title: Temporal transcriptomics suggest that twin-peaking genes reset the clock.
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.
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: William G
authors.initials: WG
authors.lastname: Pembroke
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Arran
authors.initials: A
authors.lastname: Babbs
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Kay E
authors.initials: KE
authors.lastname: Davies
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Chris P
authors.identifier: http://orcid.org/0000-0003-0202-7816
authors.initials: CP
authors.lastname: Ponting
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Oliver
mesh_terms: D000818:Animals; D001683:Biological Clocks; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D061346:Laser Capture Microdissection; D008809:Mice, Inbred C3H; D017423:Sequence Analysis, RNA; D013493:Suprachiasmatic Nucleus / Q000502:physiology*; D014158:Transcription, Genetic
keywords: circadian rhythm; evolutionary biology; genomics; mouse; neuroscience; non-coding RNA; transcriptomics