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GEO accession GSE195609 is currently private and is scheduled to be released on Nov 01, 2025.

ABSTRACT: GEO accession GSE195609 is currently private and is scheduled to be released on Nov 01, 2025.

PROVIDER: PRJNA801473 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17799100_1.fastq.gz	Fastqsanger.gz
	SRR17799100_2.fastq.gz	Fastqsanger.gz
	SRR17799101_1.fastq.gz	Fastqsanger.gz
	SRR17799101_2.fastq.gz	Fastqsanger.gz
	SRR17799102_1.fastq.gz	Fastqsanger.gz

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Pou5f3 and Nanog organize active chromatin in three dimensions

Project description:Zygotic genome in zebrafish embryogenesis is activated by transcription factors Pou5f3, Sox19b and Nanog. While it was previously demonstrated, that these factors displace nucleosomes and create the regions of open chromatin, their role in three-dimensional genome organisation was not studied. Here we show, that large-scale chromatin structures, TADs and compartments, form independently of Pou5f3, Sox19b and Nanog. However, Pou5f3 and Nanog are required for formation of small-scale 3D active chromatin structures which we call "fountains".

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Temporal transcriptome in Pou5f3, Nanog and Sox19b mutant zebrafish embryos

Project description:To understand the role of Pou5f3, Sox19b and Nanog during zebrafish zygotic genome activation, RNA-seq time-series for single, double and triple maternal-zygotic (MZ) zebrafish mutants for Pou5f3, Nanog, Sox19b, as well as the wild-type.

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Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation.

Project description:Purpose: Find out the consequences of Pou5f3/Oct4 and Nanog binding to the nucleosome distribution before and after Zygotic Genome Activation Methods: MNase-seq of the wild-type(WT), Pou5f3 (MZspg) and Nanog (MZnanog) mutant zebrafish embryos at 512-cell stage and dome stage. Results: Nanog, Sox19b and Pou5f3 bind to the High Nucleosome Affinity Regions (HNARs). HNARs are spanning over 600 bp, featuring high in vivo and predicted in vitro nucleosome occupancy and high predicted propeller twist DNA shape value. We suggest a two-step model, where the same intrinsic DNA properties of HNAR promote both high nucleosome occupancy and differential binding of TFs. In the first step, already prior to ZGA, Pou5f3 and Nanog reduce nucleosome occupancy on HNARs genome-wide. In the second step, Nanog and Pou5f3/SoxB1 complex maintain open chromatin state on the subset of HNARs, acting synergistically. Nanog binds to the HNAR center, while the Pou5f3/SoxB1 complex stabilizes the flanks.

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Temporal transcriptome in Pou5f3, Nanog and Sox19b mutant zebrafish embryos

Project description:Temporal transcriptome in Pou5f3, Nanog and Sox19b mutant zebrafish embryos

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Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.

Project description:In many organisms, early embryonic development is driven by maternally provided transcription factors until the controlled onset of transcription during zygotic genome activation (ZGA). The regulation of chromatin accessibility and its relationship to gene activity during this transition remains poorly understood. Here, we generated chromatin accessibility maps for the early stages of zebrafish development spanning genome activation and the onset of lineage specification. We find that during this period, chromatin accessibility increases at regulatory elements. This is independent of RNA pol II-mediated transcription, with the exception of the miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors pou5f3, sox19b, and nanog, which are known to be required for zebrafish ZGA, results in decreased accessibility at regulatory elements. Finally, we show that accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Together, our results suggest that maternally provided transcription factors prime genes for activity during zygotic genome activation.

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Project description:In zebrafish embryos, the maternal transcription factors (TFs)Nanog, Pou5f3 and Sox19b activate the early zygotic gene expression. To evaluate the role of Nanog, we examined the changes in H3K27ac and H3K4me3 chromatin modifications in the MZnanog embryos mutant by maternal and zygotic Nanog.

2020-05-07 | GSE143439 | GEO

Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation.

Project description:Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation.

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Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.

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Project description:Pou5f3 and Sox19b transcription factors promote chromatin accessibility and activate zygotic transcription in zebrafish embryos. It is poorly understood how two transcription factors act together on chromatin. To answer this question, we performed Omni-ATAC-seq on the zebrafish embryos, single and double mutants by Pou5f3 and Sox19b, as well as the wild-type, at two blastula developmental stages, oblong and dome. We report, that chromatin accessibility on 48% of all putative enhancers depends on Pou5f3 and Sox19b. Out of them, accessibility on 33% enhancers is reduced in the double mutant and of 15% is increased. Enhancers with reduced and increased chromatin accessibility differ in GC content and transcription factors binding motif frequency, and are linked to early and late developmental regulatory genes, respectively. Our results indicate that Pou5f3 and Sox19b not only activate early zygotic genes, but also prevent premature activation of late developmental enhancers.

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