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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.

Original publication

DOI

10.7554/eLife.10518

Type

Journal article

Journal

Elife

Publication Date

02/11/2015

Volume

4

Keywords

circadian rhythm, evolutionary biology, genomics, mouse, neuroscience, non-coding RNA, transcriptomics, Animals, Biological Clocks, Gene Expression Profiling, Gene Expression Regulation, Laser Capture Microdissection, Mice, Inbred C3H, Sequence Analysis, RNA, Suprachiasmatic Nucleus, Transcription, Genetic