The mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal gene transcription in the SCN is vital for daily timekeeping. So far, the regulatory elements assisting circadian gene transcription have only been studied in peripheral tissues, lacking the critical neuronal dimension intrinsic to the role of the SCN as central brain pacemaker. By using histone-ChIP-seq, we identified SCN-enriched gene regulatory elements that associated with temporal gene expression. Based on tissue-specific H3K27ac and H3K4me3 marks, we successfully produced the first-ever SCN gene-regulatory map. We found that a large majority of SCN enhancers not only show robust 24-h rhythmic modulation in H3K27ac occupancy, peaking at distinct times of day, but also possess canonical E-box (CACGTG) motifs potentially influencing downstream cycling gene expression. To establish enhancer–gene relationships in the SCN, we conducted directional RNA-seq at six distinct times across the day and night, and studied the association between dynamically changing histone acetylation and gene transcript levels. About 35% of the cycling H3K27ac sites were found adjacent to rhythmic gene transcripts, often preceding the rise in mRNA levels. We also noted that enhancers encompass noncoding, actively transcribing enhancer RNAs (eRNAs) in the SCN, which in turn oscillate, along with cyclic histone acetylation, and correlate with rhythmic gene transcription. Taken together, these findings shed light on genome-wide pretranscriptional regulation operative in the central clock that confers its precise and robust oscillation necessary to orchestrate daily timekeeping in mammals.

中文翻译：

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哺乳动物生物钟所在地视交叉上核基因组增强子元件的动态调节

哺乳动物的视交叉上核（SCN）位于下丘脑腹侧，根据环境和内脏线索同步并维持全身的日常细胞和生理节律。因此，SCN 中时空基因转录的系统调节对于日常计时至关重要。迄今为止，协助昼夜节律基因转录的调控元件仅在外周组织中进行了研究，缺乏视视上核作为中枢大脑起搏器的作用所固有的关键神经元维度。通过使用组蛋白 ChIP-seq，我们鉴定了与时间基因表达相关的富含 SCN 的基因调控元件。基于组织特异性H3K27ac和H3K4me3标记，我们成功制作了第一个SCN基因调控图谱。我们发现，绝大多数 SCN 增强子不仅在 H3K27ac 占用中表现出强大的 24 小时节律调节，在一天中的不同时间达到峰值，而且还具有可能影响下游循环基因表达的规范 E-box (CACGTG) 基序。为了在 SCN 中建立增强子与基因的关系，我们在白天和晚上的六个不同时间进行了定向 RNA 测序，并研究了动态变化的组蛋白乙酰化与基因转录水平之间的关联。大约 35% 的循环 H3K27ac 位点被发现与节律基因转录物相邻，通常先于 mRNA 水平的上升。我们还注意到，增强子包含 SCN 中的非编码、主动转录增强子 RNA (eRNA)，这些增强子 RNA 反过来会随着循环组蛋白乙酰化而振荡，并与节律性基因转录相关。