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.
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
Niches are often found in specific positions in tissues relative to the stem cells they support. Consistency of niche position suggests that placement is important for niche function. However, the complexity of most niches has precluded a thorough understanding of how their proper placement is established. To address this, we investigated the formation of a genetically tractable niche, the Drosophila Posterior Signaling Center (PSC), the assembly of which had not been previously explored. This niche controls hematopoietic progenitors of the lymph gland (LG). PSC cells were previously shown to be specified laterally in the embryo, but ultimately reside dorsally, at the LG posterior. Here, using live-imaging, we show that PSC cells migrate as a tight collective and associate with multiple tissues during their trajectory to the LG posterior. We find that Slit emanating from two extrinsic sources, visceral mesoderm and cardioblasts, is required for the PSC to remain a collective, and for its attachment to cardioblasts during migration. Without proper Slit-Robo signaling, PSC cells disperse, form aberrant contacts, and ultimately fail to reach their stereotypical position near progenitors. Our work characterizes a novel example of niche formation and identifies an extrinsic signaling relay that controls precise niche positioning.
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- Neuroscience
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Parkinson’s disease (PD) is a multifactorial disease caused by irreversible progressive loss of dopaminergic neurons (DANs). Recent studies have reported the successful conversion of astrocytes into DANs by repressing polypyrimidine tract binding protein 1 (PTBP1), which led to the rescue of motor symptoms in a chemically-induced mouse model of PD. However, follow-up studies have questioned the validity of this astrocyte-to-DAN conversion model. Here, we devised an adenine base editing strategy to downregulate PTBP1 in astrocytes and neurons in a chemically-induced PD mouse model. While PTBP1 downregulation in astrocytes had no effect, PTBP1 downregulation in neurons of the striatum resulted in the expression of the DAN marker tyrosine hydroxylase (TH) in non-dividing neurons, which was associated with an increase in striatal dopamine concentrations and a rescue of forelimb akinesia and spontaneous rotations. Phenotypic analysis using multiplexed iterative immunofluorescence imaging further revealed that most of these TH-positive cells co-expressed the dopaminergic marker DAT and the pan-neuronal marker NEUN, with the majority of these triple-positive cells being classified as mature GABAergic neurons. Additional research is needed to fully elucidate the molecular mechanisms underlying the expression of the observed markers and understand how the formation of these cells contributes to the rescue of spontaneous motor behaviors. Nevertheless, our findings support a model where downregulation of neuronal, but not astrocytic, PTBP1 can mitigate symptoms in PD mice.
