title: Selection for drinking in the dark alters brain gene coexpression networks.
abstract: BACKGROUND
  Heterogeneous stock (HS/NPT) mice have been used to create lines selectively bred in replicate for elevated drinking in the dark (DID). Both selected lines routinely reach a blood ethanol (EtOH) concentration (BEC) of 1.00 mg/ml or greater at the end of the 4-hour period of access in Day 2. The mechanisms through which genetic differences influence DID are currently unclear. Therefore, the current study examines the transcriptome, the first stage at which genetic variability affects neurobiology. Rather than focusing solely on differential expression (DE), we also examine changes in the ways that gene transcripts collectively interact with each other, as revealed by changes in coexpression patterns.
  
  
  METHODS
  Naïve mice (N = 48/group) were genotyped using the Mouse Universal Genotyping Array, which provided 3,683 informative markers. Quantitative trait locus (QTL) analysis used a marker-by-marker strategy with the threshold for a significant logarithm of odds (LOD) set at 10.6. Gene expression in the ventral striatum was measured using the Illumina Mouse 8.2 array. Differential gene expression and the weighted gene coexpression network analysis (WGCNA) were implemented largely as described elsewhere.
  
  
  RESULTS
  Significant QTLs for elevated BECs after DID were detected on chromosomes 4, 14, and 16; the latter 2 were associated with gene-poor regions. None of the QTLs overlapped with known QTLs for EtOH preference drinking. Ninety-four transcripts were detected as being differentially expressed in both selected lines versus HS controls; there was no overlap with known preference genes. The WGCNA revealed 2 modules as showing significant effects of both selections on intramodular connectivity. A number of genes known to be associated with EtOH phenotypes (e.g., Gabrg1, Glra2, Grik1, Npy2r, and Nts) showed significant changes in connectivity.
  
