A long nuclear‐retained non‐coding RNA regulates synaptogenesis by modulating gene expression

[1]  Howard Y. Chang,et al.  Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis , 2010, Nature.

[2]  Alok K. Sharma,et al.  Son Is Essential for Nuclear Speckle Organization and Cell Cycle Progression , 2010, Molecular biology of the cell.

[3]  J. Mattick,et al.  Non‐coding RNAs: regulators of disease , 2010, The Journal of pathology.

[4]  S. C. Lakhotia,et al.  The Developmentally Active and Stress-Inducible Noncoding hsrω Gene Is a Novel Regulator of Apoptosis in Drosophila , 2009, Genetics.

[5]  G. Carmichael,et al.  Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. , 2009, Molecular cell.

[6]  C. Beattie,et al.  Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick? , 2009, Nature Reviews Neuroscience.

[7]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[8]  D. Spector,et al.  Long noncoding RNAs: functional surprises from the RNA world. , 2009, Genes & development.

[9]  John N. Hutchinson,et al.  An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. , 2009, Molecular cell.

[10]  J. Mattick,et al.  Long non-coding RNAs: insights into functions , 2009, Nature Reviews Genetics.

[11]  T. Mituyama,et al.  MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles , 2009, Proceedings of the National Academy of Sciences.

[12]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[13]  Jennifer A. Mitchell,et al.  The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin , 2008, Science.

[14]  David L. Spector,et al.  3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA , 2008, Cell.

[15]  T. Shibata,et al.  Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs , 2008, Nature.

[16]  Jeannie T. Lee,et al.  X chromosome dosage compensation: how mammals keep the balance. , 2008, Annual review of genetics.

[17]  S. Warren,et al.  Fragile X Syndrome: Loss of Local mRNA Regulation Alters Synaptic Development and Function , 2008, Neuron.

[18]  Paulo P. Amaral,et al.  Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. , 2008, Genome research.

[19]  C. Glass,et al.  Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription , 2008, Nature.

[20]  Celso A. Espinoza,et al.  Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. , 2008, Molecular cell.

[21]  Stefan Stamm,et al.  Regulation of Alternative Splicing by Reversible Protein Phosphorylation* , 2008, Journal of Biological Chemistry.

[22]  S. Sunkin,et al.  Specific expression of long noncoding RNAs in the mouse brain , 2008, Proceedings of the National Academy of Sciences.

[23]  A. Feinberg,et al.  Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA , 2008, Nature.

[24]  T. Möröy,et al.  The impact of alternative splicing in vivo: mouse models show the way. , 2007, RNA.

[25]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[26]  M. Kuroda,et al.  Noncoding RNAs and Intranuclear Positioning in Monoallelic Gene Expression , 2007, Cell.

[27]  M. Karin,et al.  A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas , 2007, Oncogene.

[28]  Ana Serra Barros,et al.  Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript , 2007, Nature.

[29]  John N. Hutchinson,et al.  A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains , 2007, BMC Genomics.

[30]  Allan R. Jones,et al.  Genome-wide atlas of gene expression in the adult mouse brain , 2007, Nature.

[31]  D. Spector,et al.  SnapShot: Cellular Bodies , 2006, Cell.

[32]  Nicolas Servant,et al.  Goulphar: rapid access and expertise for standard two-color microarray normalization methods , 2006, BMC Bioinformatics.

[33]  D. Haussler,et al.  An RNA gene expressed during cortical development evolved rapidly in humans , 2006, Nature.

[34]  John S Mattick,et al.  Non‐coding RNAs in the nervous system , 2006, The Journal of physiology.

[35]  Robert H. Brown,et al.  Molecular biology of amyotrophic lateral sclerosis: insights from genetics , 2006, Nature Reviews Neuroscience.

[36]  C. Disteche,et al.  Dosage compensation in mammals: fine-tuning the expression of the X chromosome. , 2006, Genes & development.

[37]  J. Lawrence,et al.  Molecular anatomy of a speckle. , 2006, The anatomical record. Part A, Discoveries in molecular, cellular, and evolutionary biology.

[38]  Brian S. Clark,et al.  The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. , 2006, Genes & development.

[39]  S. Tilghman,et al.  Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. , 2006, Genes & development.

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

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

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

[43]  J. Levinson,et al.  Building Excitatory and Inhibitory Synapses: Balancing Neuroligin Partnerships , 2005, Neuron.

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

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

[46]  P. Scheiffele,et al.  Control of Excitatory and Inhibitory Synapse Formation by Neuroligins , 2005, Science.

[47]  T. Südhof,et al.  Selective Capability of SynCAM and Neuroligin for Functional Synapse Assembly , 2005, The Journal of Neuroscience.

[48]  Ann Marie Craig,et al.  Neurexins Induce Differentiation of GABA and Glutamate Postsynaptic Specializations via Neuroligins , 2004, Cell.

[49]  P. Rostaing,et al.  Morphologically identified glycinergic synapses in the hippocampus , 2004, Molecular and Cellular Neuroscience.

[50]  B. Pettmann,et al.  Foxo3a induces motoneuron death through the Fas pathway in cooperation with JNK , 2004, BMC Neuroscience.

[51]  Mark H. Ellisman,et al.  Hypophosphorylated SR splicing factors transiently localize around active nucleolar organizing regions in telophase daughter nuclei , 2004, The Journal of cell biology.

[52]  Thomas Ried,et al.  From Silencing to Gene Expression Real-Time Analysis in Single Cells , 2004, Cell.

[53]  Bing Zhang,et al.  GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies , 2004, BMC Bioinformatics.

[54]  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.

[55]  Michael Thomas,et al.  MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer , 2003, Oncogene.

[56]  David L. Spector,et al.  Nuclear speckles: a model for nuclear organelles , 2003, Nature Reviews Molecular Cell Biology.

