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.
- Miguel R Branco
- Christopher D Todd
- Darren Taylor
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Deborah Bourc'his, Institut Curie, France
- Received: December 12, 2018
- Accepted: April 20, 2019
- Accepted Manuscript published: April 23, 2019 (version 1)
© 2019, Todd et al.
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