Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA.
Alcohol Clin Exp Res. 2013 Aug;37(8):1295-303. doi: 10.1111/acer.12100. Epub 2013 Mar 29.
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.
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.
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.
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.
异质 stock（HS/NPT）小鼠已被用于创建选择性繁殖的品系，以在黑暗中增加饮酒量（DID）。在第 2 天的 4 小时接触期结束时，两条选择的品系通常都达到了 1.00 毫克/毫升或更高的血液乙醇（EtOH）浓度（BEC）。目前尚不清楚遗传差异影响 DID 的机制。因此，本研究检查了转录组，这是遗传变异影响神经生物学的第一阶段。我们不仅关注差异表达（DE），还研究了基因转录本集体相互作用方式的变化，这些变化反映在共表达模式的变化中。
使用 Mouse Universal Genotyping Array 对 48 只/组的无经验小鼠进行基因分型，该阵列提供了 3683 个有信息的标记。使用标记到标记的策略进行数量性状位点（QTL）分析，显著对数优势（LOD）的阈值设定为 10.6。使用 Illumina Mouse 8.2 阵列测量腹侧纹状体中的基因表达。差异基因表达和加权基因共表达网络分析（WGCNA）的实施主要如其他地方所述。
在 DID 后，BEC 升高的显著 QTL 检测到在染色体 4、14 和 16 上；后 2 个与基因贫乏区域相关。没有一个 QTL 与已知的 EtOH 偏好饮酒的 QTL 重叠。在两个选择品系与 HS 对照之间，检测到 94 个转录本差异表达；与已知的偏好基因没有重叠。WGCNA 显示 2 个模块显示出选择对模块内连接性的显著影响。一些已知与 EtOH 表型相关的基因（例如，Gabrg1、Glra2、Grik1、Npy2r 和 Nts）的连接性发生了显著变化。
我们发现选择对共表达模式有明显而一致的影响；DE 变化更为温和，一致性较低。这里检测到的 QTL 和差异表达基因与偏好表型不同。这与行为数据一致，表明 DID 和偏好表型在遗传上有很大的不同。
