Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA400171 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The vegetal pole cytoplasm represents a crucial source of maternal dorsal determinants for patterning the dorsoventral axis of the early embryo. Removal of the vegetal yolk in the zebrafish fertilised egg before the completion of the first cleavage results in embryonic ventralisation, but removal of this part at the two-cell stage leads to embryonic dorsalisation. How this is achieved remains unknown. Here, we report a novel mode of maternal regulation of BMP signaling during dorsoventral patterning in zebrafish. We identify Vrtn as a novel vegetally localised maternal factor with dorsalising activity and rapid transport towards the animal pole region after fertilisation. Co-injection of vrtn mRNA with vegetal RNAs from different cleavage stages suggests the presence of putative vegetally localised Vrtn antagonists with slower animal pole transport. Thus, vegetal ablation at the two-cell stage could remove most of the Vrtn antagonists, and allows Vrtn to produce the dorsalising effect. Mechanistically, Vrtn binds a bmp2b regulatory sequence and acts as a repressor to inhibit its zygotic transcription. Analysis of maternal-zygotic vrtn mutants further shows that Vrtn is required to constrain excessive bmp2b expression in the margin. Our work unveils a novel maternal mechanism regulating zygotic BMP gradient in dorsoventral patterning.
2017-08-26 | GSE103090 | GEO
Project description:PPARγ agonist-induced disruption of dorsoventral patterning in zebrafish
| PRJNA544341 | ENA
Project description:The functions of igf2bp3 during zebrafish early development
| PRJNA565584 | ENA
Project description:The functions of m6A and Ythdf2 during zebrafish early development
| PRJNA315314 | ENA
Project description:Knockdown of a zebrafish aryl hydrocarbon receptor repressor (ahrra) affects expression of genes related to photoreceptor development and hematopoiesis.
| PRJNA227196 | ENA
Project description:Lysine succinylation (Ksu) is a novel identified post-translational modification that conserved from prokaryote to eukaryotes. As a kind of acylation, Ksu was reported to have different functions with others acylation at lysine residue. However, recently studies on the Ksu mainly focus on the plants and bacterial, there are still very rare studies in the vertebrate. Therefore, the biological role of succinylation remains largely unknown in mammal. In this study, we performed global Ksu mapping in Danio rerio (zebrafish) using mass spectrometry-based proteomics with enrichment of Ksu peptides by immunoprecipitation technology. As a result, we totally identified 552 Ksu sites in 164 proteins. Compared with our previous studies on lysine acetylation and crotonylation, Ksu plays a major role in a diverse metabolic process, such as carbon metabolism and tricarboxylic acid circle. In addition, we defined 5 new succinylation motifs: (su)KA, (suc)KxxxxA, (su)KxxxxL, (su)KxA, (su)KxV. In conclusion, our result provides proteome-wide database for study of Ksu in zebrafish and our bioinformatics result facilitated the understanding of the Ksu in the role of central metabolism.
2019-09-09 | PXD013173 | Pride
Project description:Effects of maternal Cd on the female reproductive functions, gametes development and genes expression of zebrafish
| PRJNA124363 | ENA
Project description:Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA-seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references, we implemented Palette to infer spatial gene expression from bulk RNA-seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates, establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps (DreAM). Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell-cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior (AP) axis, and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally, we difined a hox score, and comprehensively demonstrated the spatial collinearity of Hox genes at single-cell resolution during development.
2024-04-08 | GSE262578 | GEO
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.
2019-07-30 | GSE135019 | GEO
Project description:Humans and animals have problems producing eggs with high embryo developmental competence, but the causes of poor egg quality are usually unknown. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading model for vertebrate development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were used to create pooled or replicated sample sets subjected to different levels of fractionation before LC-MS/MS. Obtained spectra were searched against a custom zebrafish proteome database and detected proteins were annotated, categorized and quantified based on their normalized spectral counts. Manual and automated enrichment analyses were highly confirmative, showing that good and poor quality eggs have disparate proteomes. Proteins involved in protein synthesis, energy metabolism, and lipid metabolism, and certain vitellogenin products were strikingly underrepresented in poor quality eggs. Poor quality eggs also had significantly higher representation of proteins related to immune system and endosome/lysosome functioning, oncogenes, and apoptosis, as well as lectins and egg envelope proteins. Quantitative comparisons of highly abundant proteins revealed 9 candidate egg quality markers warranting further study. In conclusion, the zebrafish egg proteome appears to be linked to embryo developmental potential, a phenomenon that begs further investigation.
2017-11-27 | PXD005137 | Pride