Temporal transcriptomics suggest that twin-peaking genes reset the clock

The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the true nature of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-Seq over a 24-hour light / dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near both the start and end of the dark phase; this twin-peaking group is significantly enriched for synaptic transmission genes that are crucial for light-induced phase-shifting of the circadian clock. 342 intergenic non-coding RNAs, together with novel exons of annotated protein-coding genes, including Cry1, also show specific circadian expression variation. Overall, our data provide an important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and allow us to propose that transcriptional timing in the SCN is gating clock resetting mechanisms. Pooled dissected tissue of the suprachiasmatic nucleus from five adult male mice provided one of three replicates for each of six timepoints over a 12:12 light/dark (LD) cycle (ZT2, 6, 10, 14, 18 and 22). Each biological replicate was sequenced over 3 seperate lanes using Illumina HiSeq.

哺乳动物视交叉上核（suprachiasmatic nucleus, SCN）驱动每日节律性行为与生理活动，但目前对其协同转录调控程序仍缺乏深入理解。为揭示哺乳动物SCN转录组中昼夜节律变异的真实本质，我们结合激光捕获显微切割（laser-capture microdissection, LCM）与RNA测序（RNA-Seq）技术，在24小时明暗周期下开展实验。研究发现，呈现经典正弦表达特征的基因数量是此前SCN相关研究中报道的7倍。另有766个基因意外呈现双峰表达模式，在黑暗阶段的起始与临近结束时均达到表达峰值；该双峰基因集显著富集于突触传递相关基因，这类基因对于生物钟受光诱导的相位重置至关重要。342个基因间非编码RNA，以及包括Cry1在内的已注释蛋白编码基因的新型外显子，同样呈现特异性的昼夜节律表达变异。总体而言，本研究的数据提供了一项重要的时间生物学研究资源（www.wgpembroke.com/shiny/SCNseq/），并支持我们提出假说：SCN内的转录时序对生物钟重置机制具有门控调控作用。本研究将5只成年雄性小鼠的视交叉上核解剖组织进行合并，以此作为12:12明暗（LD）周期下6个时间点（ZT2、6、10、14、18与22）各自三份生物学重复样本中的一份。每份生物学重复样本均通过Illumina HiSeq测序平台在3个独立泳道完成测序。