High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

  1. Arnaud Krebs
  2. Sophie Dessus-Babus
  3. Lukas Burger
  4. Dirk Schübeler  Is a corresponding author
  1. Friedrich Miescher Institute, Switzerland
  2. Friedrich Miescher Institute, Basel, Switzerland

Abstract

The majority of mammalian promoters are CpG islands; regions of high CG density that require protection from DNA methylation to be functional. Importantly, how sequence architecture mediates this unmethylated state remains unclear. To address this question in a comprehensive manner, we developed a method to interrogate methylation states of hundreds of sequence variants inserted at the same genomic site in mouse embryonic stem cells. Using this assay, we were able to quantify the contribution of various sequence motifs towards the resulting DNA methylation state. Surprisingly, modeling of this comprehensive dataset revealed that CG density alone is a minor determinant of their unmethylated state. Instead, these data argue for a principal role for transcription factor binding sites, a prediction confirmed by testing synthetic mutant libraries. Taken together, these findings establish the hierarchy between the two cis-encoded mechanisms that define the DNA methylation state and thus the transcriptional competence of CpG islands.

Article and author information

Author details

  1. Arnaud Krebs

    Friedrich Miescher Institute, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. Sophie Dessus-Babus

    Friedrich Miescher Institute, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  3. Lukas Burger

    Friedrich Miescher Institute, Basel, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Dirk Schübeler

    Friedrich Miescher Institute, Basel, Switzerland
    For correspondence
    Dirk.Schubeler@fmi.ch
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Anne C Ferguson-Smith, University of Cambridge, United Kingdom

Version history

  1. Received: July 18, 2014
  2. Accepted: September 24, 2014
  3. Accepted Manuscript published: September 26, 2014 (version 1)
  4. Version of Record published: October 21, 2014 (version 2)

Copyright

© 2014, Krebs 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. Arnaud Krebs
  2. Sophie Dessus-Babus
  3. Lukas Burger
  4. Dirk Schübeler
(2014)
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
eLife 3:e04094.
https://doi.org/10.7554/eLife.04094

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https://doi.org/10.7554/eLife.04094

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