Unknown

Dataset Information

0

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells.


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.

SUBMITTER: Todd CD 

PROVIDER: S-EPMC6544436 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

altmetric image

Publications

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells.

Todd Christopher D CD   Deniz Özgen Ö   Taylor Darren D   Branco Miguel R MR  

eLife 20190423


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 est  ...[more]

Similar Datasets

2018-12-18 | GSE122856 | GEO
2018-12-18 | GSE122855 | GEO
2018-12-18 | GSE122854 | GEO
| PRJNA506704 | ENA
| S-EPMC3177211 | biostudies-literature
| PRJNA506706 | ENA
| PRJNA506708 | ENA
| S-EPMC8240256 | biostudies-literature
| S-EPMC6318327 | biostudies-literature
| S-EPMC5716208 | biostudies-literature