Computational analysis of gene regulation in animal sleep deprivation

Physiological Genomics

Volumn 42, Issue 3, 2010, Pages 427-436

  Wang, Haifang ^a   Liu, Yuting ^a   Briesemann, Marko ^a   Yan, Jun ^a  

^a MAX PLANCK INSTITUTE   (Germany)

Author keywords

Brain; Short term sleep deprivation

Indexed keywords

ANIMAL BEHAVIOR; ANIMAL EXPERIMENT; ARTICLE; BRAIN REGION; CYCLIC AMP RESPONSIVE ELEMENT; FLY; GENE CONTROL; GENE EXPRESSION; GENE REGULATORY NETWORK; MALE; MICROARRAY ANALYSIS; MOUSE; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; RAT; SLEEP DEPRIVATION; SLEEP TIME; SPARROW; SYNAPTOGENESIS;

ANIMALS; BEHAVIOR, ANIMAL; COMPUTATIONAL BIOLOGY; DROSOPHILA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; META-ANALYSIS AS TOPIC; MICE; MICE, INBRED C57BL; MICE, MUTANT STRAINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; SLEEP DEPRIVATION; SPARROWS;

ANIMALIA; MUS; RATTUS;

EID: 77955719183     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00205.2009     Document Type: Article

References (39)

