Gene expression in the rat brain during sleep deprivation and recovery sleep: an Affymetrix GeneChip® study

Abstract

Previous studies have demonstrated that macromolecular synthesis in the brain is modulated in association with the occurrence of sleep and wakefulness. Similarly, the spectral composition of electroencephalographic activity that occurs during sleep is dependent on the duration of prior wakefulness. Since this homeostatic relationship between wake and sleep is highly conserved across mammalian species, genes that are truly involved in the electroencephalographic response to sleep deprivation (SD) might be expected to be conserved across mammalian species. Therefore, in the rat cerebral cortex, we have studied the effects of SD on the expression of immediate early gene (IEG) and heat shock protein (HSP) mRNAs previously shown to be upregulated in the mouse brain in SD and in recovery sleep (RS) after SD. We find that the molecular response to SD and RS in the brain is highly conserved between these two mammalian species, at least in terms of expression of IEG and HSP family members. Using Affymetrix Neurobiology U34 GeneChips ® , we also screened the rat cerebral cortex, basal forebrain, and hypothalamus for other genes whose expression may be modulated by SD or RS. We find that the response of the basal forebrain to SD is more similar to that of the cerebral cortex than to the hypothalamus. Together, these results suggest that sleep-dependent changes in gene expression in the cerebral cortex are similar across rodent species and therefore may underlie sleep historydependent changes in sleep electroencephalographic activity. KeywordsTaqman analysis; sleep deprivation; immediate early genes; basal forebrain; cerebral cortex; hypothalamus HHS Public Access Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptSleep is a homeostatic process in that the time spent asleep and the continuity of sleep states are directly related to the duration of prior wakefulness. Although sleep duration and the time spent in each of its stages are parameters commonly measured in sleep studies, sleep also has an intensity dimension, measurable by slow wave activity (SWA) in the electroencephalogram (EEG) during non-rapid eye movement (NREM) sleep. The amplitude of EEG SWA is directly proportional to the duration of prior wake and consequently has been proposed as a marker for the homeostatic regulation of sleep in mammals (Borbely and Achermann, 2000). Accordingly, sleep need, measurable as EEG SWA once sleep is initiated, is thought to accrue during wakefulness. Conversely, the decline of EEG SWA amplitude across a sleep bout is thought to reflect the diminution of the sleep-dependent "Process S" that reflects recovery from prior waking activities.The temporal dynamics of the sleep-dependent discharge of sleep need (reflected in the decay of the sleep-dependent Process S) is conserved among genetically distinct rodent strains (Franken et al., 2001). The conserved nature of Process S supports the concept that EEG SWA may be an electrophysiological marker of restorative neurochemical processes that occur during...

Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts

“…Spontaneous sleep-wakefulness or natural sleep is less well studied, based on the short, rapid cycling of sleep-wake bouts in rodents, the requirement to dissociate circadian and homeostatic influences, and the possible effects on cellular activities resulting from the practical difficulty of sacrificing a sleeping animal without first waking him up. Such technical considerations further elaborate the complexities involved in studies designed to understand the intracellular response to sleep.More recent microarray analyses showed that a small percentage of genes (i.e., 1-5%) were differentially expressed across sleep and waking states, independent of the time of day (TOD) or the brain region studied [Cirelli et al, 2004;Terao et al, 2006]. These patterns were conserved across rodent species [Terao et al, 2006] and encoded proteins associated with a variety of housekeeping functions, including energy metabolism, synaptic plasticity, membrane trafficking and maintenance, and cholesterol biosynthesis [Cirelli et al, 2004;Terao et al, 2006].…”

“…These patterns were conserved across rodent species [Terao et al, 2006] and encoded proteins associated with a variety of housekeeping functions, including energy metabolism, synaptic plasticity, membrane trafficking and maintenance, and cholesterol biosynthesis [Cirelli et al, 2004;Terao et al, 2006]. In addition, a subset of state-dependent mRNAs was common to two or more brain regions [Cirelli et al, 2004;Terao et al, 2006], suggesting that sleep influences global as well as regional brain function(s). While these studies provided valuable insights regarding the intracellular impact of sleep at the nucleic acid level, alterations in mRNA levels often do not reflect corresponding protein expression [Anderson and Seilhamer, 1997;Abbott et al, 1999;Gygi et al, 1999;Ideker et al, 2001;Takahashi, 2004], a more direct functional indicator of the cellular response to sleep.…”

“…To confirm the 2DE results and begin examination of cellular mechanisms associated with sleep, the expression of two sleep-related proteins was monitored following SD by mRNA and Western analyses. Frontal cortex tissue was analyzed, as this region exhibits the electrical activities characteristic of spontaneous sleep-wakefulness [Steriade and Timofeev, 2003] and SD [Borbely and Achermann, 1999], mediates some of the cognitive deficits associated with SD [Rogers et al, 2003;Van Dongen et al, 2003] and shows alterations in mRNA profiles after periods of spontaneous sleep-wakefulness [Cirelli et al, 2004] and SD [Cirelli et al, 2004;Terao et al, 2006]. …”

“…More recent microarray analyses showed that a small percentage of genes (i.e., 1-5%) were differentially expressed across sleep and waking states, independent of the time of day (TOD) or the brain region studied [Cirelli et al, 2004;Terao et al, 2006]. These patterns were conserved across rodent species [Terao et al, 2006] and encoded proteins associated with a variety of housekeeping functions, including energy metabolism, synaptic plasticity, membrane trafficking and maintenance, and cholesterol biosynthesis [Cirelli et al, 2004;Terao et al, 2006].…”

“…These patterns were conserved across rodent species [Terao et al, 2006] and encoded proteins associated with a variety of housekeeping functions, including energy metabolism, synaptic plasticity, membrane trafficking and maintenance, and cholesterol biosynthesis [Cirelli et al, 2004;Terao et al, 2006]. In addition, a subset of state-dependent mRNAs was common to two or more brain regions [Cirelli et al, 2004;Terao et al, 2006], suggesting that sleep influences global as well as regional brain function(s).…”