Chromatin accessibility dynamics across C. elegans development and ageing

Jürgen Jänes; Yan Dong; Michael Schoof; Jacques Serizay; Alex Appert; Chiara Cerrato; Carson Woodbury; Ron Chen; Carolina Gemma; Ni Huang; Djem Kissiov; Przemyslaw Stempor; Annette Steward; Eva Zeiser; Sascha Sauer; Julie Ahringer

doi:10.7554/eLife.37344

eLife (Oct 2018)

Chromatin accessibility dynamics across C. elegans development and ageing

Jürgen Jänes,
Yan Dong,
Michael Schoof,
Jacques Serizay,
Alex Appert,
Chiara Cerrato,
Carson Woodbury,
Ron Chen,
Carolina Gemma,
Ni Huang,
Djem Kissiov,
Przemyslaw Stempor,
Annette Steward,
Eva Zeiser,
Sascha Sauer,
Julie Ahringer

Affiliations

Jürgen Jänes: ORCiD; Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Yan Dong: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Michael Schoof: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Jacques Serizay: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Alex Appert: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Chiara Cerrato: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Carson Woodbury: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Ron Chen: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Carolina Gemma: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Ni Huang: ORCiD; Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Djem Kissiov: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Przemyslaw Stempor: ORCiD; Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Annette Steward: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Eva Zeiser: Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
Sascha Sauer: Max Delbrück Center for Molecular Medicine, Berlin, Germany; Max Planck Institute for Molecular Genetics, Otto-Warburg Laboratories, Berlin, Germany
Julie Ahringer: ORCiD; Department of Genetics, University of Cambridge, Cambridge, United Kingdom; The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom

DOI: https://doi.org/10.7554/eLife.37344
Journal volume & issue: Vol. 7

Abstract

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An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here, we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one Caenorhabditis elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

Published in eLife

ISSN: 2050-084X (Online)
Publisher: eLife Sciences Publications Ltd
Country of publisher: United Kingdom
LCC subjects: Medicine; Science: Biology (General)
Website: https://elifesciences.org

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