Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency
- Institut Curie, France
- The Buck Institute for Research on Aging, United States
- Université Paris-Saclay, France
Abstract
During early mammalian development, the chromatin landscape undergoes profound transitions. The Zdbf2 gene-involved in growth control-provides a valuable model to study this window: upon exit from naïve pluripotency and prior to tissue differentiation, it undergoes a switch from a distal to a proximal promoter usage, accompanied by a switch from polycomb to DNA methylation occupancy. Using an embryonic stem cell (ESC) system to mimic this period, we show here that four enhancers contribute to the Zdbf2 promoter switch, concomitantly with dynamic changes in chromatin architecture. In ESCs, the locus is partitioned to facilitate enhancer contacts with the distal Zdbf2 promoter. Relieving the partition enhances proximal Zdbf2 promoter activity, as observed during differentiation or with genetic mutants. Importantly, we show that 3D regulation occurs upstream of the polycomb and DNA methylation pathways. Our study reveals the importance of multi-layered regulatory frameworks to ensure proper spatio-temporal activation of developmentally important genes.
Data availability
Sequencing data have been deposited in GEO under accession code GSE121405.
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An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cellsNCBI Gene Expression Omnibus, GSE71593.
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The landscape of accessible chromatin in mammalian pre-implantation embryosNCBI Gene Expression Omnibus, GSE66390.
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Distinct features in establishing H3K4me3 and H3K27me3 in pre-implantation embryosNCBI Gene Expression Omnibus, GSE73952.
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Reorganization of enhancer patterns in transition from naïve to primed pluripotencyNCBI Gene Expression Omnibus, GSE56138.
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Enhancing the Potency of Mouse Embryonic Stem CellsNCBI Gene Expression Omnibus, GSE99494.
Article and author information
Author details
Maxim Van Cleef Greenberg
Funding
H2020 European Research Council (Cog EpiRepro)
- Deborah Bourc'his
European Molecular Biology Organization (LTF 457-2013)
- Maxim Van Cleef Greenberg
Fondation ARC pour la Recherche sur le Cancer (Post-doc Fellowship)
- Maxim Van Cleef Greenberg
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2019, Greenberg 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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Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency
eLife 8:e44057.
https://doi.org/10.7554/eLife.44057
Further reading
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Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
