Genome-Wide Profiling of the Activity-Dependent Hippocampal Transcriptome

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Hermey, Guido ^a   Mahlke, Claudia ^a   Gutzmann, Jakob J ^a   Schreiber, Jörg ^b   Blüthgen, Nils ^c   Kuhl, Dietmar ^a  

^a UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^b MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

^c CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

3' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; ARTICLE; BRAIN NERVE CELL; CONTROLLED STUDY; EXON; GENE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE INDUCTION; HIPPOCAMPUS; IN SITU HYBRIDIZATION; MALE; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; TRANSCRIPTOMICS; ZWINT GENE;

3' UNTRANSLATED REGIONS; ALTERNATIVE SPLICING; ANIMALS; BINDING SITES; CLUSTER ANALYSIS; EXONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HIPPOCAMPUS; MALE; MICE; MOLECULAR SEQUENCE ANNOTATION; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84885739058     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0076903     Document Type: Article

References (47)

1. Kauer JA, Malenka RC, (2007) Synaptic plasticity and addiction. Nat Rev Neurosci 8: 844-858.
2. Milner B, Squire LR, Kandel ER, (1998) Cognitive neuroscience and the study of memory. Neuron 20: 445-468.
3. Duman RS, (2002) Synaptic plasticity and mood disorders. Mol Psychiatry 7Suppl 1: S29-34.
4. Goelet P, Castellucci VF, Schacher S, Kandel ER, (1986) The long and the short of long-term memory-a molecular framework. Nature 322: 419-422.
5. Flavell SW, Greenberg ME, (2008) Signaling mechanisms linking neuronal activity to gene expression and plasticity of the nervous system. Annu Rev Neurosci 31: 563-590.
6. Sheng M, Greenberg ME, (1990) The regulation and function of c-fos and other immediate early genes in the nervous system. Neuron 4: 477-485.
7. Nedivi E, Hevroni D, Naot D, Israeli D, Citri Y, (1993) Numerous candidate plasticity-related genes revealed by differential cDNA cloning. Nature 363: 718-722.
8. Qian Z, Gilbert ME, Colicos MA, Kandel ER, Kuhl D, (1993) Tissue-Plasminogen Activator Is Induced as an Immediate Early Gene during Seizure, Kindling and Long-Term Potentiation. Nature 361: 453-457.
9. Yamagata K, Andreasson KI, Kaufmann WE, Barnes CA, Worley PF, (1993) Expression of a Mitogen-Inducible Cyclooxygenase in Brain Neurons- Regulation by Synaptic Activity and Glucocorticoids. Neuron 11: 371-386.
10. Leslie JH, Nedivi E, (2011) Activity-regulated genes as mediators of neural circuit plasticity. Prog Neurobiol 94: 223-237.
11. Altar CA, Laeng P, Jurata LW, Brockman JA, Lemire A, et al. (2004) Electroconvulsive seizures regulate gene expression of distinct neurotrophic signaling pathways. J Neurosci 24: 2667-2677.
12. French PJ, O'Connor V, Voss K, Stean T, Hunt SP, et al. (2001) Seizure-induced gene expression in area CA1 of the mouse hippocampus. European Journal of Neuroscience 14: 2037-2041.
13. Hunsberger JG, Bennett AH, Selvanayagam E, Duman RS, Newton SS, (2005) Gene profiling the response to kainic acid induced seizures. Brain Res Mol Brain Res 141: 95-112.
14. Park CS, Gong R, Stuart J, Tang SJ, (2006) Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus. J Biol Chem 281: 30195-30211.
15. Jacobs GH, Stockwell PA, Tate WP, Brown CM, (2006) Transterm-extended search facilities and improved integration with other databases. Nucleic Acids Res 34: D37-40.
16. Kielbasa SM, Klein H, Roider HG, Vingron M, Bluthgen N, (2010) TransFind-predicting transcriptional regulators for gene sets. Nucleic Acids Res 38Suppl: W275-280.
17. McLin JP, Steward O, (2006) Comparison of seizure phenotype and neurodegeneration induced by systemic kainic acid in inbred, outbred, and hybrid mouse strains. Eur J Neurosci 24: 2191-2202.
18. Guzowski JF, Lyford GL, Stevenson GD, Houston FP, McGaugh JL, et al. (2000) Inhibition of activity-dependent arc protein expression in the rat hippocampus impairs the maintenance of long-term potentiation and the consolidation of long-term memory. J Neurosci 20: 3993-4001.
19. Plath N, Ohana O, Dammermann B, Errington ML, Schmitz D, et al. (2006) Arc/Arg3.1 is essential for the consolidation of synaptic plasticity and memories. Neuron 52: 437-444.
20. Chowdhury S, Shepherd JD, Okuno H, Lyford G, Petralia RS, et al. (2006) Arc/Arg3.1 interacts with the endocytic machinery to regulate AMPA receptor trafficking. Neuron 52: 445-459.
