Effects of selection for ethanol preference on gene expression in the nucleus accumbens of HS-CC mice.

paper Cited Public

Authors: Colville, A M; Iancu, O D; Oberbeck, D L; Darakjian, P; Zheng, C L; Walter, N A R; Harrington, C A; Searles, R P; McWeeney, S; Hitzemann, R J
Year: 2017
Journal: Genes, brain, and behavior
PMID: 28058793
DOI: 10.1111/gbb.12367
PMCID: PMC5671806

#	Section	Preview
20	Results — Selection effects on gene-level expression	It was of interest to note that among the affected hub nodes in the greenyellow and lightcyan…
21	Results — Selection effects on gene cosplicing	The cosplicing network was formed as described elsewhere (Iancu et al. 2015). Twenty-nine genes…
22	Results — Selection effects on gene cosplicing	The DW and splicing network data were integrated to focus on those nodes that are hubs in only one…
23	Discussion	Brain gene expression data are available for mice selectively bred for ethanol preference from F2…
24	Discussion	Three generations of breeding were sufficient for significant segregation of the high and low…
25	Discussion	As described by Grahame et al. (1999) and Oberlin et al. (2011), replicate lines of high alcohol…
26	Discussion	studies focused on the effects of selection and the apparent inverse genetic relationship between…
27	Discussion	The RNA-Seq data were analyzed at both the gene and exon level. Both analysis strategies confirmed…
28	Discussion	The DV gene expression statistic is one approach for assessing whether there are differences in the…
29	Discussion	The DV genes were highly enriched (P < 10−42) in a single coexpression module (greenyellow). The…
30	Discussion	Fyn has been implicated in the regulation of a variety of ethanol phenotypes; Fyn knockout (KO) mice…
31	Discussion	The DW gene expression statistic assesses the change in connectivity of a single gene to all other…
32	Discussion	including 4 cadherin and 18 protocadherin genes. Previous studies have implicated Cdh11, Cdh12,…
33	Discussion	Preference selection had a marked effect on alternative splicing. The mammalian genome contains over…
34	Discussion	The Mantel correlations, similar to the Pearson correlations for coexpression, were used to assess…
35	Discussion	TBC1 domain family member 9 (Tbc1d9), nucleoporin 50 [Nup50, cytoplasmic FMR1-interacting protein 1…
36	Discussion	Thirty-six splicing hub nodes were significantly (FDR < 0.05) affected by selection. In contrast,…
37	Discussion	Beginning with the selection of the long-sleep and short-sleep mice (see references in McClearn &…
38	Discussion	our observation that when comparing striatal gene regulation among F2, HS4 and HS-CC mice (Iancu et…

Name	Type
129Sv/Im local	cohort
acute ethanol withdrawal local	phenotype
acute preference consumption local	phenotype
ADD2 local	gene
Adra1a	gene
A/J local	cohort
alcohol	phenotype
alcoholism	phenotype
alcohol preference	phenotype
alcohol-related phenotypes	phenotype
alcohol self-administration	phenotype
alternative splicing	drug
Arcturus Picopure Kit	drug
brain	anatomy
brown local	cohort
brown module	cohort
C57BL/6J	cohort
CAST/Ei local	cohort
CBL local	gene
Cdh11 local	gene
CDH11 local	gene
CDH12	gene
CDH13	gene
Cdh19 local	gene
CDH19 local	gene
Cdkl5 local	gene
CDKL5 local	gene
cell adhesion molecules local	drug
cell–cell adhesion local	phenotype
Chrna7	gene
chromosome 2 local	variant
chronic preference consumption local	phenotype
Cyfip1 local	gene
CYFIP1 local	gene
DCC	gene
differentially wired (DW) local	phenotype
DOCK1 local	gene
DO mice local	cohort
Dpp6	gene
drug dependence	phenotype
DW local	cohort
DW local	phenotype
DW genes local	cohort
Eco-Fresh bedding	drug
ethanol consumption	phenotype
ethanol preference	phenotype
ethanol preference consumption local	phenotype
excessive preference consumption local	phenotype
F2 local	cohort
F2 intercross local	cohort
Fyn	gene
Fzd3	gene
G23 local	cohort
Gabrb2	gene
genes	gene
GLUTAMATE_SECRETION local	phenotype
Gm12356 local	gene
Gm26672 local	gene
GPR63 local	gene
green module	cohort
greenyellow local	cohort
greenyellow module local	cohort
GREENYELLOW_MODULE local	cohort
GRIA1	gene
GRIA3	gene
Grid2	gene
GRIK2	gene
GRIN2A	gene
GRIN2B	gene
GRM1	gene
GRM3	gene
GRM4	gene
GRM7	gene
GSE65950 local	cohort
high alcohol preference	phenotype
high line	cohort
high preference local	phenotype
high preference line	cohort
HS4 local	cohort
HS-CC	cohort
HS-CC founders	cohort
HS-CC mice	cohort
HS/Ibg local	cohort
HS/Npt	cohort
Htr2a	gene
Htr5a	gene
Igf1r	gene
inbred strains	cohort
Kcna4	gene
Kcnab1 local	gene
Kcnb1	gene
Kcnb2	gene
Kcnd2	gene
Kif1a	gene
Kif1b local	gene
Kif5a local	gene
Kif5b local	gene
Kif5c local	gene
KIT	gene
lightcyan local	cohort
lightcyan module local	cohort
long non-coding RNAs local	drug
long-sleep mice local	phenotype
loss of righting reflex	phenotype
low alcohol preference	phenotype
low line	cohort
low preference local	phenotype
low preference line	cohort
low preferring lines local	cohort
Mapk1	gene
Mapk8ip3 local	gene
MegaMUGA mouse genotyping array local	drug
meiotic drive locus local	variant
mice	cohort
M. musculus local	cohort
NAc	anatomy
NAc shell	anatomy
Naive S4 mice local	cohort
Ndrg1	gene
NEURONAL_CELL_BODY local	phenotype
neuron part local	phenotype
NFKB1	gene
NOD/Lt local	cohort
Nploc4	gene
NP rats	cohort
nucleus accumbens shell	anatomy
Nup50 local	gene
NUP50 local	gene
NZO/HILt local	cohort
Oprd1	cohort
Pcdh15	gene
PCDHGA2 local	gene
PCDHGA5 local	gene
Pcdhga6	gene
PCDHGA7B2 local	gene
Pcdhgb5	gene
PCDHGB7 local	gene
Pchha9 local	gene
PCHHA9 local	gene
Pcsk1	gene
Pdch15 local	gene
Pde10a local	gene
Pde4b	gene
Pde4d	gene
pink local	cohort
PINK_MODULE local	cohort
Portland VA Medical Center	cohort
preference for ethanol	phenotype
preference risk local	phenotype
preferring rats local	cohort
PSEN1	gene
Purina 5001 chow	drug
PWK/Ph local	cohort
Rab local	gene
Rap local	gene
Ras GTPase local	gene
Ras/MAPK pathway local	drug
RESPONSE_TO_ENDOGENOUS_STIMULUS local	phenotype
RI strains local	cohort
S0 mice	cohort
S4 alcohol-naïve pups local	cohort
S4 animals local	cohort
saccharin	drug
selected lines	cohort
sex	phenotype
SHANK3	gene
shell	anatomy
short-sleep mice local	phenotype
short-term selection (STS) local	cohort
SIGNALING_RECEPTOR_ACTIVITY local	phenotype
single nucleotide polymorphisms	variant
Slc6a15	gene
Snap25	gene
Sod1	gene
SORT1	gene
Sos1 local	gene
SOS1 local	gene
Srga local	gene
striatum	anatomy
synaptic function	phenotype
Tbc1d9 local	gene
TBC1D9 local	gene
TCFAP2A local	gene
Tmem208 local	gene
Tnik local	gene
Two-bottle choice preference test local	phenotype
water	drug
WSB alleles local	variant
WSB/EiJ local	cohort
WSB/EiJ inbred strain local	cohort
WSB founder strain local	cohort
yellow local	cohort
yellow module	cohort
ZBT7A local	gene

