title: Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.
abstract: Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep).
  
  
  
  In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV). RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1-3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h) do so on average with a time constant that is similar to the time constant for the discharge of sleep need.
  
  
  
  We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally distinct classes of genes.
authors: Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
authors: Jason R
authors: JR
authors: Gerstner
authors: Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
authors: John N
authors: JN
authors: Koberstein
authors: Department of Neuroscience, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, 19104, USA.
authors: Adam J
authors: AJ
authors: Watson
authors: Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
authors: Nikolai
authors: N
authors: Zapero
authors: Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA.
authors: Davide
authors: D
authors: Risso
authors: Department of Statistics, University of California, Berkeley, CA, USA.|Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia.|Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
authors: Terence P
authors: TP
authors: Speed
authors: Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA. marcos.frank@wsu.edu.
authors: Marcos G
authors: MG
authors: Frank
authors: Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA. lucia.peixoto@wsu.edu.
authors: Lucia
authors: L
authors: Peixoto
mesh_terms: D000818:Animals; D002540:Cerebral Cortex / Q000502:physiology*; D002940:Circadian Rhythm / Q000235:genetics; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006706:Homeostasis / Q000235:genetics*; D008297:Male; D051379:Mice; D012890:Sleep / Q000235:genetics*; D012892:Sleep Deprivation / Q000235:genetics; D059467:Transcriptome
keywords: Circadian; Gene; Microarray; Sleep; Sleep deprivation; Transcriptomics; mRNA