The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing (original) (raw)

• Rossler W, Salize HJ, van Os J, Riecher-Rossler A . Size of burden of schizophrenia and psychotic disorders. Eur Neuropsychopharmacol 2005; 15: 399–409.
  Article Google Scholar
• Small SA, Schobel SA, Buxton RB, Witter MP, Barnes CA . A pathophysiological framework of hippocampal dysfunction in ageing and disease. Nat Rev Neurosci 2011; 12: 585–601.
  Article CAS Google Scholar
• Sullivan PF, Kendler KS, Neale MC . Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. Arch Gen Psychiatry 2003; 60: 1187–1192.
  Article Google Scholar
• Girard SL, Gauthier J, Noreau A, Xiong L, Zhou S, Jouan L et al. Increased exonic de novo mutation rate in individuals with schizophrenia. Nat Genet 2011; 43: 860–863.
  Article CAS Google Scholar
• Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, Levy S et al. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet 2011; 43: 864–868.
  Article CAS Google Scholar
• Morikawa T, Manabe T . Aberrant regulation of alternative pre-mRNA splicing in schizophrenia. Neurochem Int 2010; 57: 691–704.
  Article CAS Google Scholar
• Nakata K, Lipska BK, Hyde TM, Ye T, Newburn EN, Morita Y et al. DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms. Proc Natl Acad Sci USA 2009; 106: 15873–15878.
  Article CAS Google Scholar
• Law AJ, Kleinman JE, Weinberger DR, Weickert CS . Disease-associated intronic variants in the ErbB4 gene are related to altered ErbB4 splice-variant expression in the brain in schizophrenia. Hum Mol Genet 2007; 16: 129–141.
  Article CAS Google Scholar
• Tsuiji H, Yoshimoto R, Hasegawa Y, Furuno M, Yoshida M, Nakagawa S . Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells 2011; 16: 479–490.
  Article CAS Google Scholar
• Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007; 316: 1484–1488.
  Article CAS Google Scholar
• Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012; 22: 1775–1789.
  Article CAS Google Scholar
• Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A et al. Landscape of transcription in human cells. Nature 2012; 489: 101–108.
  Article CAS Google Scholar
• Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489: 57–74.
  Article CAS Google Scholar
• Guttman M, Rinn JL . Modular regulatory principles of large non-coding RNAs. Nature 2012; 482: 339–346.
  Article CAS Google Scholar
• Wang KC, Chang HY . Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43: 904–914.
  Article CAS Google Scholar
• Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477: 295–300.
  Article CAS Google Scholar
• Wapinski O, Chang HY . Long noncoding RNAs and human disease. Trends Cell Biol 2011; 21: 354–361.
  Article CAS Google Scholar
• Chen LL, Carmichael GG . Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol 2010; 22: 357–364.
  Article CAS Google Scholar
• Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 2006; 51: 1087–1099.
  Article CAS Google Scholar
• Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP et al. Genomic analysis of mouse retinal development. PLoS Biol 2004; 2: E247.
  Article Google Scholar
• Rapicavoli NA, Blackshaw S . New meaning in the message: noncoding RNAs and their role in retinal development. Dev Dyn 2009; 238: 2103–2114.
  Article CAS Google Scholar
• Rapicavoli NA, Poth EM, Blackshaw S . The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 2010; 10: 49.
  Article Google Scholar
• Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS et al. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 2010; 11: 14.
  Article Google Scholar
• Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS . Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 2008; 105: 716–721.
  Article CAS Google Scholar
• Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S . The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 2007; 120: 2498–2506.
  Article CAS Google Scholar
• Albertson DN, Schmidt CJ, Kapatos G, Bannon MJ . Distinctive profiles of gene expression in the human nucleus accumbens associated with cocaine and heroin abuse. Neuropsychopharmacology 2006; 31: 2304–2312.
  Article CAS Google Scholar
• Michelhaugh SK, Lipovich L, Blythe J, Jia H, Kapatos G, Bannon MJ . Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. J Neurochem 2011; 116: 459–466.
  Article CAS Google Scholar
• Di Chiara G, Bassareo V, Fenu S, De Luca MA, Spina L, Cadoni C et al. Dopamine and drug addiction: the nucleus accumbens shell connection. Neuropharmacology 2004; 47 (Suppl 1): 227–241.
