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Pou5f3 and Nanog organize active chromatin in three dimensions

ABSTRACT: 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".

ORGANISM(S): Danio rerio

PROVIDER: GSE195609 | GEO | 2025/12/01

REPOSITORIES: GEO

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			Action	DRS
		Other
	GSE195609_MZnanog_2.75.1000.mcool	Other
	GSE195609_MZnanog_5.3.1000.mcool	Other
	GSE195609_MZsox19b_5.3.1000.mcool	Other
	GSE195609_MZspg_2.75.1000.mcool	Other

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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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