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In this knowledge base

Title	Year	PMID
Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.	2021	31477794

External

Title	Authors	Journal	Year	Link
Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice - The Central Nucleus of the Amygdala.	Anderson JQ et al.	—	2025	→
Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala	Anderson JQ et al.	—	2025	—
Modeling Brain Gene Expression in Alcohol Use Disorder with Genetic Animal Models.	Hitzemann R et al.	—	2025	→
Brain gene expression differences related to ethanol preference in the collaborative cross founder strains.	Anderson JQ et al.	—	2022	→
Alcohol Dependence in Rats Is Associated with Global Changes in Gene Expression in the Central Amygdala.	Kisby BR et al.	—	2021	→
Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.	Rao X et al.	—	2021	→
Effect of chronic ethanol consumption in rhesus macaques on the nucleus accumbens core transcriptome.	Walter N et al.	—	2021	→
Heritability of ethanol consumption and pharmacokinetics in a genetically diverse panel of collaborative cross mouse strains and their inbred founders.	Bagley JR et al.	—	2021	→
On the Use of Heterogeneous Stock Mice to Map Transcriptomes Associated With Excessive Ethanol Consumption.	Hitzemann R et al.	—	2021	→
The escalation in ethanol consumption following chronic intermittent ethanol exposure is blunted in mice expressing ethanol-resistant GluN1 or GluN2A NMDA receptor subunits.	Zamudio PA et al.	—	2021	→
Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46.	Walter NAR et al.	—	2020	→
Knock-in Mice Expressing an Ethanol-Resistant GluN2A NMDA Receptor Subunit Show Altered Responses to Ethanol.	Zamudio PA et al.	—	2020	→
Phenotypic and gene expression features associated with variation in chronic ethanol consumption in heterogeneous stock collaborative cross mice.	Hitzemann R et al.	—	2020	→
RNA-Seq Analysis of Genetic and Transcriptome Network Effects of Dual-Trait Selection for Ethanol Preference and Withdrawal Using SOT and NOT Genetic Models.	Kozell LB et al.	—	2020	→
High-Diversity Mouse Populations for Complex Traits.	Saul MC et al.	—	2019	→
Regional Analysis of the Brain Transcriptome in Mice Bred for High and Low Methamphetamine Consumption.	Hitzemann R et al.	—	2019	→
Cross-species molecular dissection across alcohol behavioral domains.	Farris SP et al.	—	2018	→
Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs.	Iancu OD et al.	—	2018	→
Genetics of metabolic syndrome: potential clues from wild-derived inbred mouse strains.	Karunakaran S et al.	—	2018	→
NMDA receptor GluN2A subunit deletion protects against dependence-like ethanol drinking.	Jury NJ et al.	—	2018	→
Regional Differences and Similarities in the Brain Transcriptome for Mice Selected for Ethanol Preference From HS-CC Founders.	Colville AM et al.	—	2018	→
Alignment of the transcriptome with individual variation in animals selectively bred for High Drinking-In-the-Dark (HDID).	Hitzemann R et al.	—	2017	→