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Danio rerio

ABSTRACT: RNAseq of wild type and maternal-zygotic Nanog mutant (MZnanog) zebrafish embryos

PROVIDER: PRJNA350823 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4457850.fastq.gz	Fastqsanger.gz
	SRR4457851.fastq.gz	Fastqsanger.gz
	SRR4457852.fastq.gz	Fastqsanger.gz
	SRR4457853.fastq.gz	Fastqsanger.gz
	SRR4457854.fastq.gz	Fastqsanger.gz

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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:Upon fertilization, the embryonic genome remains transcriptionally inactive until the mid-blastula transition. Zygotic genome activation (ZGA) of vertebrate embryos has been extensively studied using nucleic acid-based strategies, but proteomics data are still scarce, impeding the full mechanistic understanding of how ZGA is executed during the maternal-to-zygotic transition (MZT). Here, we performed quantitative proteomics to decipher the proteome landscape of zebrafish embryos during the MZT, quantifying nearly 5,000 proteins across four embryonic stages. The stage-specific clustering based on protein expression pattern revealed that helicases (i.e., eif4a2 and ruvbl1) facilitate pluripotency factors (i.e., nanog, pou5f3, ctcf, and hmga1) triggering ZGA in zebrafish, accompanied by the maternal product decay with P-bodies and ubiquitin dependent proteolytic pathway. Dozens of transcription factors show wave-like expression patterns during MZT, implying their diverse functions in triggering the ZGA and modulating differentiation for organ development. The combination of morpholino knockdown and quantitative proteomics demonstrated that maternal Nanog is required for proper embryogenesis by regulating 1) interactions with other pluripotency factors, 2) F-actin band formation, 3) cell cycle checkpoints and 4) maternal product degradation. This study represents the most systematic proteomics survey of developmentally regulated proteins and their expression profiles accompanying MZT in zebrafish, which is a valuable proteome resource for understanding ZGA.

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Project description:Ikk2 regulates cytokinesis during vertebrate development (Trancriptome profiling from the wild-type and Ikk2 maternal-zygotic mutant zebrafish)

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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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