1. Adamantidis A, de Lecea L. Sleep and metabolism: shared circuits, new connections. Trends Endocrinol Metab 19: 362-370, 2008.
2. Born J, Rasch B, Gais S. Sleep to remember. Neuroscientist 12: 410-424, 2006.
3. Carter JH, Lefebvre JM, Wiest DL, Tourtellotte WG. Redundant role for early growth response transcriptional regulators in thymocyte differentiation and survival. J Immunol 178: 6796-6805, 2007. (Pubitemid 46847404)
4. Cirelli C, Gutierrez CM, Tononi G. Extensive and divergent effects of sleep and wakefulness on brain gene expression. Neuron 41: 35-43, 2004.
5. Cirelli C, LaVaute TM, Tononi G. Sleep and wakefulness modulate gene expression in Drosophila. J Neurochem 94: 1411-1419, 2005.
6. Cirelli C, Tononi G. Is sleep essential? PLoS Biol 6: e216, 2008.
7. de Magalhaes JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 25: 875-881, 2009.
8. Durchdewald M, Guinea-Viniegra J, Haag D, Riehl A, Lichter P, Hahn M, Wagner EF, Angel P, Hess J. Podoplanin is a novel Fos target gene in skin carcinogenesis. Cancer Res 68: 6877-6883, 2008.
9. Espana RA, Scammell TE. Sleep neurobiology for the clinician. Sleep 27: 811-820, 2004.
10. Frank MG. The mystery of sleep function: current perspectives and future directions. Rev Neurosci 17: 375-392, 2006.
11. Franken P, Dijk DJ. Circadian clock genes and sleep homeostasis. Eur J Neurosci 29: 1820-1829, 2009.
12. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80, 2004.
13. Gilestro GF, Tononi G, Cirelli C. Widespread changes in synaptic markers as a function of sleep and wakefulness in Drosophila. Science 324: 109-112, 2009.
14. Han T, Wang J, Tong W, Moore MM, Fuscoe JC, Chen T. Microarray analysis distinguishes differential gene expression patterns from large and small colony thymidine kinase mutants of L5178Y mouse lymphoma cells. BMC Bioinformatics 7, Suppl 2: S9, 2006. (Pubitemid 46442970)
15. Hayaishi O, Urade Y. Prostaglandin D2 in sleep-wake regulation: recent progress and perspectives. Neuroscientist 8: 12-15, 2002.
16. Hendricks JC, Williams JA, Panckeri K, Kirk D, Tello M, Yin JC, Sehgal A. A non-circadian role for cAMP signaling and CREB activity in Drosophila rest homeostasis. Nat Neurosci 4: 1108-1115, 2001. (Pubitemid 34116556)
17. Hunter P. To sleep, perchance to live. Sleeping is vital for health, cognitive function, memory and long life. EMBO Rep 9: 1070-1073, 2008.
18. Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, McWeeney S, Dunn JJ, Mandel G, Goodman RH. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell 119: 1041-1054, 2004.
19. Jones S, Pfister-Genskow M, Benca RM, Cirelli C. Molecular correlates of sleep and wakefulness in the brain of the white-crowned sparrow. J Neurochem 105: 46-62, 2008.
20. Latchman DS. Transcription factors: bound to activate or repress. Trends Biochem Sci 26: 211-213, 2001.
21. Mackiewicz M, Shockley KR, Romer MA, Galante RJ, Zimmerman JE, Naidoo N, Baldwin DA, Jensen ST, Churchill GA, Pack AI. Macromolecule biosynthesis: a key function of sleep. Physiol Genomics 31: 441-457, 2007.
22. Mackiewicz M, Zimmerman JE, Shockley KR, Churchill GA, Pack AI. What are microarrays teaching us about sleep? Trends Mol Med 15: 79-87, 2009.
23. Maret S, Dorsaz S, Gurcel L, Pradervand S, Petit B, Pfister C, Hagenbuchle O, O'Hara BF, Franken P, Tafti M. Homer1a is a core brain molecular correlate of sleep loss. Proc Natl Acad Sci USA 104: 20090-20095, 2007.
24. Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA. Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol 2: 2006.0017, 2006.
25. Peng Y, Jahroudi N. The NFY transcription factor functions as a repressor and activator of the von Willebrand factor promoter. Blood 99: 2408-2417, 2002. (Pubitemid 34525426)
26. Schenk M. Learn, sleep and remember. Dtsch Med Wochenschr 133: p39, 2008.
27. Siegel JM. Sleep viewed as a state of adaptive inactivity. Nat Rev Neurosci 10: 747-753, 2009.
28. Szymusiak R, McGinty D. Hypothalamic regulation of sleep and arousal. Ann NY Acad Sci 1129: 275-286, 2008.
29. Tafti M, Franken P. Molecular analysis of sleep. Cold Spring Harb Symp Quant Biol 72: 573-578, 2007.
30. Terao A, Steininger TL, Hyder K, Apte-Deshpande A, Ding J, Rishipathak D, Davis RW, Heller HC, Kilduff TS. Differential increase in the expression of heat shock protein family members during sleep deprivation and during sleep. Neuroscience 116: 187-200, 2003.
31. Terao A, Wisor JP, Peyron C, Apte-Deshpande A, Wurts SW, Edgar DM, Kilduff TS. Gene expression in the rat brain during sleep deprivation and recovery sleep: an Affymetrix GeneChip study. Neuroscience 137: 593-605, 2006.
32. Vyazovskiy VV, Cirelli C, Pfister-Genskow M, Faraguna U, Tononi G. Molecular and electrophysiological evidence for net synaptic potentiation in wake and depression in sleep. Nat Neurosci 11: 200-208, 2008.
33. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R, Pruss M, Schacherer F, Thiele S, Urbach S. The TRANSFAC system on gene expression regulation. Nucleic Acids Res 29: 281-283, 2001.
34. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28: 316-319, 2000.
35. Yan J, Wang H, Liu Y, Shao C. Analysis of gene regulatory networks in the mammalian circadian rhythm. PLoS Comput Biol 4: e1000193, 2008.
36. Zhang GC, Mao LM, Liu XY, Parelkar NK, Arora A, Yang L, Hains M, Fibuch EE, Wang JQ. In vivo regulation of Homer1a expression in the striatum by cocaine. Mol Pharmacol 71: 1148-1158, 2007.
37. Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci USA 102: 4459-4464, 2005.
38. Zimmerman JE, Naidoo N, Raizen DM, Pack AI. Conservation of sleep: insights from non-mammalian model systems. Trends Neurosci 31: 371-376, 2008.
39. Zimmerman JE, Rizzo W, Shockley KR, Raizen DM, Naidoo N, Mackiewicz M, Churchill GA, Pack AI. Multiple mechanisms limit the duration of wakefulness in Drosophila brain. Physiol Genomics 27: 337-350, 2006.