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Danio rerio

ABSTRACT: Whole genome methylation profiling in developing and developed Zebrafish

PROVIDER: PRJNA226701 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1024320_1.fastq.gz	Fastqsanger.gz
	SRR1024320_2.fastq.gz	Fastqsanger.gz
	SRR1024311_1.fastq.gz	Fastqsanger.gz
	SRR1024311_2.fastq.gz	Fastqsanger.gz
	SRR1024321_1.fastq.gz	Fastqsanger.gz

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WGBS and RNA-seq of Danio rerio in HSPC generation

Project description:In this study, we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First, we generated a comprehensive DNA methylation landscape of EHT, which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1-deficient embryos, we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically, we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling, thus contributing to defects in the EHT in dnmt1-deficient embryos. Herein, we identified that DNA methylation, as epigenetic regulator, participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish.

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Role of the Exon Junction Complex in Danio rerio

Project description:The exon junction complex (EJC) is composed of three core proteins Rbm8a, Magoh and Eif4a3 and is thought to play a role in several post-transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome-wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing (RIP-Seq). We find that, as in human cells, zebrafish EJC is deposited about 24 nts upstream of exon-exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA-seq from rbm8a mutant, magoh mutant and wild-type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants.

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