Abstract

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 C. 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.

Data availability

Sequencing data have been deposited in GEO under accession code GSE114494.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Jürgen Jänes

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  2. Yan Dong

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  3. Michael Schoof

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  4. Jacques Serizay

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  5. Alex Appert

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  6. Chiara Cerrato

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  7. Carson Woodbury

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  8. Ron Chen

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  9. Carolina Gemma

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  10. Ni Huang

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8849-038X
  11. Djem Kissiov

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  12. Przemyslaw Stempor

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9464-7475
  13. Annette Steward

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  14. Eva Zeiser

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  15. Sascha Sauer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
    Competing interests
    No competing interests declared.
  16. Julie Ahringer

    The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    ja219@cam.ac.uk
    Competing interests
    Julie Ahringer, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7074-4051

Funding

Wellcome (101863)

  • Jürgen Jänes
  • Yan Dong
  • Alex Appert
  • Chiara Cerrato
  • Ron Chen
  • Carolina Gemma
  • Ni Huang
  • Przemyslaw Stempor
  • Annette Steward
  • Eva Zeiser
  • Julie Ahringer

Medical Research Council

  • Jacques Serizay

European Commission (FP7/2007-2013)

  • Sascha Sauer
  • Julie Ahringer

Wellcome (97679)

  • Jürgen Jänes

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Siu Sylvia Lee, Cornell University, United States

Version history

  1. Received: April 7, 2018
  2. Accepted: October 25, 2018
  3. Accepted Manuscript published: October 26, 2018 (version 1)
  4. Version of Record published: November 12, 2018 (version 2)

Copyright

© 2018, Jänes et al.

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.

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  1. Jürgen Jänes
  2. Yan Dong
  3. Michael Schoof
  4. Jacques Serizay
  5. Alex Appert
  6. Chiara Cerrato
  7. Carson Woodbury
  8. Ron Chen
  9. Carolina Gemma
  10. Ni Huang
  11. Djem Kissiov
  12. Przemyslaw Stempor
  13. Annette Steward
  14. Eva Zeiser
  15. Sascha Sauer
  16. Julie Ahringer
(2018)
Chromatin accessibility dynamics across C. elegans development and ageing
eLife 7:e37344.
https://doi.org/10.7554/eLife.37344

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https://doi.org/10.7554/eLife.37344