Journal of cell biology.

[143]  S. Hunt,et al.  Contextual fear conditioning regulates the expression of brain‐specific small nucleolar RNAs in hippocampus , 2003, The European journal of neuroscience.