  Article CAS Google Scholar
• Takahashi S, Ohtsuki T, Yu SY, Tanabe E, Yara K, Kamioka M et al. Significant linkage to chromosome 22q for exploratory eye movement dysfunction in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2003; 123B: 27–32.
  Article Google Scholar
• Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y et al. DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 2003; 302: 890–893.
  Article CAS Google Scholar
• Smyth GK . Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3, Article 3.
  Article Google Scholar
• Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A et al. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007; 23: 2700–2707.
  Article CAS Google Scholar
• Smyth GK, Speed T . Normalization of cDNA microarray data. Methods 2003; 31: 265–273.
  Article CAS Google Scholar
• Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P et al. Genome-wide analysis of long noncoding RNA stability. Genome Res 2012; 22: 885–898.
  Article CAS Google Scholar
• Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res 2010; 38: W210–W213.
  Article CAS Google Scholar
• Wickham H . ggplot2: Elegant Graphics for Data Analysis. Springer: New York, 2009.
  Book Google Scholar
• Chen H, Boutros PC . VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 2011; 12: 35.
  Article Google Scholar
• Xu RH, Peck RM, Li DS, Feng X, Ludwig T, Thomson JA . Basic FGF and suppression of BMP signaling sustain undifferentiated proliferation of human ES cells. Nat Methods 2005; 2: 185–190.
  Article CAS Google Scholar
• Vetter I . Development and Optimization of FLIPR high throughput calcium assays for ion channels and GPCRs. Adv Exp Med Biol 2012; 740: 45–82.
  Article CAS Google Scholar
• Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J et al. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics 2012; 11: O111.016253.
  Article Google Scholar
• Fok V, Mitton-Fry RM, Grech A, Steitz JA . Multiple domains of EBER 1, an Epstein-Barr virus noncoding RNA, recruit human ribosomal protein L22. RNA 2006; 12: 872–882.
  Article CAS Google Scholar
• Beveridge NJ, Tooney PA, Carroll AP, Gardiner E, Bowden N, Scott RJ et al. Dysregulation of miRNA 181b in the temporal cortex in schizophrenia. Hum Mol Genet 2008; 17: 1156–1168.
  Article CAS Google Scholar
• Wu JQ, Wang X, Beveridge NJ, Tooney PA, Scott RJ, Carr VJ et al. Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia. PLoS ONE 2012; 7: e36351.
  Article CAS Google Scholar
• Lyons MR, West AE . Mechanisms of specificity in neuronal activity-regulated gene transcription. Prog Neurobiol 2011; 94: 259–295.
  Article CAS Google Scholar
• Bredy TW, Lin Q, Wei W, Baker-Andresen D, Mattick JS . MicroRNA regulation of neural plasticity and memory. Neurobiol Learn Mem 2011; 96: 89–94.
  Article CAS Google Scholar
• Siemen H, Colas D, Heller HC, Brustle O, Pera RA . Pumilio-2 function in the mouse nervous system. PLoS ONE 2011; 6: e25932.
  Article CAS Google Scholar
• Lahmann I, Fabienke M, Henneberg B, Pabst O, Vauti F, Minge D et al. The hnRNP and cytoskeletal protein raver1 contributes to synaptic plasticity. Exp Cell Res 2008; 314: 1048–1060.
  Article CAS Google Scholar
• Kundel M, Jones KJ, Shin CY, Wells DG . Cytoplasmic polyadenylation element-binding protein regulates neurotrophin-3-dependent beta-catenin mRNA translation in developing hippocampal neurons. J Neurosci 2009; 29: 13630–13639.
  Article CAS Google Scholar
• Zearfoss NR, Alarcon JM, Trifilieff P, Kandel E, Richter JD . A molecular circuit composed of CPEB-1 and c-Jun controls growth hormone-mediated synaptic plasticity in the mouse hippocampus. J Neurosci 2008; 28: 8502–8509.
  Article CAS Google Scholar
• Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25: 1915–1927.
  Article CAS Google Scholar
• Englund C, Fink A, Lau C, Pham D, Daza RA, Bulfone A et al. Pax6, Tbr2, and Tbr1 are expressed sequentially by radial glia, intermediate progenitor cells, and postmitotic neurons in developing neocortex. J Neurosci 2005; 25: 247–251.
  Article CAS Google Scholar
• Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J 2010; 29: 3082–3093.
  Article CAS Google Scholar
• Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010; 39: 925–938.
  Article CAS Google Scholar
• Aberg K, Saetre P, Jareborg N, Jazin E . Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia. Proc Natl Acad Sci USA 2006; 103: 7482–7487.
