The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6 weeks, and the liver samples were collected starting at 9:00 AM (CT1), and every 4 h in a 24-h cycle (CT5, CT9, CT13, CT17 and CT21). Total RNA was extracted and subjected to RNA-Seq data (deposited as GSE 133342, L-DD). To compare gene oscillation pattern under normal light-dark condition (LD, GSE114400) and short time (2 days) dark-dark condition (S-DD, GSE70497), these data were retried from GEO database, and the trimmed mean of M-values normalization was used to normalize the three RNA-seq data followed by MetaCycle analysis. Approximate 12.1% of the genes under L-DD exhibited significant rhythmically expression. The top 5 biological processes enriched in L-DD oscillation genes were mRNA processing, aromatic compound catabolic process, mitochondrion organization, heterocycle catabolic process and cellular nitrogen compound mitotic catabolic process. The endogenous circadian rhythms of clock genes, P450 genes and lipid metabolism genes under L-DD were further compared with LD and S-DD. The oscillation patterns were similar but the period and amplitude of those oscillation genes were slightly altered. RT-qPCR confirmed the selected RNA sequence findings. This is the first study to profile oscillation gene expressions under L-DD. Our data indicate that clock genes, P450 genes and lipid metabolism genes expressed rhythmically under L-DD. Light was not the necessary factor for persisting circadian rhythm but influenced the period and amplitude of oscillation genes.

中文翻译：

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持续黑暗下小鼠肝脏内源性昼夜节律时间基因的表达

昼夜节律调节生理功能和新陈代谢。昼夜节律时间（CT）是量化内源生物钟节律的单位，与光的影响无关。为了了解整个 CT 期间的基因表达变化，将 C57BL/6 J 小鼠维持在恒定黑暗 (DD) 下 6 周，并从上午 9:00 (CT1) 开始收集肝脏样本，并在 24 小时内每 4 小时收集一次。 h 周期（CT5、CT9、CT13、CT17 和 CT21）。提取总 RNA 并进行 RNA-Seq 数据处理（保藏号为 GSE 133342，L-DD）。为了比较正常明暗条件（LD，GSE114400）和短时间（2天）暗-暗条件（S-DD，GSE70497）下的基因振荡模式，这些数据从GEO数据库中重试，并且M-使用值归一化对三个 RNA-seq 数据进行归一化，然后进行 MetaCycle 分析。L-DD下大约12.1%的基因表现出显着的节律性表达。L-DD振荡基因富集的前5位生物过程是mRNA加工、芳香化合物分解代谢过程、线粒体组织、杂环分解代谢过程和细胞氮化合物有丝分裂分解代谢过程。进一步将L-DD下的时钟基因、P450基因和脂代谢基因的内源性昼夜节律与LD和S-DD进行比较。振荡模式相似，但这些振荡基因的周期和幅度略有改变。RT-qPCR 证实了选定的 RNA 序列结果。这是第一个在 L-DD 下分析振荡基因表达的研究。我们的数据表明时钟基因、P450 基因和脂质代谢基因在 L-DD 下有节奏地表达。光不是持续昼夜节律的必要因素，但影响振荡基因的周期和幅度。