1. Chromosomes and Gene Expression
  2. Genetics and Genomics
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Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

  1. Christopher D Todd
  2. Özgen Deniz
  3. Darren Taylor
  4. Miguel R Branco  Is a corresponding author
  1. Queen Mary University of London, United Kingdom
Research Article
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Cite this article as: eLife 2019;8:e44344 doi: 10.7554/eLife.44344

Abstract

Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that they play significant roles in gene regulation. Here we tested a set of long terminal repeat TE families for roles as enhancers in mouse embryonic and trophoblast stem cells. Epigenomic and transcriptomic data suggested that a large number of TEs helped to establish tissue-specific gene expression programmes. Genetic editing of individual TEs confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a subset of TEs are important for gene regulation in early mouse development, and highlight the importance of functional experiments when evaluating gene regulatory roles of TEs.

Article and author information

Author details

  1. Christopher D Todd

    Blizard Institute, Queen Mary University of London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Özgen Deniz

    Blizard Institute, Queen Mary University of London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Darren Taylor

    Blizard Institute, Queen Mary University of London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Miguel R Branco

    Blizard Institute, Queen Mary University of London, London, United Kingdom
    For correspondence
    m.branco@qmul.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9447-1548

Funding

Wellcome (Sir Henry Dale Fellowship 101225/Z/13/Z)

  • Miguel R Branco

The Medical College of Saint Bartholomew's Hospital Trust (Donald Hunter Studentship)

  • Christopher D Todd

Biotechnology and Biological Sciences Research Council (BB/R505997/1)

  • Darren Taylor

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

Reviewing Editor

  1. Deborah Bourc'his, Institut Curie, France

Publication history

  1. Received: December 12, 2018
  2. Accepted: April 20, 2019
  3. Accepted Manuscript published: April 23, 2019 (version 1)

Copyright

© 2019, Todd 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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