[57]  Jinhua Wang,et al.  ESEfinder: a web resource to identify exonic splicing enhancers , 2003, Nucleic Acids Res..

[58]  T. Südhof,et al.  SynCAM, a Synaptic Adhesion Molecule That Drives Synapse Assembly , 2002, Science.

[59]  T. Pawson,et al.  The Receptor Tyrosine Kinase EphB2 Regulates NMDA-Dependent Synaptic Function , 2001, Neuron.

[60]  J. Mattick.  Non‐coding RNAs: the architects of eukaryotic complexity , 2001, EMBO reports.

[61]  D. Benson,et al.  Stages of Synapse Development Defined by Dependence on F-Actin , 2001, The Journal of Neuroscience.

[62]  Stormy J. Chamberlain,et al.  The Prader-Willi syndrome imprinting center activates the paternally expressed murine Ube3a antisense transcript but represses paternal Ube3a. , 2001, Genomics.

[63]  M. Pfaffl,et al.  A new mathematical model for relative quantification in real-time RT-PCR. , 2001, Nucleic acids research.

[64]  K. Fukunaga,et al.  A working model of CaM kinase II activity in hippocampal long-term potentiation and memory , 2000, Neuroscience Research.

[65]  Susanne E. Ahmari,et al.  Assembly of presynaptic active zones from cytoplasmic transport packets , 2000, Nature Neuroscience.

[66]  J. Kaplan,et al.  CaMKII regulates the density of central glutamatergic synapses in vivo , 1999, Nature.

[67]  O. Steward,et al.  Synaptic Clustering of AMPA Receptors by the Extracellular Immediate-Early Gene Product Narp , 1999, Neuron.

[68]  Neil J McKenna,et al.  A Steroid Receptor Coactivator, SRA, Functions as an RNA and Is Present in an SRC-1 Complex , 1999, Cell.

[69]  J. Manley,et al.  Phosphorylation–dephosphorylation differentially affects activities of splicing factor ASF/SF2 , 1998, The EMBO journal.

[70]  A. Krainer,et al.  Serine Phosphorylation of SR Proteins Is Required for Their Recruitment to Sites of Transcription In Vivo , 1998, The Journal of cell biology.

[71]  Tobias Meyer,et al.  CaMKIIβ Functions As an F-Actin Targeting Module that Localizes CaMKIIα/β Heterooligomers to Dendritic Spines , 1998, Neuron.

[72]  H. Cline,et al.  Stabilization of dendritic arbor structure in vivo by CaMKII. , 1998, Science.

[73]  M. Garcia-Blanco,et al.  Both phosphorylation and dephosphorylation of ASF/SF2 are required for pre-mRNA splicing in vitro. , 1997, RNA.

[74]  E G Jones,et al.  Inhibitory synaptogenesis in mouse somatosensory cortex. , 1997, Cerebral cortex.

[75]  Tom Misteli,et al.  The dynamics of a pre-mRNA splicing factor in living cells , 1997, Nature.

[76]  B. Chabot,et al.  The nuclear matrix phosphoprotein p255 associates with splicing complexes as part of the [U4/U6.U5] tri-snRNP particle. , 1995, Nucleic Acids Research.

[77]  David Ish-Horowicz,et al.  Expression of a Delta homologue in prospective neurons in the chick , 1995, Nature.

[78]  T. Deerinck,et al.  In vivo analysis of the stability and transport of nuclear poly(A)+ RNA , 1994, The Journal of cell biology.

[79]  N. Schaeren-Wiemers,et al.  A single protocol to detect transcripts of various types and expression levels in neural tissue and cultured cells: in situ hybridization using digoxigenin-labelled cRNA probes , 1993, Histochemistry.

[80]  J. Bachellerie,et al.  Intranuclear distribution of poly(A) RNA determined by electron microscope in situ hybridization. , 1993, Experimental cell research.

[81]  O. Steward,et al.  Selective localization of polyribosomes beneath developing synapses: A quantitative analysis of the relationships between polyribosomes and developing synapses in the hippocampus and dentate gyrus , 1991, The Journal of comparative neurology.

[82]  J. Lawrence,et al.  Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus , 1991, The Journal of cell biology.

[83]  P. De Camilli,et al.  The distribution of synapsin I and synaptophysin in hippocampal neurons developing in culture , 1991, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[84]  O. Steward,et al.  Protein-synthetic machinery at postsynaptic sites during synaptogenesis: a quantitative study of the association between polyribosomes and developing synapses , 1986, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[85]  R. Mcgee.  Regulation of presynaptic cellular function , 1980, Molecular and Cellular Biochemistry.

[86]  T. Barrett.  Splicing in vitro? , 1979, Nature.

[87]  Paulo P. Amaral,et al.  MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. , 2009, Genome research.

[88]  J. Cáceres,et al.  The SR protein family of splicing factors: master regulators of gene expression. , 2009, The Biochemical journal.

[89]  D. Spector,et al.  Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. , 2007, Genes & development.

[90]  P. Glees,et al.  The time course of synapse formation of mouse neuroblastoma cells in monolayer cultures , 2004, Cell and Tissue Research.

[91]  Dmitri A. Nusinow,et al.  Xist RNA and the mechanism of X chromosome inactivation. , 2002, Annual review of genetics.

[92]  K. Shen,et al.  CaMKIIbeta functions as an F-actin targeting module that localizes CaMKIIalpha/beta heterooligomers to dendritic spines. , 1998, Neuron.

[93]  Shin Heu,et al.  Experimental Validation of , 1991 .

[94]  R. Mcgee.  Regulation of presynaptic cellular function. Biochemical studies using clonal neuronal cells. , 1980, Molecular and cellular biochemistry.