Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains
Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains
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DOI：
10.1111/j.1530-0277.2007.00397.x
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发表时间：
2007-07-01
影响因子：
3.2
通讯作者：
Edenberg, Howard J.
中科院分区：
文献类型：
--
作者：
Carr, Lucinda G.;Kimpel, Mark W.;Edenberg, Howard J.
背景：通过分析iP大鼠和iNP大鼠的杂交，在4号染色体上发现了一个影响酒精偏好的高度显著的数量性状位点（QTL）。与iNP背景菌株相比，将iP染色体4 QTL区间转移到iNP的同源菌株（NP.P）表现出预期的酒精消耗增加。本研究旨在鉴定4号染色体QTL区间的基因，这些基因可能导致酒精初始基因菌株和背景菌株之间酒精消耗的差异。方法：从6个NP的5个脑区提取RNA。在Affymetrix大鼠基因组230 2.0芯片上分别标记和分析P和6 iNP大鼠，寻找顺式调控和反式调控基因。使用鲁棒多芯片平均（RMA）将表达水平归一化。采用实时定量聚合酶链反应验证差异基因表达。分析了五个单独的大脑区域（伏隔核、额叶皮质、杏仁核、海马和纹状体），以检测渗入QTL区间内基因的差异表达，以及该区域外的基因。为了提高检测差异表达基因的能力，还进行了联合分析（平均每只动物的5个离散脑区数据）。结果：集中分析QTL区间内基因的单个脑区分析在所有5个脑区均检测到差异表达；至少1个区域共检测到35个基因，从伏隔核的6个基因到额叶皮质的22个基因不等。全基因组分析发现QTL外的差异表达基因很少。跨大脑区域的综合分析更为有力。对QTL区间内的基因进行分析，确认了个别区域检测到的19个基因，并检测到另外15个基因。全基因组分析检测到区间外1个差异表达基因。结论：通过基因芯片分析携带酒精偏好QTL的同源动物的基因表达差异，确定了顺式调节的酒精消耗候选基因。
Background: A highly significant quantitative trait locus (QTL) on chromosome 4 that influenced alcohol preference was identified by analyzing crosses between the iP and iNP rats. Congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP (NP.P) exhibited the expected increase in alcohol consumption compared with the iNP background strain. This study was undertaken to identify genes in the chromosome 4 QTL interval that might contribute to the differences in alcohol consumption between the alcohol-naive congenic and background strains.Methods: RNA from 5 brain regions from each of 6 NP.P and 6 iNP rats was labeled and analyzed separately on an Affymetrix Rat Genome 230 2.0 microarray to look for both cis-regulated and trans-regulated genes. Expression levels were normalized using robust multi-chip average (RMA). Differential gene expression was validated using quantitative real-time polymerase chain reaction. Five individual brain regions (nucleus accumbens, frontal cortex, amygdala, hippocampus, and striatum) were analyzed to detect differential expression of genes within the introgressed QTL interval, as well as genes outside that region. To increase the power to detect differentially expressed genes, combined analyses (averaging data from the 5 discrete brain regions of each animal) were also carried out.Results: Analyses within individual brain regions that focused on genes within the QTL interval detected differential expression in all 5 brain regions; a total of 35 genes were detected in at least 1 region, ranging from 6 genes in the nucleus accumbens to 22 in the frontal cortex. Analysis of the whole genome detected very few differentially expressed genes outside the QTL. Combined analysis across brain regions was more powerful. Analysis focused on the genes within the QTL interval confirmed 19 of the genes detected in individual regions and detected 15 additional genes. Whole genome analysis detected 1 differentially expressed gene outside the interval.Conclusions: Cis-regulated candidate genes for alcohol consumption were identified using microarray profiling of gene expression differences in congenic animals carrying a QTL for alcohol preference.