The pioneer factor OCT4 requires BRG1 to functionally mature gene regulatory elements in mouse embryonic stem cells
- University of Oxford, United Kingdom
Abstract
Pioneer transcription factors recognise and bind their target sequences in inaccessible chromatin to establish new transcriptional networks during development and cellular reprogramming. During this process, pioneer factors establish an accessible chromatin state to facilitate additional transcription factor binding, yet how different pioneer factors achieve this remains unclear. Here, we discover that the pluripotency-associated pioneer factor OCT4 binds chromatin to shape accessibility, transcription factor co-binding, and regulatory element function in mouse embryonic stem cells. Chromatin accessibility at OCT4-bound sites requires the chromatin remodeller BRG1, which is recruited to these sites by OCT4. BRG1 occupancy supports transcription factor binding and expression of the pluripotency-associated transcriptome. Furthermore, the requirement for BRG1 in shaping OCT4 binding reflects how these target sites are used during cellular reprogramming and early mouse development. Together this reveals a distinct requirement for a chromatin remodeller in shaping the activity of the pioneer factor OCT4 and regulating the pluripotency network.
Data availability
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The pioneer factor OCT4 requires BRG1 to functionally mature gene regulatory elements in mouse embryonic stem cellsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE87822).
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A comparative encyclopedia of DNA elements in the mouse genomePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE49847).
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Enhancer Decommissioning by LSD1 During Embryonic Stem Cell DifferentiationPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE27844).
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DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of WashingtonPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE37074).
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INO80 complex in the core regulatory network governing ESC self-renewal [ChIP-Seq]Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE49137).
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Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cellsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE64825).
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Multiphasic and dynamic changes in alternative splicing during induction of pluripotency are coordinated by numerous RNA binding proteins [iPS]Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE70022).
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Expression data from OSKM-mediated 2nd reprogramming cells and the corresponding iPS cell linePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE67462).
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The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE66581).
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Establishing Chromatin Regulatory Landscape during Mouse Preimplantation DevelopmentPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE76642).
Article and author information
Author details
Funding
Wellcome (098024/Z/11/Z)
- Robert J Klose
European Research Council (681440)
- Robert J Klose
Exeter College, University of Oxford (Monsanto Senior Research Fellowship)
- Robert J Klose
Lister Institute of Preventive Medicine
- Robert J Klose
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Irwin Davidson, Institut de Génétique et de Biologie Moléculaire et Cellulaire, France
Version history
- Received: October 26, 2016
- Accepted: March 9, 2017
- Accepted Manuscript published: March 13, 2017 (version 1)
- Accepted Manuscript updated: March 15, 2017 (version 2)
- Version of Record published: April 21, 2017 (version 3)
Copyright
© 2017, King & Klose
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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The pioneer factor OCT4 requires BRG1 to functionally mature gene regulatory elements in mouse embryonic stem cells
eLife 6:e22631.
https://doi.org/10.7554/eLife.22631
Further reading
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- Developmental Biology
- Stem Cells and Regenerative Medicine
Co-regulated genes of the Imprinted Gene Network are involved in the control of growth and body size, and imprinted gene dysfunction underlies human paediatric disorders involving the endocrine system. Imprinted genes are highly expressed in the pituitary gland, among them, Dlk1, a paternally expressed gene whose membrane-bound and secreted protein products can regulate proliferation and differentiation of multiple stem cell populations. Dosage of circulating DLK1 has been previously implicated in the control of growth through unknown molecular mechanisms. Here we generate a series of mouse genetic models to modify levels of Dlk1 expression in the pituitary gland and demonstrate that the dosage of DLK1 modulates the process of stem cell commitment with lifelong impact on pituitary gland size. We establish that stem cells are a critical source of DLK1, where embryonic disruption alters proliferation in the anterior pituitary, leading to long-lasting consequences on growth hormone secretion later in life.
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- Developmental Biology
- Stem Cells and Regenerative Medicine
Using embryonic stem cells (ESCs) in regenerative medicine or in disease modeling requires a complete understanding of these cells. Two main distinct developmental states of ESCs have been stabilized in vitro, a naïve pre-implantation stage and a primed post-implantation stage. Based on two recently published CRISPR-Cas9 knockout functional screens, we show here that the exit of the naïve state is impaired upon heme biosynthesis pathway blockade, linked in mESCs to the incapacity to activate MAPK- and TGFβ-dependent signaling pathways after succinate accumulation. In addition, heme synthesis inhibition promotes the acquisition of 2 cell-like cells in a heme-independent manner caused by a mitochondrial succinate accumulation and leakage out of the cell. We further demonstrate that extracellular succinate acts as a paracrine/autocrine signal, able to trigger the 2C-like reprogramming through the activation of its plasma membrane receptor, SUCNR1. Overall, this study unveils a new mechanism underlying the maintenance of pluripotency under the control of heme synthesis.
