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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- Chromosomes and Gene Expression
- Evolutionary Biology
Gene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind. In prokaryotes, gene expression requires a stretch of DNA called a promoter, which contains two motifs called –10 and –35 boxes. However, these motifs may occur in both promoters and non-promoter DNA in multiple copies. They have been implicated in some studies to improve promoter activity, and in others to repress it. Here, we ask whether the presence of such motifs in different genetic sequences influences promoter evolution and emergence. To understand whether and how promoter motifs influence promoter emergence and evolution, we start from 50 ‘promoter islands’, DNA sequences enriched with –10 and –35 boxes. We mutagenize these starting ‘parent’ sequences, and measure gene expression driven by 240,000 of the resulting mutants. We find that the probability that mutations create an active promoter varies more than 200-fold, and is not correlated with the number of promoter motifs. For parent sequences without promoter activity, mutations created over 1500 new –10 and –35 boxes at unique positions in the library, but only ~0.3% of these resulted in de-novo promoter activity. Only ~13% of all –10 and –35 boxes contribute to de-novo promoter activity. For parent sequences with promoter activity, mutations created new –10 and –35 boxes in 11 specific positions that partially overlap with preexisting ones to modulate expression. We also find that –10 and –35 boxes do not repress promoter activity. Overall, our work demonstrates how promoter motifs influence promoter emergence and evolution. It has implications for predicting and understanding regulatory evolution, de novo genes, and phenotypic evolution.
