Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells

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Abstract

In embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute to cis-regulation in mouse ESCs, we assayed two massively parallel reporter assay (MPRA) libraries composed of binding sites for SOX2, POU5F1 (OCT4), KLF4, and ESRRB. Comparisons between synthetic cis-regulatory elements and genomic sequences with comparable binding site configurations revealed some aspects of a regulatory grammar. The expression of synthetic elements is influenced by both the number and arrangement of binding sites. This grammar plays only a small role for genomic sequences, as the relative activities of genomic sequences are best explained by the predicted affinity of binding sites, regardless of binding site identity and positioning. Our results suggest that the effects of transcription factor binding sites (TFBS) are influenced by the order and orientation of sites, but that in the genome the overall occupancy of TFs is the primary determinant of activity.

Data availability

Sequencing data has been deposited in GEO under accession code GSE120240.Any additional data generated during this study are included in the manuscript and supporting files.

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Article and author information

Author details

Dana M King

Edison Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4635-5272
Clarice Kit Yee Hong

Edison Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.
James L Shepherdson

Edison Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.
David M Granas

Edison Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.
Brett B Maricque

Edison Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.
Barak Cohen

Edison Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, United States

For correspondence
cohen@wustl.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3350-2715

Funding

National Institutes of Health (R01 GM092910)

Barak Cohen

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

Copyright

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.