miRNA Regulation of Gene Expression: A Predictive Bioinformatics Analysis in the Postnatally Developing Monkey Hippocampus

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Favre, Grégoire ^a   Banta Lavenex, Pamela ^a   Lavenex, Pierre ^a  

^a UNIVERSITY OF FRIBOURG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; ASTROCYTE; BIOINFORMATICS; BRAIN DEVELOPMENT; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CONSERVATION; HAPLORHINI; HIPPOCAMPAL CA1 REGION; HIPPOCAMPAL CA3 REGION; HIPPOCAMPUS; MALE; MICROARRAY ANALYSIS; NERVE CELL; NONHUMAN; OLIGODENDROGLIA; POSTNATAL DEVELOPMENT;

ANIMALS; ASTROCYTES; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; DOWN-REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HAPLORHINI; HIPPOCAMPUS; HUMANS; MACACA MULATTA; MALE; MICRORNAS; MODELS, GENETIC; NEURONS; OLIGODENDROGLIA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

MAMMALIA; PRIMATES; RODENTIA;

EID: 84865461065     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043435     Document Type: Article

References (62)

1. Banta Lavenex P, Amaral DG, Lavenex P, (2006) Hippocampal lesion prevents spatial relational learning in adult macaque monkeys. J Neurosci 26: 4546-4558.
2. Banta Lavenex P, Lavenex P, (2009) Spatial memory and the monkey hippocampus: not all space is created equal. Hippocampus 19: 8-19.
3. Morris RG (2007) Theories of Hippocampal Function. In: Andersen P, Morris RG, Amaral DG, Bliss TV, O'Keefe J, editors. The Hippocampus Book. Oxford: University Press. 581-713.
4. Squire LR, Zola SM, (1996) Structure and function of declarative and nondeclarative memory systems. Proc Natl Acad Sci U S A 93: 13515-13522.
5. Milner B, Squire LR, Kandel ER, (1998) Cognitive neuroscience and the study of memory. Neuron 20: 445-468.
6. Jabes A, Banta Lavenex P, Amaral DG, Lavenex P, (2011) Postnatal development of the hippocampal formation: A stereological study in macaque monkeys. J Comp Neurol 519: 1051-1070.
7. Lavenex P, Sugden SG, Davis RR, Gregg JP, Banta Lavenex P, (2011) Developmental regulation of gene expression and astrocytic processes may explain selective hippocampal vulnerability. Hippocampus 21: 142-149.
8. Lavenex P, Banta Lavenex P, Amaral DG, (2007) Postnatal development of the primate hippocampal formation. Dev Neurosci 29: 179-192.
9. Hobert O, (2008) Gene regulation by transcription factors and microRNAs. Science 319: 1785-1786.
10. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
11. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
12. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, et al. (2004) Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 5: R13.
13. 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.
14. Vo N, Klein ME, Varlamova O, Keller DM, Yamamoto T, et al. (2005) A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis. Proc Natl Acad Sci U S A 102: 16426-16431.
15. Yu JY, Chung KH, Deo M, Thompson RC, Turner DL, (2008) MicroRNA miR-124 regulates neurite outgrowth during neuronal differentiation. Exp Cell Res 314: 2618-2633.
16. Fiore R, Schratt G, (2007) MicroRNAs in vertebrate synapse development. ScientificWorldJournal 7: 167-177.
17. Jose AM, Hunter CP, (2007) Transport of sequence-specific RNA interference information between cells. Annu Rev Genet 41: 305-330.
18. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. JR Statist Soc B 57: 289-300.
19. Betel D, Wilson M, Gabow A, Marks DS, Sander C, (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36: D149-153.
20. Lewis BP, Burge CB, Bartel DP, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
21. Wang X, (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14: 1012-1017.
22. Wang X, El Naqa IM, (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24: 325-332.
23. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158.
24. Griffiths-Jones S, (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342: 129-138.
25. Sethupathy P, Megraw M, Hatzigeorgiou AG, (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3: 881-886.
26. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG, (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 37: D155-158.
27. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
28. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
29. Artzi S, Kiezun A, Shomron N, (2008) miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics 9: 39.
30. Fiore R, Khudayberdiev S, Christensen M, Siegel G, Flavell SW, et al. (2009) Mef2-mediated transcription of the miR379-410 cluster regulates activity-dependent dendritogenesis by fine-tuning Pumilio2 protein levels. EMBO J 28: 697-710.
31. Peng S, Zhang Y, Zhang J, Wang H, Ren B, (2010) ERK in learning and memory: A review of recent research. Int J Mol Sci 11: 222-232.
32. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, et al. (2008) A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 28: 264-278.
33. Dinger ME, Mercer TR, Mattick JS, (2008) RNAs as extracellular signaling molecules. J Mol Endocrinol 40: 151-159.
34. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
35. Altemus KL, Lavenex P, Ishizuka N, Amaral DG, (2005) Morphological characteristics and electrophysiological properties of CA1 pyramidal neurons in macaque monkeys. Neuroscience 136: 741-756.
36. Abe K, Chisaka O, Van Roy F, Takeichi M, (2004) Stability of dendritic spines and synaptic contacts is controlled by alpha N-catenin. Nat Neurosci 7: 357-363.
37. Xie K, Allen KL, Kourrich S, Colon-Saez J, Thomas MJ, et al. (2010) Gbeta5 recruits R7 RGS proteins to GIRK channels to regulate the timing of neuronal inhibitory signaling. Nat Neurosci 13: 661-663.
38. Zhang R, Wang YQ, Su B, (2008) Molecular evolution of a primate-specific microRNA family. Mol Biol Evol 25: 1493-1502.
39. Parsons MJ, Grimm CH, Paya-Cano JL, Sugden K, Nietfeld W, et al. (2008) Using hippocampal microRNA expression differences between mouse inbred strains to characterise miRNA function. Mamm Genome 19: 552-560.
40. Flavell SW, Cowan CW, Kim TK, Greer PL, Lin Y, et al. (2006) Activity-dependent regulation of MEF2 transcription factors suppresses excitatory synapse number. Science 311: 1008-1012.
41. Altier C, Garcia-Caballero A, Simms B, You H, Chen L, et al. (2011) The Cavbeta subunit prevents RFP2-mediated ubiquitination and proteasomal degradation of L-type channels. Nat Neurosci 14: 173-180.
42. Glazov EA, McWilliam S, Barris WC, Dalrymple BP, (2008) Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol 25: 939-948.
43. Peter ME, (2010) Targeting of mRNAs by multiple miRNAs: the next step. Oncogene 29: 2161-2164.
44. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
45. Nishikura K, (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79: 321-349.
46. Duxbury MS, Ashley SW, Whang EE, (2005) RNA interference: a mammalian SID-1 homologue enhances siRNA uptake and gene silencing efficacy in human cells. Biochem Biophys Res Commun 331: 459-463.
47. Flexner JB, Flexner LB, Stellar E, (1963) Memory in mice as affected by intracerebral puromycin. Science 141: 57-59.
48. Stanton PK, Sarvey JM, (1984) Blockade of long-term potentiation in rat hippocampal CA1 region by inhibitors of protein synthesis. J Neurosci 4: 3080-3088.
49. Lopez-Salon M, Alonso M, Vianna MR, Viola H, Mello e Souza T, et al. (2001) The ubiquitin-proteasome cascade is required for mammalian long-term memory formation. Eur J Neurosci 14: 1820-1826.
50. Mabb AM, Ehlers MD, (2010) Ubiquitination in postsynaptic function and plasticity. Annu Rev Cell Dev Biol 26: 179-210.
51. Jabes A, Banta Lavenex P, Amaral DG, Lavenex P, (2010) Quantitative analysis of postnatal neurogenesis and neuron number in the macaque monkey dentate gyrus. Eur J Neurosci 31: 273-285.
52. Bani-Yaghoub M, Tremblay RG, Lei JX, Zhang D, Zurakowski B, et al. (2006) Role of Sox2 in the development of the mouse neocortex. Dev Biol 295: 52-66.
53. Sahni V, Mukhopadhyay A, Tysseling V, Hebert A, Birch D, et al. (2010) BMPR1a and BMPR1b signaling exert opposing effects on gliosis after spinal cord injury. J Neurosci 30: 1839-1855.
54. Boneva NB, Kaplamadzhiev DB, Sahara S, Kikuchi H, Pyko IV, et al. (2011) Expression of fatty acid-binding proteins in adult hippocampal neurogenic niche of postischemic monkeys. Hippocampus 21: 162-171.
55. Oberheim NA, Wang X, Goldman S, Nedergaard M, (2006) Astrocytic complexity distinguishes the human brain. Trends Neurosci 29: 547-553.
56. Kelleher RJ, 3rd, Bear MF (2008) The autistic neuron: troubled translation? Cell 135: 401-406.
57. Cui Y, Costa RM, Murphy GG, Elgersma Y, Zhu Y, et al. (2008) Neurofibromin regulation of ERK signaling modulates GABA release and learning. Cell 135: 549-560.
58. Denayer E, Ahmed T, Brems H, Van Woerden G, Borgesius NZ, et al. (2008) Spred1 is required for synaptic plasticity and hippocampus-dependent learning. J Neurosci 28: 14443-14449.
59. Bauer PJ, (2006) Constructing a past in infancy: a neuro-developmental account. Trends Cogn Sci 10: 175-181.
60. Luo L, O'Leary DD, (2005) Axon retraction and degeneration in development and disease. Annu Rev Neurosci 28: 127-156.
61. Squire LR, (1992) Memory and the Hippocampus- a Synthesis From Findings With Rats, Monkeys, and Humans. Psychol Rev 99: 195-231.
62. Allen NC, Bagade S, McQueen MB, Ioannidis JP, Kavvoura FK, et al. (2008) Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database. Nat Genet 40: 827-834.