Temporal transcriptomics suggest that twin-peaking genes reset the clock

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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 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. 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.

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William G Pembroke

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Arran Babbs

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Kay Davies

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Chris P Ponting

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Peter L Oliver

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

For correspondence
peter.oliver@dpag.ox.ac.uk

Competing interests
The authors declare that no competing interests exist.

Ethics

Animal experimentation: All experiments were conducted in adherence to the guidelines set forth by the UK Home Office regulations under Project Licence number 30/2792, and with the approval of the University of Oxford Ethical Review Board.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.