miRNA Regulons Associated with Synaptic Function

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Paschou, Maria ^a   Paraskevopoulou, Maria D ^b   Vlachos, Ioannis S ^b   Koukouraki, Pelagia ^a   Hatzigeorgiou, Artemis G ^b,c   Doxakis, Epaminondas ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING   (Greece)

^c UNIVERSITY OF THESSALY   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; SYNAPSE RECEPTOR;

3' UNTRANSLATED REGION; ALGORITHM; ARTICLE; BINDING SITE; DENDRITIC SPINE; HYDROLYSIS; NERVE CELL PLASTICITY; POSTSYNAPTIC POTENTIAL; PRESYNAPTIC POTENTIAL; PROTEIN ASSEMBLY; PROTEIN LOCALIZATION; PROTEIN SYNTHESIS; REGULON; RNA BINDING; SYNAPSE; TRANSCRIPTION REGULATION;

3' UNTRANSLATED REGIONS; HUMANS; MICRORNAS; NERVE TISSUE PROTEINS; REGULON; SYNAPSES;

EID: 84867325304     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046189     Document Type: Article

References (69)

1. Sudhof TC, (2008) Neuroligins and neurexins link synaptic function to cognitive disease. Nature 455: 903-911.
2. Hirokawa N, Niwa S, Tanaka Y, (2010) Molecular motors in neurons: transport mechanisms and roles in brain function, development, and disease. Neuron 68: 610-638.
3. Santos MS, Li H, Voglmaier SM, (2009) Synaptic vesicle protein trafficking at the glutamate synapse. Neuroscience 158: 189-203.
4. Liu-Yesucevitz L, Bassell GJ, Gitler AD, Hart AC, Klann E, et al. (2011) Local RNA translation at the synapse and in disease. J Neurosci 31: 16086-16093.
5. Swanger SA, Bassell GJ, (2011) Making and breaking synapses through local mRNA regulation. Curr Opin Genet Dev 21: 414-421.
6. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T, (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
7. Lau NC, Lim LP, Weinstein EG, Bartel DP, (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
8. Lee RC, Ambros V, (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
9. Bartel DP, Chen CZ, (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5: 396-400.
10. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, et al. (2006) miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell metabolism 3: 87-98.
11. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, et al. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438: 685-689.
12. Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
13. Wienholds E, Plasterk RH, (2005) MicroRNA function in animal development. FEBS Lett 579: 5911-5922.
14. Lai EC, (2005) miRNAs: whys and wherefores of miRNA-mediated regulation. Curr Biol 15: R458-460.
15. Lugli G, Torvik VI, Larson J, Smalheiser NR, (2008) Expression of microRNAs and their precursors in synaptic fractions of adult mouse forebrain. J Neurochem 106: 650-661.
16. Lugli G, Larson J, Martone ME, Jones Y, Smalheiser NR, (2005) Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain-dependent manner. J Neurochem 94: 896-905.
17. Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, et al. (2010) Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs. Cell 141: 618-631.
18. Cheng D, Hoogenraad CC, Rush J, Ramm E, Schlager MA, et al. (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Molecular & cellular proteomics: MCP 5: 1158-1170.
19. Hahn CG, Banerjee A, Macdonald ML, Cho DS, Kamins J, et al. (2009) The post-synaptic density of human postmortem brain tissues: an experimental study paradigm for neuropsychiatric illnesses. PLoS One 4: e5251.
20. Sheng M, Hoogenraad CC, (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annual review of biochemistry 76: 823-847.
21. Yoshimura Y, Yamauchi Y, Shinkawa T, Taoka M, Donai H, et al. (2004) Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J Neurochem 88: 759-768.
22. Ziv NE, Garner CC, (2004) Cellular and molecular mechanisms of presynaptic assembly. Nat Rev Neurosci 5: 385-399.
23. Matsumoto M, Setou M, Inokuchi K, (2007) Transcriptome analysis reveals the population of dendritic RNAs and their redistribution by neural activity. Neurosci Res 57: 411-423.
24. Bruses JL, (2010) Identification of gene transcripts expressed by postsynaptic neurons during synapse formation encoding cell surface proteins with presumptive synaptogenic activity. Synapse 64: 47-60.
25. Ule J, Ule A, Spencer J, Williams A, Hu JS, et al. (2005) Nova regulates brain-specific splicing to shape the synapse. Nat Genet 37: 844-852.
26. Stryker E, Johnson KG, (2007) LAR, liprin alpha and the regulation of active zone morphogenesis. J Cell Sci 120: 3723-3728.
27. Vessey JP, Karra D, (2007) More than just synaptic building blocks: scaffolding proteins of the post-synaptic density regulate dendritic patterning. J Neurochem 102: 324-332.
28. Spangler SA, Hoogenraad CC, (2007) Liprin-alpha proteins: scaffold molecules for synapse maturation. Biochem Soc Trans 35: 1278-1282.
29. Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D, (1997) GeneCards: integrating information about genes, proteins and diseases. Trends Genet 13: 163.
30. Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, et al. (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011: bar030.
31. Garcia DM, Baek D, Shin C, Bell GW, Grimson A, et al. (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18: 1139-1146.
32. Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG, (2012) Functional microRNA targets in protein coding sequences. Bioinformatics 28: 771-776.
33. Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, et al. (2012) DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res 40: W498-W504.
34. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG, (2009) Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25: 3049-3055.
35. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093.
36. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
37. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348.
38. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57: 289-300.
39. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
40. Gu S, Jin L, Zhang F, Sarnow P, Kay MA, (2009) Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16: 144-150.
41. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB, (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320: 1643-1647.
42. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
43. Hsu R, Schofield CM, Dela Cruz CG, Jones-Davis DM, Blelloch R, et al. (2012) Loss of microRNAs in pyramidal neurons leads to specific changes in inhibitory synaptic transmission in the prefrontal cortex. Mol Cell Neurosci 50: 283-292.
44. Davis TH, Cuellar TL, Koch SM, Barker AJ, Harfe BD, et al. (2008) Conditional loss of Dicer disrupts cellular and tissue morphogenesis in the cortex and hippocampus. J Neurosci 28: 4322-4330.
45. Li Q, Bian S, Hong J, Kawase-Koga Y, Zhu E, et al. (2011) Timing specific requirement of microRNA function is essential for embryonic and postnatal hippocampal development. PLoS One 6: e26000.
46. An JJ, Gharami K, Liao GY, Woo NH, Lau AG, et al. (2008) Distinct role of long 3′ UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons. Cell 134: 175-187.
47. Ji Z, Lee JY, Pan Z, Jiang B, Tian B, (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106: 7028-7033.
48. Bergauer T, Krueger U, Lader E, Pilk S, Wolter I, et al. (2009) Analysis of putative miRNA binding sites and mRNA 3′ ends as targets for siRNA-mediated gene knockdown. Oligonucleotides 19: 41-52.
49. Majoros WH, Ohler U, (2007) Spatial preferences of microRNA targets in 3′ untranslated regions. BMC Genomics 8: 152.
50. Beveridge NJ, Cairns MJ, (2012) MicroRNA dysregulation in schizophrenia. Neurobiology of disease 46: 263-271.
51. Smalheiser NR, Lugli G, Rizavi HS, Torvik VI, Turecki G, et al. (2012) MicroRNA expression is down-regulated and reorganized in prefrontal cortex of depressed suicide subjects. PLoS One 7: e33201.
52. Inukai S, de Lencastre A, Turner M, Slack F, (2012) Novel MicroRNAs Differentially Expressed during Aging in the Mouse Brain. PLoS One 7: e40028.
53. Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, et al. (2011) Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics 12: 277.
54. Agostini M, Tucci P, Steinert JR, Shalom-Feuerstein R, Rouleau M, et al. (2011) microRNA-34a regulates neurite outgrowth, spinal morphology, and function. Proc Natl Acad Sci U S A 108 (52) (): 21099-21104.
55. Agostini M, Tucci P, Killick R, Candi E, Sayan BS, et al. (2011) Neuronal differentiation by TAp73 is mediated by microRNA-34a regulation of synaptic protein targets. Proc Natl Acad Sci U S A 108 (52) (): 21093-21098.
56. Wang WX, Huang Q, Hu Y, Stromberg AJ, Nelson PT, (2011) Patterns of microRNA expression in normal and early Alzheimer's disease human temporal cortex: white matter versus gray matter. Acta Neuropathol 121: 193-205.
57. Kim AH, Reimers M, Maher B, Williamson V, McMichael O, et al. (2010) MicroRNA expression profiling in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders. Schizophr Res 124: 183-191.
58. Sano T, Reynolds JP, Jimenez-Mateos EM, Matsushima S, Taki W, et al. (2012) MicroRNA-34a upregulation during seizure-induced neuronal death. Cell death & disease 3: e287.
59. Zovoilis A, Agbemenyah HY, Agis-Balboa RC, Stilling RM, Edbauer D, et al. (2011) microRNA-34c is a novel target to treat dementias. EMBO J 30: 4299-4308.
60. Haramati S, Navon I, Issler O, Ezra-Nevo G, Gil S, et al. (2011) MicroRNA as repressors of stress-induced anxiety: the case of amygdalar miR-34. J Neurosci 31: 14191-14203.
61. Magill ST, Cambronne XA, Luikart BW, Lioy DT, Leighton BH, et al. (2010) microRNA-132 regulates dendritic growth and arborization of newborn neurons in the adult hippocampus. Proc Natl Acad Sci U S A 107: 20382-20387.
62. Pathania M, Torres-Reveron J, Yan L, Kimura T, Lin TV, et al. (2012) miR-132 Enhances Dendritic Morphogenesis, Spine Density, Synaptic Integration, and Survival of Newborn Olfactory Bulb Neurons. PLoS One 7: e38174.
63. Tognini P, Putignano E, Coatti A, Pizzorusso T, (2011) Experience-dependent expression of miR-132 regulates ocular dominance plasticity. Nat Neurosci 14: 1237-1239.
64. Cheng HY, Papp JW, Varlamova O, Dziema H, Russell B, et al. (2007) microRNA modulation of circadian-clock period and entrainment. Neuron 54: 813-829.
65. Lee K, Kim JH, Kwon OB, An K, Ryu J, et al. (2012) An activity-regulated microRNA, miR-188, controls dendritic plasticity and synaptic transmission by downregulating neuropilin-2. J Neurosci 32: 5678-5687.
66. Zhou S, Yu B, Qian T, Yao D, Wang Y, et al. (2011) Early changes of microRNAs expression in the dorsal root ganglia following rat sciatic nerve transection. Neuroscience letters 494: 89-93.
67. Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME, et al. (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439: 283-289.
68. Siegel G, Obernosterer G, Fiore R, Oehmen M, Bicker S, et al. (2009) A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nature cell biology 11: 705-716.
69. Jimenez-Mateos EM, Engel T, Merino-Serrais P, McKiernan RC, Tanaka K, et al. (2012) Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nature medicine 18 (7) (): 1087-1094.