21. Messaoudi E, Kanhema T, Soule J, Tiron A, Dagyte G, et al. (2007) Sustained Arc/Arg3.1 synthesis controls long-term potentiation consolidation through regulation of local actin polymerization in the dentate gyrus in vivo. J Neurosci 27: 10445-10455.
22. Shepherd JD, Rumbaugh G, Wu J, Chowdhury S, Plath N, et al. (2006) Arc/Arg3.1 mediates homeostatic synaptic scaling of AMPA receptors. Neuron 52: 475-484.
23. Brakeman PR, Lanahan AA, O'Brien R, Roche K, Barnes CA, et al. (1997) Homer: a protein that selectively binds metabotropic glutamate receptors. Nature 386: 284-288.
24. Link W, Konietzko U, Kauselmann G, Krug M, Schwanke B, et al. (1995) Somatodendritic expression of an immediate early gene is regulated by synaptic activity. Proc Natl Acad Sci U S A 92: 5734-5738.
25. Lyford GL, Yamagata K, Kaufmann WE, Barnes CA, Sanders LK, et al. (1995) Arc, a growth factor and activity-regulated gene, encodes a novel cytoskeleton-associated protein that is enriched in neuronal dendrites. Neuron 14: 433-445.
26. Hermey G, (2009) The Vps10p-domain receptor family. Cell Mol Life Sci 66: 2677-2689.
27. Hermey G, Plath N, Hubner CA, Kuhl D, Schaller HC, et al. (2004) The three sorCS genes are differentially expressed and regulated by synaptic activity. J Neurochem 88: 1470-1476.
28. Vezzani A, Sperk G, Colmers WF, (1999) Neuropeptide Y: emerging evidence for a functional role in seizure modulation. Trends Neurosci 22: 25-30.
29. Bottai D, Guzowski JF, Schwarz MK, Kang SH, Xiao B, et al. (2002) Synaptic activity-induced conversion of intronic to exonic sequence in Homer 1 immediate early gene expression. J Neurosci 22: 167-175.
30. Kato A, Ozawa F, Saitoh Y, Hirai K, Inokuchi K, (1997) vesl, a gene encoding VASP/Ena family related protein, is upregulated during seizure, long-term potentiation and synaptogenesis. FEBS Lett 412: 183-189.
31. Chen CY, Shyu AB, (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem Sci 20: 465-470.
32. Jacobsen A, Wen J, Marks DS, Krogh A, (2010) Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res 20: 1010-1019.
33. Lai EC, Tam B, Rubin GM, (2005) Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev 19: 1067-1080.
34. Flavell SW, Kim TK, Gray JM, Harmin DA, Hemberg M, et al. (2008) Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60: 1022-1038.
35. Lonze BE, Ginty DD, (2002) Function and regulation of CREB family transcription factors in the nervous system. Neuron 35: 605-623.
36. Barnes G, Puranam RS, Luo Y, McNamara JO, (2003) Temporal specific patterns of semaphorin gene expression in rat brain after kainic acid-induced status epilepticus. Hippocampus 13: 1-20.
37. Moore MJ, (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309: 1514-1518.
38. Famulski JK, Vos L, Sun X, Chan G, (2008) Stable hZW10 kinetochore residency, mediated by hZwint-1 interaction, is essential for the mitotic checkpoint. J Cell Biol 180: 507-520.
39. Lee HK, Safieddine S, Petralia RS, Wenthold RJ, (2002) Identification of a novel SNAP25 interacting protein (SIP30). J Neurochem 81: 1338-1347.
40. van Vlijmen T, Vleugel M, Evers M, Mohammed S, Wulf PS, et al. (2008) A unique residue in rab3c determines the interaction with novel binding protein Zwint-1. FEBS Lett 582: 2838-2842.
41. Sala C, Futai K, Yamamoto K, Worley PF, Hayashi Y, et al. (2003) Inhibition of dendritic spine morphogenesis and synaptic transmission by activity-inducible protein Homer1a. J Neurosci 23: 6327-6337.
42. Schoch S, Gundelfinger ED, (2006) Molecular organization of the presynaptic active zone. Cell Tissue Res 326: 379-391.
43. Abel T, Martin KC, Bartsch D, Kandel ER, (1998) Memory suppressor genes: inhibitory constraints on the storage of long-term memory. Science 279: 338-341.
44. Abel T, Kandel E, (1998) Positive and negative regulatory mechanisms that mediate long-term memory storage. Brain Res Brain Res Rev 26: 360-378.
45. Zucman-Rossi J, Legoix P, Thomas G, (1996) Identification of new members of the Gas2 and Ras families in the 22q12 chromosome region. Genomics 38: 247-254.
46. Elam C, Hesson L, Vos MD, Eckfeld K, Ellis CA, et al. (2005) RRP22 is a farnesylated, nucleolar, Ras-related protein with tumor suppressor potential. Cancer Res 65: 3117-3125.
47. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, et al. (2002) Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415: 436-442.