What are microarrays teaching us about sleep?

Trends in Molecular Medicine

Volumn 15, Issue 2, 2009, Pages 79-87

  Mackiewicz, Miroslaw ^a   Zimmerman, John E ^a   Shockley, Keith R ^b   Churchill, Gary A ^b   Pack, Allan I ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR CLOCK;

BRAIN REGION; CELL STRESS; DISEASE MARKER; DNA SEQUENCE; DOWN REGULATION; ENDOPLASMIC RETICULUM STRESS; ENERGY METABOLISM; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC DIFFERENCE; GENETIC TRANSCRIPTION; HOMEOSTASIS; HUMAN; LIPID METABOLISM; MICROARRAY ANALYSIS; NERVE CELL PLASTICITY; NONHUMAN; QUANTITATIVE TRAIT LOCUS; REVIEW; SIGNAL TRANSDUCTION; SLEEP; SLEEP APNEA SYNDROME; SLEEP DEPRIVATION; SLEEP DISORDER; SOMNOLENCE; WAKEFULNESS;

GENE EXPRESSION PROFILING; GENETIC VARIATION; HUMANS; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; QUANTITATIVE TRAIT LOCI; SLEEP; SLEEP DISORDERS; WAKEFULNESS;

EID: 60649083558     PISSN: 14714914     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molmed.2008.12.002     Document Type: Review

References (101)

