Abstract
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 finer details of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-seq over a 24 hr 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. 341 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.
Highlights
The suprachiasmatic nucleus (SCN) of the hypothalamus is the seat of the principal circadian clock in mammals
Sequencing RNA in each replicate generated up to 133 million paired-end reads of which 45–65% were subsequently mapped to the mouse genome allowing for gene expression level estimation
Global expression differences were apparent between timepoints, as revealed by principal component analysis (PCA) (Figure 1—figure supplement 1B)
Summary
The suprachiasmatic nucleus (SCN) of the hypothalamus is the seat of the principal circadian clock in mammals. These data reveal many hundreds of novel cycling transcripts and provide evidence that the temporal variation in a specific group of genes plays a role in modulating light-induced phase resetting of the circadian clock.
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