Temporal profiles of hepatic gene expression in PAR bZip triple knockout mice

The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. Mouse knockout models of different parts of the circadian clock network (Bmal1, Cry1/2, and Hlf/Dbp/Tef) exposed to controlled feeding regimens (ad libitum, night restricted feeding) were generated and analyzed for their temporal hepatic transcriptome. A genetical ablation of core loop elements altered feeding patterns that were restored by night restricted feeding. Mainly genes with a high amplitude were driven by the circadian clock but natural feeding patterns equally contributed to rhythmic gene expression with lower amplitude. We observed that Bmal1 and Cry1/2 KOs differed in rhythmic gene expression and identified differences in mean expression levels as a predictor for rhythmic gene expression. In Hlf/Dbp/Tef KO, mRNA levels of Hlf/Dbp/Tef target genes were decreased, albeit rhythmicity was overall preserved potentially due to the activity of the D-Box binding repressor NFIL3. Genes that lost rhythmicity in Hlf/Dbp/Tef KOs were identified to be no direct targets of PARbZip factors and presumably lost rhythmicity due to indirect effects. Collectively, our findings provide unprecedent insights into the diurnal transcriptome in mouse liver and defines the contribution of subloops of the circadian clock network and natural feeding cycles. The developed algorithm and a webapp to browse the outcomes of the study are publicly available to serve as a resource for the scientific community. RNA-Seq from mRNA of mouse liver across the course of a day. Time-series include mRNA profiles of PARbZip proficient (Hlf+/+/Dbp+/+/Tef+/+) and deficient (Hlf-/-/Dbp-/-/Tef-/-) mice under an ad libitum feeding regimen.昼夜节律钟（circadian clock）与节律性进食均为肝脏节律性基因表达的重要调控因子。然而，目前尚不清楚昼夜节律钟网络与自然进食节律在多大程度上共同影响节律性基因表达。 为系统性解答这一科学问题，我们开发了一款算法，用于探究不同数量实验条件间的差异节律性。我们构建了接受可控进食方案（自由进食（ad libitum）、夜间限饲（night restricted feeding））处理的昼夜节律钟网络不同组分的小鼠敲除模型（Bmal1、Cry1/2及Hlf/Dbp/Tef），并对其肝脏时序转录组（hepatic transcriptome）进行了分析。 昼夜节律核心环路元件的遗传敲除会改变小鼠进食模式，而夜间限饲可恢复该异常进食模式。 主要以高振幅表达的基因受昼夜节律钟调控，而自然进食模式同样可对低振幅节律性基因的表达产生贡献。 我们发现Bmal1与Cry1/2敲除小鼠的节律性基因表达存在显著差异，并确定平均表达水平差异可作为节律性基因表达的预测因子。 在Hlf/Dbp/Tef敲除小鼠中，Hlf/Dbp/Tef靶基因的mRNA水平有所降低，尽管整体节律性得以保留，这可能得益于D盒结合阻遏因子NFIL3（D-Box binding repressor NFIL3）的调控活性。 在Hlf/Dbp/Tef敲除小鼠中丧失节律性的基因并非PARbZip家族因子的直接靶标，其节律性丧失推测由间接效应导致。 综上，本研究为小鼠肝脏的日间转录组提供了前所未有的见解，并明确了昼夜节律钟网络亚环路与自然进食周期的具体贡献。本研究开发的算法与用于浏览研究结果的网页应用已公开可用，可为全球科研共同体提供宝贵的研究资源。 本数据集包含小鼠肝脏mRNA的全日RNA测序（RNA-Seq）数据，时序序列涵盖了自由进食方案下PARbZip功能正常（Hlf+/+/Dbp+/+/Tef+/+）与功能缺陷（Hlf-/-/Dbp-/-/Tef-/-）小鼠的mRNA表达谱。