1. Mackiewicz M., and Pack A.I. Functional genomics of sleep. Respir. Physiol. Neurobiol. 135 (2003) 207-220
2. Rhyner T.A., et al. Molecular cloning of forebrain mRNAs which are modulated by sleep deprivation. Eur. J. Neurosci. 2 (1990) 1063-1073
3. Liang P., and Pardee A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257 (1992) 967-971
4. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
5. Gupta B.P., and Sternberg P.W. The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Genome Biol. 4 (2003) 238
6. Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science 287 (2000) 2185-2195
7. Quackenbush J. Computational analysis of microarray data. Nat. Rev. Genet. 2 (2001) 418-427
8. Kerr M.K., and Churchill G.A. Statistical design and the analysis of gene expression microarray data. Genet. Res. 77 (2001) 123-128
9. Mignot E. Why we sleep: the temporal organization of recovery. PLoS Biol. 6 (2008) e106
10. Cirelli C., and Bushey D. Sleep and wakefulness in Drosophila melanogaster. Ann. N. Y. Acad. Sci. 1129 (2008) 323-329
11. Cirelli C., and Tononi G. Is sleep essential?. PLoS Biol. 6 (2008) e216
12. Colten H.R., and Altevogt B.M. Sleep Disorders and Sleep Deprivation: an Unmet Public Health Problem (2006), The National Academies Press
13. Cirelli C., et al. Extensive and divergent effects of sleep and wakefulness on brain gene expression. Neuron 41 (2004) 35-43
14. Cirelli C., et al. Sleep and wakefulness modulate gene expression in Drosophila. J. Neurochem. 94 (2005) 1411-1419
15. Cirelli C., and Tononi G. Locus ceruleus control of state-dependent gene expression. J. Neurosci. 24 (2004) 5410-5419
16. Jones S., et al. Molecular correlates of sleep and wakefulness in the brain of the white-crowned sparrow. J. Neurochem. 105 (2008) 46-62
17. Mackiewicz M., et al. Macromolecule biosynthesis: a key function of sleep. Physiol. Genomics 31 (2007) 441-457
18. Maret S., et al. Homer1a is a core brain molecular correlate of sleep loss. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 20090-20095
19. Zimmerman J.E., et al. Multiple mechanisms limit the duration of wakefulness in Drosophila brain. Physiol. Genomics 27 (2006) 337-350
20. Hendricks J.C., et al. Rest in Drosophila is a sleep-like state. Neuron 25 (2000) 129-138
21. Shaw P.J., et al. Correlates of sleep and waking in Drosophila melanogaster. Science 287 (2000) 1834-1837
22. Zimmerman J.E., et al. Conservation of sleep: insights from non-mammalian model systems. Trends Neurosci. 31 (2008) 371-376
23. Yokogawa T., et al. Characterization of sleep in zebrafish and insomnia in hypocretin receptor mutants. PLoS Biol. 5 (2007) e277
24. Prober D.A., et al. Hypocretin/orexin overexpression induces an insomnia-like phenotype in zebrafish. J. Neurosci. 26 (2006) 13400-13410
25. Zhdanova I.V., et al. Melatonin promotes sleep-like state in zebrafish. Brain Res. 903 (2001) 263-268
26. Raizen D.M., et al. Lethargus is a Caenorhabditis elegans sleep-like state. Nature 451 (2008) 569-572
27. Allada R., and Siegel J.M. Unearthing the phylogenetic roots of sleep. Curr. Biol. 18 (2008) R670-R679
28. Youngsteadt E. Genetics. Simple sleepers. Science 321 (2008) 334-337
29. Olofsson B., and de Bono M. Sleep: dozy worms and sleepy flies. Curr. Biol. 18 (2008) R204-R206
30. Graves L.A., et al. Genetic evidence for a role of CREB in sustained cortical arousal. J. Neurophysiol. 90 (2003) 1152-1159
31. Hendricks J.C., et al. A non-circadian role for cAMP signaling and CREB activity in Drosophila rest homeostasis. Nat. Neurosci. 4 (2001) 1108-1115
32. Foltenyi K., et al. Activation of EGFR and ERK by rhomboid signaling regulates the consolidation and maintenance of sleep in Drosophila. Nat. Neurosci. 10 (2007) 1160-1167
33. Van Buskirk C., and Sternberg P.W. Epidermal growth factor signaling induces behavioral quiescence in Caenorhabditis elegans. Nat. Neurosci. 10 (2007) 1300-1307
34. Tononi G., and Cirelli C. Sleep and synaptic homeostasis: a hypothesis. Brain Res. Bull. 62 (2003) 143-150
35. Tononi G., and Cirelli C. Sleep function and synaptic homeostasis. Sleep Med. Rev. 10 (2006) 49-62
36. Vyazovskiy V., et al. Unilateral vibrissae stimulation during waking induces interhemispheric EEG asymmetry during subsequent sleep in the rat. J. Sleep Res. 9 (2000) 367-371
37. Vyazovskiy V.V., et al. Regional pattern of metabolic activation is reflected in the sleep EEG after sleep deprivation combined with unilateral whisker stimulation in mice. Eur. J. Neurosci. 20 (2004) 1363-1370
