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Temporal transcriptome in Pou5f3, Nanog and Sox19b mutant zebrafish embryos

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

PROVIDER: PRJNA681822 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13174600_1.fastq.gz	Fastqsanger.gz
	SRR13174600_2.fastq.gz	Fastqsanger.gz
	SRR13174601_1.fastq.gz	Fastqsanger.gz
	SRR13174601_2.fastq.gz	Fastqsanger.gz
	SRR13174602_1.fastq.gz	Fastqsanger.gz

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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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Temporal transcriptome in Pou5f3 and Sox19b mutant zebrafish embryos

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Temporal transcriptome in Pou5f3 and Sox19b mutant zebrafish embryos

Project description:We applied time-series SE50bp RNA-seq with 35M reads per sample in wild-type, MZsox19b, MZspg, and double MZspgsox19b mutants in zebrafish embryos to understand the role of Pou5f3 and Sox19b during zebrafish zygotic genome activation. In total we sequenced 4 biological replicates (rep1-4) for WT time curve and 2 biological replicates (rep1-2) for each mutant. WT rep5 are technical replicates for WT rep1, while MZsox19b rep3 and MZspg rep3 are techical replicates for MZsox19b rep1 and MZspg rep1, respectively.

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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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Regulation of chromatin accessibility in early zebrafish embryos by Pou5f3 and Sox19b transcription factors.

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

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

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

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