Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells
- Washington University in St Louis School of Medicine, United States
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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Massively Parallel Reporter Assay for pluripotency factors in mESCsNCBI Gene Expression Omnibus, GSE120240.
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Mapping of transcription factor binding sites in mouse embryonic stem cellsNCBI Gene Expression Omnibus, GSE11431.
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Genome-wide maps of REST and its cofactors in mouse E14 cellsNCBI Gene Expression Omnibus, GSE28233.
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MTF2 recruits Polycomb Repressive Complex 2 by helical shape-selective DNA bindingNCBI Gene Expression Omnibus, GSE94300.
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The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)NCBI Gene Expression Omnibus, GSE66581.
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The conserved organization of the human and mouse transcriptomesNCBI Gene Expression Omnibus, GSE49417.
Article and author information
Author details
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.
Reviewing Editor
- Patricia J Wittkopp, University of Michigan, United States
Version history
- Received: August 20, 2018
- Accepted: February 7, 2020
- Accepted Manuscript published: February 11, 2020 (version 1)
- Version of Record published: March 17, 2020 (version 2)
Copyright
© 2020, King 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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Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells
eLife 9:e41279.
https://doi.org/10.7554/eLife.41279
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