38. Simons K., and Toomre D. Lipid rafts and signal transduction. Nat. Rev. Mol. Cell Biol. 1 (2000) 31-39
39. Butchbach M.E., et al. Association of excitatory amino acid transporters, especially EAAT2, with cholesterol-rich lipid raft microdomains: importance for excitatory amino acid transporter localization and function. J. Biol. Chem. 279 (2004) 34388-34396
40. Eroglu C., et al. Glutamate-binding affinity of Drosophila metabotropic glutamate receptor is modulated by association with lipid rafts. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 10219-10224
41. Hering H., et al. Lipid rafts in the maintenance of synapses, dendritic spines, and surface AMPA receptor stability. J. Neurosci. 23 (2003) 3262-3271
42. Schrattenholz A., and Soskic V. NMDA receptors are not alone: dynamic regulation of NMDA receptor structure and function by neuregulins and transient cholesterol-rich membrane domains leads to disease-specific nuances of glutamate-signalling. Curr. Top. Med. Chem. 6 (2006) 663-686
43. Van Dongen H.P., et al. The cumulative cost of additional wakefulness: dose-response effects on neurobehavioral functions and sleep physiology from chronic sleep restriction and total sleep deprivation. Sleep 26 (2003) 117-126
44. Franken P., et al. The homeostatic regulation of sleep need is under genetic control. J. Neurosci. 21 (2001) 2610-2621
45. Franken P., et al. Genetic determinants of sleep regulation in inbred mice. Sleep 22 (1999) 155-169
46. Shaw P.J., et al. Stress response genes protect against lethal effects of sleep deprivation in Drosophila. Nature 417 (2002) 287-291
47. Naidoo N., et al. Sleep deprivation induces the unfolded protein response in mouse cerebral cortex. J. Neurochem. 92 (2005) 1150-1157
48. Terao A., et al. Differential increase in the expression of heat shock protein family members during sleep deprivation and during sleep. Neuroscience 116 (2003) 187-200
49. Kaufman R.J. Orchestrating the unfolded protein response in health and disease. J. Clin. Invest. 110 (2002) 1389-1398
50. Ma Y., and Hendershot L.M. The mammalian endoplasmic reticulum as a sensor for cellular stress. Cell Stress Chaperones 7 (2002) 222-229
51. Schroder M., and Kaufman R.J. The mammalian unfolded protein response. Annu. Rev. Biochem. 74 (2005) 739-789
52. Hobson J.A. Sleep is of the brain, by the brain and for the brain. Nature 437 (2005) 1254-1256
53. Cirelli C., et al. Reduced sleep in Drosophila Shaker mutants. Nature 434 (2005) 1087-1092
54. Koh K., et al. Identification of SLEEPLESS, a sleep-promoting factor. Science 321 (2008) 372-376
55. Wu M.N., et al. A genetic screen for sleep and circadian mutants reveals mechanisms underlying regulation of sleep in Drosophila. Sleep 31 (2008) 465-472
56. Raizen D.M., et al. A novel gain-of-function mutant of the cyclic GMP-dependent protein kinase egl-4 affects multiple physiological processes in Caenorhabditis elegans. Genetics 173 (2006) 177-187
57. Metaxakis A., et al. Minos as a genetic and genomic tool in Drosophila melanogaster. Genetics 171 (2005) 571-581
58. Thibault S.T., et al. A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat. Genet. 36 (2004) 283-287
59. Spradling A.C., et al. The Berkeley Drosophila Genome Project gene disruption project: single P element insertions mutating 25% of vital Drosophila genes. Genetics 153 (1999) 135-177
60. Dietzl G., et al. A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448 (2007) 151-156
61. McGuire S.E., et al. Spatiotemporal gene expression targeting with the TARGET and gene-switch systems in Drosophila. Sci. STKE 2004 (2004) pl6
62. Naidoo N., et al. A role for the molecular chaperone protein BiP/GRP78 in Drosophila sleep homeostasis. Sleep 30 (2007) 557-565
63. Dorner A.J., et al. Overexpression of GRP78 mitigates stress induction of glucose regulated proteins and blocks secretion of selective proteins in Chinese hamster ovary cells. EMBO J. 11 (1992) 1563-1571
64. Bertolotti A., et al. Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response. Nat. Cell Biol. 2 (2000) 326-332
65. Kerkhof G.A., and Van Dongen H.P. Morning-type and evening-type individuals differ in the phase position of their endogenous circadian oscillator. Neurosci. Lett. 218 (1996) 153-156
66. Gottlieb D.J., et al. Genome-wide association of sleep and circadian phenotypes. BMC Med. Genet. 8 Suppl 1 (2007) S9
67. Franken P., et al. Genetic variation in EEG activity during sleep in inbred mice. Am. J. Physiol. 275 (1998) R1127-R1137
