mRNA Levels in the Rat Liver Display Strain-Specific, Hereditary and AHR-Dependent Components. Rattus norvegicus

Background The rat is a major model organism in toxicogenomics and pharmacogenomics, and the use of steady-state hepatic mRNA levels to predict and understand drug toxicity and mechanism is well-established. Surprisingly, the inter- and intra-strain variability of rat mRNA expression has not been evaluated, nor has the extent of its hereditability been established. We address these issues by studying three rat strains (Long-Evans, Hans/Wistar, and Sprague-Dawley) and two F2 lines derived from Long-Evans x Hans/Wistar crosses. Results Using three independent techniques – variance analysis, linear modelling, and unsupervised pattern recognition – we characterize large amounts of both intra- and inter-strain variability in mRNA levels. Importantly, both sources of variability are highly non-random, and are enriched for specific functional groups. Specific transcription-factor binding-sites are enriched in their promoter regions, and these genes occur in “islands” throughout the rat genome. Using the two F2 crosses we study the hereditability of hepatic mRNA levels and show that the majority of rat genes appear to exhibit directional genetics, with only a small fraction having evidence for interacting loci. Finally, a comparison of inter-strain heterogeneity between mouse and rat orthologs shows more heterogeneity in rats than mice, and find that rat and mouse heterogeneity are uncorrelated. Conclusions Our results establish that hepatic mRNA levels are relatively homogeneous within rat strains, but highly variable between them. This variability may be related to increased activity specific transcription-factors, and has clear functional consequences. Future toxicogenomic and pharmacogenomic studies may take advantage of this phenomenon by surveying panels of rat strains. Keywords: Inter-Strain Comparison Overall design: We profiled the basal mRNA levels in three strains and two lines of rat, each using four biological replicates.

【背景】大鼠是毒理基因组学（toxicogenomics）与药物基因组学（pharmacogenomics）领域的核心模式生物，利用稳态肝脏mRNA水平（steady-state hepatic mRNA levels）预测、解析药物毒性及其作用机制的方法已得到广泛验证。令人意外的是，目前尚未有研究评估大鼠mRNA表达的品系间与品系内变异，也未明确其遗传力（heritability）的分布范围。本研究通过分析3种大鼠品系（Long-Evans、Hans/Wistar与Sprague-Dawley）以及2个由Long-Evans与Hans/Wistar杂交获得的F2代品系，对上述问题展开了探讨。

【结果】本研究采用方差分析（variance analysis）、线性建模（linear modelling）与无监督模式识别（unsupervised pattern recognition）三种独立技术，对mRNA水平中大量存在的品系内与品系间变异进行了系统表征。值得注意的是，两类变异均呈现高度非随机性，且显著富集于特定功能类群（functional groups）。这些基因的启动子区域（promoter regions）中富集了特定的转录因子结合位点（transcription-factor binding-sites），且此类基因在大鼠基因组中呈“岛屿状”分布。通过对两个F2杂交系的分析，我们探究了肝脏mRNA水平的遗传力，结果显示绝大多数大鼠基因呈现定向遗传，仅少数基因存在互作位点（interacting loci）的相关证据。最后，通过比较小鼠与大鼠直系同源基因（orthologs）的品系间异质性（heterogeneity），我们发现大鼠的异质性显著高于小鼠，且二者的异质性并无相关性。

【结论】本研究结果证实，大鼠品系内的肝脏mRNA水平相对同质，但品系间差异显著。此类变异可能与特定转录因子的活性升高相关，并具有明确的功能影响。未来的毒理基因组学与药物基因组学研究可通过筛查大鼠品系组，利用这一现象开展相关工作。

关键词：品系间比较（Inter-Strain Comparison）

【实验整体设计】我们对3种大鼠品系及2个F2代品系的基础mRNA水平进行了检测，每个组别均设置4次生物学重复（biological replicates）。