  
  CONCLUSIONS
  We found marked and consistent effects of selection on coexpression patterns; DE changes were more modest and less concordant. The QTLs and differentially expressed genes detected here are distinct from the preference phenotype. This is consistent with behavioral data and suggests that the DID and preference phenotypes are markedly different genetically.
authors.affiliation: Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA. iancuo@ohsu.edu
authors.forename: Ovidiu D
authors.initials: OD
authors.lastname: Iancu
authors.forename: Denesa
authors.initials: D
authors.lastname: Oberbeck
authors.forename: Priscila
authors.initials: P
authors.lastname: Darakjian
authors.forename: Pamela
authors.initials: P
authors.lastname: Metten
authors.forename: Shannon
authors.initials: S
authors.lastname: McWeeney
authors.forename: John C
authors.initials: JC
authors.lastname: Crabbe
authors.forename: Robert
authors.initials: R
authors.lastname: Hitzemann
mesh_terms: D000428:Alcohol Drinking / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D001479:Basal Ganglia / Q000378:metabolism*; D001923:Brain Chemistry / Q000235:genetics*; D003624:Darkness; D005260:Female; D053263:Gene Regulatory Networks; D008297:Male; D051379:Mice; D040641:Quantitative Trait Loci; D012641:Selection, Genetic
keywords: Alcohol; Binge; Drinking in the Dark; Microarray; Mouse; Selection; Weighted Gene Coexpression Network Analysis
references.citation: BMC Genomics. 2010 Oct 19;11:585
references.pmid: 20959017
references.citation: J Neural Transm (Vienna). 2012 Apr;119(4):425-33
references.pmid: 22072270
references.citation: Neuroscience. 1999;93(1):227-36
references.pmid: 10430486
references.citation: BMC Syst Biol. 2007 Nov 21;1:54
references.pmid: 18031580
references.citation: Alcohol Clin Exp Res. 2011 Apr;35(4):659-70
references.pmid: 21223303
references.citation: BMC Bioinformatics. 2008 Dec 29;9:559
references.pmid: 19114008
references.citation: Ann N Y Acad Sci. 2011 Jan;1216:24-40
references.pmid: 21272009
references.citation: Behav Genet. 1999 Jan;29(1):47-57
references.pmid: 10371758
references.citation: Neuropharmacology. 2011 Jun;60(7-8):1269-80
references.pmid: 21185315
references.citation: Curr Pharm Des. 2010;16(19):2141-8
references.pmid: 20482509
references.citation: J Pharmacol Exp Ther. 1994 Nov;271(2):969-76
references.pmid: 7965819
references.citation: Addict Biol. 2012 Jan;17(1):13-32
references.pmid: 21955048
references.citation: Alcohol. 2011 Aug;45(5):427-40
references.pmid: 21194877
references.citation: Behav Genet. 2006 Mar;36(2):248-60
references.pmid: 16482403
references.citation: Addict Biol. 2011 Apr;16(2):238-50
references.pmid: 21182574
references.citation: Alcohol Clin Exp Res. 2009 Aug;33(8):1382-90
references.pmid: 19426171
references.citation: Alcohol Clin Exp Res. 2000 Dec;24(12):1873-82
references.pmid: 11141048
references.citation: Eur J Neurosci. 2006 Dec;24(12):3496-506
references.pmid: 17229098
references.citation: PLoS Comput Biol. 2011 Jan 20;7(1):e1001057
references.pmid: 21283776
references.citation: Addict Biol. 2006 Sep;11(3-4):195-269
references.pmid: 16961758
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12149-54
references.pmid: 21730162
references.citation: Bioinformatics. 2012 Jun 15;28(12):1592-7
references.pmid: 22556371
references.citation: Alcohol Clin Exp Res. 2008 Nov;32(11):1962-8
references.pmid: 18782340
references.citation: Mamm Genome. 2001 Dec;12(12):893-9
references.pmid: 11707775
references.citation: Psychopharmacology (Berl). 2009 May;203(4):713-22
references.pmid: 19052728
references.citation: Mamm Genome. 2007 Jul;18(6-7):473-81
references.pmid: 17674098
references.citation: Physiol Behav. 2005 Jan 31;84(1):53-63
references.pmid: 15642607
references.citation: Genes Brain Behav. 2012 Feb;11(1):29-37
references.pmid: 21967164
references.citation: Neuropharmacology. 2012 Jun;62(7):2430-9
references.pmid: 22387532
references.citation: Psychopharmacology (Berl). 2005 Apr;178(4):471-80
references.pmid: 15765261
references.citation: Alcohol Clin Exp Res. 2011 Jan;35(1):99-107
references.pmid: 21039631
references.citation: J Neurosci. 2008 Jan 2;28(1):264-78
references.pmid: 18171944
references.citation: Neuropsychopharmacology. 2009 Apr;34(5):1245-54
references.pmid: 18818659
references.citation: Neuropsychopharmacology. 2012 May;37(6):1409-21
references.pmid: 22218088
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6368-73
references.pmid: 16618939
references.citation: J Neurosci. 2003 Oct 29;23(30):9752-60
references.pmid: 14586002
references.citation: Genes Brain Behav. 2007 Feb;6(1):1-18
references.pmid: 17233637
references.citation: Genetics. 1992 Jun;131(2):479-91
references.pmid: 1644282
references.citation: Brain Res. 2009 Dec 11;1305 Suppl:S27-36
references.pmid: 19781529
references.citation: J Neurochem. 2004 Jun;89(5):1175-85
references.pmid: 15147510
references.citation: EMBO J. 2009 Apr 22;28(8):1170-9
references.pmid: 19229292
references.citation: Brain Res. 2007 Feb 23;1134(1):148-61
references.pmid: 17198693
references.citation: Nat Rev Neurosci. 2012 Feb 15;13(3):169-82
references.pmid: 22334212
references.citation: Bioinformatics. 2008 Mar 1;24(5):719-20
references.pmid: 18024473
references.citation: J Pharmacol Exp Ther. 1996 Aug;278(2):510-7
references.pmid: 8768698
references.citation: Behav Genet. 1997 Jan;27(1):55-66
references.pmid: 9145544
references.citation: Genes Brain Behav. 2012 Jun;11(4):424-35
references.pmid: 22405477
references.citation: Stat Appl Genet Mol Biol. 2005;4:Article17
references.pmid: 16646834
references.citation: Mamm Genome. 2006 Dec;17(12):1193-204
references.pmid: 17143586
references.citation: Physiol Behav. 2012 Jun 6;106(3):325-31
references.pmid: 22245775
references.citation: Biol Psychiatry. 2009 Apr 15;65(8):662-70
references.pmid: 19095222
references.citation: Bioinformatics. 2008 Jul 1;24(13):1547-8
references.pmid: 18467348
references.citation: JAMA. 2007 Oct 10;298(14):1641-51
references.pmid: 17925516