The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function 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 throughout development and cellular reprogramming. During this process, pioneer factors establish an accessible chromatin state to facilitate additional transcription factor binding, yet it remains unclear how different pioneer factors achieve this. 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 to support additional 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 promoting 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.
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 the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
eLife 6:e22631.
https://doi.org/10.7554/eLife.22631
Further reading
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- Stem Cells and Regenerative Medicine
The lateral wall of the mouse subventricular zone harbors neural stem cells (NSC, B cells) which generate proliferating transient-amplifying progenitors (TAP, C cells) that ultimately give rise to neuroblasts (NB, A cells). Molecular profiling at the single-cell level struggles to distinguish these different cell types. Here, we combined transcriptome analyses of FACS-sorted cells and single-cell RNAseq to demonstrate the existence of an abundant, clonogenic and multipotent population of immature neuroblasts (iNB cells) at the transition between TAP and migrating NB (mNB). iNB are reversibly engaged in neuronal differentiation. Indeed, they keep molecular features of both undifferentiated progenitors, plasticity and unexpected regenerative properties. Strikingly, they undergo important progressive molecular switches, including changes in the expression of splicing regulators leading to their differentiation in mNB subdividing them into two subtypes, iNB1 and iNB2. Due to their plastic properties, iNB could represent a new target for regenerative therapy of brain damage.
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- Biochemistry and Chemical Biology
- Stem Cells and Regenerative Medicine
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. In this study, we characterise the proteomes of multiple hiPSC and hESC lines derived from independent donors and find that while they express a near-identical set of proteins, they show consistent quantitative differences in the abundance of a subset of proteins. hiPSCs have increased total protein content, while maintaining a comparable cell cycle profile to hESCs, with increased abundance of cytoplasmic and mitochondrial proteins required to sustain high growth rates, including nutrient transporters and metabolic proteins. Prominent changes detected in proteins involved in mitochondrial metabolism correlated with enhanced mitochondrial potential, shown using high-resolution respirometry. hiPSCs also produced higher levels of secreted proteins, including growth factors and proteins involved in the inhibition of the immune system. The data indicate that reprogramming of fibroblasts to hiPSCs produces important differences in cytoplasmic and mitochondrial proteins compared to hESCs, with consequences affecting growth and metabolism. This study improves our understanding of the molecular differences between hiPSCs and hESCs, with implications for potential risks and benefits for their use in future disease modelling and therapeutic applications.
