Transcriptome analysis of wild-type and maternal ybx1 mutant zebrafish embryos during early development
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA429172 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6451494.fastq.gz | Fastqsanger.gz | |||
| SRR6451495.fastq.gz | Fastqsanger.gz | |||
| SRR6451496.fastq.gz | Fastqsanger.gz | |||
| SRR6451497.fastq.gz | Fastqsanger.gz |
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Project description:To study the function of zebrafish Ybx1 during early embryogenesis, we generated maternal ybx1 (Mybx1) mutant using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic loss of maternal mRNA decay and zygotic genome activation in Mybx1 embryos during maternal-to-zygotic transition.
2018-09-01 | GSE108924 | GEO
Project description:The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic-driven programing. However, how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) in zebrafish early embryos, we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box-binding protein 1 (Ybx1) prefers to recognizing m5C-modified mRNAs through p-p interaction with a key residue Trp45 in its cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation-regulated maternal mRNA stability during zebrafish MZT, highlighting the critical role of m5C mRNA methylation in early development.
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Project description:To study the function of zebrafish nuclear pores during early embryogenesis, we generated maternal zygotic double mutant of nup85;nup133 (MZnup85;nup133) using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal-to-zygotic transition.
2023-03-04 | GSE146394 | GEO
Project description:The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic-driven programing. However, how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) in zebrafish early embryos, we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box-binding protein 1 (Ybx1) prefers to recognizing m5C-modified mRNAs through p-p interaction with a key residue Trp45 in its cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation-regulated maternal mRNA stability during zebrafish MZT, highlighting the critical role of m5C mRNA methylation in early development.
2019-08-07 | GSE120643 | GEO
Project description:In mammals, maternal gene products decay and zygotic genome activation (ZGA) onsets during maternal to zygotic transition (MZT). Y-box binding protein YBX1 plays vital roles in RNA stabilization and transcriptional regulation, but its roles in pre-implantation development remain to be elucidated. In the present study, we aim to investigate the role of YBX1 during goat MZT and further explore the molecular mechanisms. The expression of YBX1 was increased during MZT in goat, bovine, human, and mice. We successfully knocked down YBX1 by microinjection of siRNA against YBX1, and the embryo development was impaired when YBX1 was knocked down. Using RNA-seq, we identified 1623 up-regulated and 3531 down-regulated genes in the 8-cell stage YBX1 knockdown embryos. GO/KEGG/GSEA enrichment analysis revealed that the down-regulated genes were enriched in regulation of RNA/mRNA stability and spliceosome, suggesting that YBX1 might medicate pre-implantation development by alternative splicing and maternal mRNA decay. To this end, we identified 3284 differential alternative splicing events and 1322 differentially expressed maternal mRNAs at the 8-cell stage YBX1 knockdown embryos compared to the controls. Moreover, the splicing factors and mRNA decay related genes were aberrantly expressed. Lastly, knockdown of YBX1 impaired transcriptional activity during ZGA in goat and mice as revealed by 5-EU staining. Our results identify that YBX1 serves an important role in maternal mRNA decay, alternative splicing, and the transcriptional activity required for early embryogenesis, which will broaden the current understanding of YBX1 functions during the stochastic reprogramming events.
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Project description:Y box-binding protein 1 (Ybx1) is critical for embryogenesis and organogenesis. In zebrafish, we identify Ybx1 is predominantly expressed in the enterocytes of intestine in day5 larvae, whereas its immediately degradation driven by ubiquitination on day6. Here we show the maternal lethality with cardiac edema in ybx1-/- larvae, and postnatal larval lethality exhibited in ybx1-/- larvae within the death window from 10dpf to 20dpf. To study the underlying mechanisms for the ybx1-/- larvae partial lethality, we performed RNA-seq and experimental results showed the increased ROS might be the underlying cause for the postnatal lethality. By ascorbic acid treatment, we found ascorbic acid exposure prevented ybx1-/- larvae from postnatal lethality, while hydrogen peroxide aggravated ybx1-/- larvae postnatal lethality during the death window. By RNA-seq analysis, we also found significantly increased expressions of mmp9 and mmp13a in ybx1-/- larvae, and by inhibition of either MMP9 or MMP13a expression partially rescue the ybx1-/- postnatal lethality during the death window. Later, we further identify the intestinal impairs on 30 dpf and further deteriorated severe intestinal disorder in Ybx1 deficiency zebrafish. By exposure of ybx1-/- zebrafish for 14 days, we discover ascorbic acid partially mend the impaired intestine in ybx1-/-. In this study, we demonstrate that ybx1-/- larvae were ROS-susceptible, and the increased inflammation in ybx1-/- larvae intestine identified enables the ybx1-/- zebrafish as good model for studying of intestinal disease.
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Project description:Goal of the experiment was to assess the differences in gene expression between maternal zygotic ezh2 mutant zebrafish embryos and wildtype embryos at 0 and 3.3 hpf.
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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:RNAseq of wild type and maternal Eevs mutant (Meevs) zebrafish embryos
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Project description:microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied. We used microarrays to detail the effect of maternal microRNA mir-34 in regulation of zygotic trancription during the initial stages of Zebrafish embryonic development from one cell stage through the maternal-zygotic transition up to 24 hours post fertilization. Zebrafish embryos were selected at specific stages of early embryonic development (1, 7, and 24 hours post fertilization). RNA was extracted and hybridized to Affymetrix microarrays. The embryos were injected with anti-microRNA LNA and were kept for constant monitoring for the indicated time points. A mockLNA was injected as a control. The embryos were visualized for any visible developmental abnormalities.
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