Similar Datasets
Project description:We aimed to expand the knowledge of Fgf and Wnt signaling in the zebrafish tailbud. Both pathways are required for proper axis elongation and segmentation and we wished to explore the genes under the control of each pathway during this process. In addition, we saught to identify crosstalk between the two pathways by determining whether pathway effector expression was being changed after time-resolved modification of each pathway using pharmacological modifiers. Embryos were treated with either 0.3M LiCl, 50uM SU5402, or E2 for 3hours or 7 hours (E2 and SU5402), followed by tailbud dissection and RNA extraction. Conditions were replicated in triplicate.
2012-07-15 | E-GEOD-38969 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6449393 | biostudies-literature
Project description:During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNAbound proteome. This protein constellation consists of many conserved RBPs, with additional embryo- and stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of RBPs in embryogenesis, we focused on hnRNP A1. iCLIP and subsequent mRNA reporter assays revealed a function for hnRNP A1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3’UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that hnRNP A1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-miR-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of hnRNP A1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that hnRNP A1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.
2017-03-27 | PXD006098 | Pride
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.
2024-05-01 | PXD036678 | Pride
Project description:We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal-to-zygotic transition
2017-03-24 | GSE76212 | GEO
Project description:Goal of this study is differential gene expression between wild type and MZnanog mutant during early zebrafish embryogenesis
2017-10-25 | GSE89245 | GEO
Project description:During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development, known as the maternal to zygotic transition (MZT), the genome becomes activated and the maternally provided mRNAs begin to degrade. In the early zebrafish embryo, when under maternal control, cells divide rapidly and synchronously with cell cycles that lack gap phases. At cell cycle ten the introduction of gap phases lengthens the cell cycle and synchronised division is lost. During the MZT, zygotic activation of microRNAs leads to the targeted degradation of a number of maternally provided mRNAs, thus linking genome activation to maternal mRNA degredation.While the MZT has been studied in several different organisms the molecular mechanisms that coordinate genome activity and mRNA degradation remain largely unknown. For example, while the bulk of zygotic transcription occurs at cell cycle ten we do not understand why there is a minor wave of transcription before this time point. Similarly maternal mRNAs degrade at different rates, with only a percentage undergoing microRNA-mediated degredation. The aparant different rates of maternal mRNA degredation may be obscured by zygotic transcription.In order to gain an understanding of the MZT I intend to establish a precise understanding of transcription in the early embryo by using solexa sequencing to perform transcript counting at five different developmental stages that span the MZT. Specifically I intend to use crosses from two different zebrafish strains SAT (Sequenced AB and Tbingen, Zv9) and WIK. This project will allow one to understand the overall transcription profiles of genes in the early embryo, but importantly, the SNPs between the two different strains will determine if transcripts are maternal or zygotic (paternal). As a proof of principle we will first use one lane of sequencing to identify transcripts from a cross of an SAT and a WIK fish. This will allow us to observe SNPs between the two different strains. This will be run over one solexa lane. We will then sequence from five different time points on four different crosses SAT male and WIK female, WIK male and SAT female, WIK male and WIK female and SAT male with SAT female. We will prepare the libraries, which will be sequenced paired-end 54 bp over a total of seven lanes of solexa.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2012-03-12 | E-ERAD-57 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6312346 | biostudies-literature
Project description:During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly-synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3′ modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.
2018-04-13 | GSE111152 | GEO
Project description: Not available
| S-EPMC5495070 | biostudies-literature