  Article Google Scholar
• Aberg K, Saetre P, Lindholm E, Ekholm B, Pettersson U, Adolfsson R et al. Human QKI, a new candidate gene for schizophrenia involved in myelination. Am J Med Genet B Neuropsychiatr Genet 2006; 141B: 84–90.
  Article Google Scholar
• Haroutunian V, Katsel P, Dracheva S, Davis KL . The human homolog of the QKI gene affected in the severe dysmyelination ‘quaking’ mouse phenotype: downregulated in multiple brain regions in schizophrenia. Am J Psychiatry 2006; 163: 1834–1837.
  Article Google Scholar
• McCullumsmith RE, Gupta D, Beneyto M, Kreger E, Haroutunian V, Davis KL et al. Expression of transcripts for myelination-related genes in the anterior cingulate cortex in schizophrenia. Schizophr Res 2007; 90: 15–27.
  Article Google Scholar
• Hashimoto R, Straub RE, Weickert CS, Hyde TM, Kleinman JE, Weinberger DR . Expression analysis of neuregulin-1 in the dorsolateral prefrontal cortex in schizophrenia. Mol Psychiatry 2004; 9: 299–307.
  Article CAS Google Scholar
• Brandon NJ, Sawa A . Linking neurodevelopmental and synaptic theories of mental illness through DISC1. Nat Rev Neurosci 2011; 12: 707–722.
  Article CAS Google Scholar
• Ishizuka K, Kamiya A, Oh EC, Kanki H, Seshadri S, Robinson JF et al. DISC1-dependent switch from progenitor proliferation to migration in the developing cortex. Nature 2011; 473: 92–96.
  Article CAS Google Scholar
• Wang Q, Charych EI, Pulito VL, Lee JB, Graziane NM, Crozier RA et al. The psychiatric disease risk factors DISC1 and TNIK interact to regulate synapse composition and function. Mol Psychiatry 2011; 16: 1006–1023.
  Article CAS Google Scholar
• Hayashi-Takagi A, Takaki M, Graziane N, Seshadri S, Murdoch H, Dunlop AJ et al. Disrupted-in-Schizophrenia 1 (DISC1) regulates spines of the glutamate synapse via Rac1. Nat Neurosci 2010; 13: 327–332.
  Article CAS Google Scholar
• Shamir A, Kwon OB, Karavanova I, Vullhorst D, Leiva-Salcedo E, Janssen MJ et al. The importance of the NRG-1/ErbB4 pathway for synaptic plasticity and behaviors associated with psychiatric disorders. J Neurosci 2012; 32: 2988–2997.
  Article CAS Google Scholar
• Veikkolainen V, Vaparanta K, Halkilahti K, Iljin K, Sundvall M, Elenius K . Function of ERBB4 is determined by alternative splicing. Cell Cycle 2011; 10: 2647–2657.
  Article CAS Google Scholar
• Beveridge NJ, Cairns MJ . MicroRNA dysregulation in schizophrenia. Neurobiol Dis 2012; 46: 263–271.
  Article CAS Google Scholar
• Beveridge NJ, Gardiner E, Carroll AP, Tooney PA, Cairns MJ . Schizophrenia is associated with an increase in cortical microRNA biogenesis. Mol Psychiatry 2010; 15: 1176–1189.
  Article CAS Google Scholar
• Gardiner E, Beveridge NJ, Wu JQ, Carr V, Scott RJ, Tooney PA et al. Imprinted DLK1-DIO3 region of 14q32 defines a schizophrenia-associated miRNA signature in peripheral blood mononuclear cells. Mol Psychiatry 2012; 17: 827–840.
  Article CAS Google Scholar
• Miller BH, Zeier Z, Xi L, Lanz TA, Deng S, Strathmann J et al. MicroRNA-132 dysregulation in schizophrenia has implications for both neurodevelopment and adult brain function. Proc Natl Acad Sci USA 2012; 109: 3125–3130.
  Article CAS Google Scholar
• Mercer TR, Dinger ME, Mattick JS . Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10: 155–159.
  Article CAS Google Scholar
• Day JJ, Sweatt JD . Epigenetic mechanisms in cognition. Neuron 2011; 70: 813–829.
  Article CAS Google Scholar
• Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD et al. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 2011; 147: 773–788.
  Article CAS Google Scholar