68. Franken P., and Tafti M. Genetics of sleep and sleep disorders. Front. Biosci. 8 (2003) e381-e397
69. Tafti M., and Franken P. Invited review: genetic dissection of sleep. J. Appl. Physiol. 92 (2002) 1339-1347
70. Mackiewicz M., et al. Analysis of the QTL for sleep homeostasis in mice: Homer1a is a likely candidate. Physiol. Genomics 33 (2008) 91-99
71. Bottai D., et al. Synaptic activity-induced conversion of intronic to exonic sequence in Homer 1 immediate early gene expression. J. Neurosci. 22 (2002) 167-175
72. Kittleson M.M., and Hare J.M. Molecular signature analysis: using the myocardial transcriptome as a biomarker in cardiovascular disease. Trends Cardiovasc. Med. 15 (2005) 130-138
73. Mohr S., and Liew C.C. The peripheral-blood transcriptome: new insights into disease and risk assessment. Trends Mol. Med. 13 (2007) 422-432
74. Seugnet L., et al. Identification of a biomarker for sleep drive in flies and humans. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 19913-19918
75. Irwin M.R., et al. Sleep deprivation and activation of morning levels of cellular and genomic markers of inflammation. Arch. Intern. Med. 166 (2006) 1756-1762
76. Hoffmann M.S., et al. Microarray studies of genomic oxidative stress and cell cycle responses in obstructive sleep apnea. Antioxid. Redox Signal. 9 (2007) 661-669
77. Khalyfa, A. et al. (2008) Genome-wide gene expression profiling in children with non-obese obstructive sleep apnea. Sleep Med.; Epub ahead of print
78. Dawson D., and McCulloch K. Managing fatigue: it's about sleep. Sleep Med. Rev. 9 (2005) 365-380
79. Jones C.B., et al. Fatigue and the criminal law. Ind. Health 43 (2005) 63-70
80. Van Dongen H.P., et al. Individual differences in adult human sleep and wakefulness: Leitmotif for a research agenda. Sleep 28 (2005) 479-496
81. Pack A.I. Advances in sleep-disordered breathing. Am. J. Respir. Crit. Care Med. 173 (2006) 7-15
82. McNicholas W.T., and Ryan S. Obstructive sleep apnoea syndrome: translating science to clinical practice. Respirology 11 (2006) 136-144
83. Arnardottir, E. et al. Molecular signatures of obstructive sleep apnea in adults: a review and perspective. Sleep (in press)
84. Methippara M.M., et al. Salubrinal, an inhibitor of protein synthesis, promotes deep slow wave sleep. Am. J. Physiol. Regul. Integr. Comp. Physiol. 296 (2009) R178-R184
85. Vyazovskiy V.V., et al. Molecular and electrophysiological evidence for net synaptic potentiation in wake and depression in sleep. Nat. Neurosci. 11 (2008) 200-208
86. Frank M.G., et al. Sleep enhances plasticity in the developing visual cortex. Neuron 30 (2001) 275-287
87. Stickgold R. Sleep-dependent memory consolidation. Nature 437 (2005) 1272-1278
88. Nakanishi H., et al. Positive correlations between cerebral protein synthesis rates and deep sleep in Macaca mulatta. Eur. J. Neurosci. 9 (1997) 271-279
89. Ramm P., and Smith C.T. Rates of cerebral protein synthesis are linked to slow wave sleep in the rat. Physiol. Behav. 48 (1990) 749-753
90. Pace-Schott E.F., and Hobson J.A. The neurobiology of sleep: genetics, cellular physiology and subcortical networks. Nat. Rev. Neurosci. 3 (2002) 591-605
91. Saper C.B., et al. Homeostatic, circadian, and emotional regulation of sleep. J. Comp. Neurol. 493 (2005) 92-98
92. Saper C.B., et al. The sleep switch: hypothalamic control of sleep and wakefulness. Trends Neurosci. 24 (2001) 726-731
93. Nelson S.B., et al. The problem of neuronal cell types: a physiological genomics approach. Trends Neurosci. 29 (2006) 339-345
94. Sultan M., et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321 (2008) 956-960
95. Knutson K.L., et al. The metabolic consequences of sleep deprivation. Sleep Med. Rev. 11 (2007) 163-178
96. Ayas N.T., et al. A prospective study of sleep duration and coronary heart disease in women. Arch. Intern. Med. 163 (2003) 205-209
97. Cirelli C., and Tononi G. Differences in gene expression between sleep and waking as revealed by mRNA differential display. Brain Res. Mol. Brain Res. 56 (1998) 293-305
98. Cirelli C., and Tononi G. Gene expression in the brain across the sleep-waking cycle. Brain Res. 885 (2000) 303-321
99. Terao A., et al. Gene expression in the rat brain during sleep deprivation and recovery sleep: an Affymetrix GeneChip study. Neuroscience 137 (2006) 593-605
100. Cirelli C., et al. Changes in brain gene expression after long-term sleep deprivation. J. Neurochem. 98 (2006) 1632-1645
101. Storey J. A direct approach to false discovery rates. J. Roy. Stat. Soc. B 64 (2002) 479-498