Effect of depletion or transgenic overexpression of nup133 or elys on zygotic genome activation (ZGA) during zebrafish early development
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ABSTRACT:
PROVIDER: PRJNA878486 | ENA |
REPOSITORIES: ENA
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Project description:To investigate the function of nuclear pore complex (NPC) in the regulation of zygotic genome activation (ZGA), we established mutants of nucleoporins, including maternal and zygotic mutant of nup133 (MZnup133) and maternal mutant of elys (Melys), for maternal depletion by CRISPR/Cas9, and transgenic embryos of nup133 (Tgnup133) for maternal overexpression through Tol2 mediated method. We then performed gene expression profiling analysis using data obtained from RNA-seq of wildtype, MZnup133, Melys and Tgnup133 at three time points.
2023-02-22 | GSE212933 | GEO
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:During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development, still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z and independent of Zelda. H2A.Z enrichment precedes ZGA and Polymerase II loading onto chromatin. In vivo knock-down of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that maternal factors and H2A.Z are master regulators of the de novo establishment of transcriptional programs during ZGA via chromatin reorganization.
2021-10-13 | GSE161589 | GEO
Project description:Zygotic transcription of ZGA staged embryos [GRO-seq]
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Project description:We generated NUP133 mutant podocytes to model human hereditary SRNS in vitro. A subtype of SRNS is caused by monogenetic mutations of the nuclear pore complex including NUP133. Human immortalized podocytes were genome edited applying the CRISPR/Cas9 technique to create NUP133 KO cells (“KO-1”). cDNA of NUP133-WT or causative variants NUP133 c.2922T>G (“Mutation-1”) or NUP133 c.3335-11T>A (“Mutation-2”) were stable expressed into this KO background by lentiviral transduction. Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis was performed in triplicate for each cell line. NUP133 mutant podocytes showed no overt transcriptional changes compared to NUP133-WT cells.
2022-04-07 | GSE189709 | GEO
Project description:Zygotic genome activation (ZGA) is a complex process which denotes the initiation of gene expression after fertilization. Deciphering the proper timing and genes involved in ZGA program is still a fundamental challenge in early embryo development. Here, we present a new ZGA gene identification framework, named ZGA-Timer, based on the timecourse pattern from RNA-seq data. By performing ZGA-Timer and siRNA technology, we confirmed Uqcc3 as a novel ZGA gene in mice. As a unique feature of ZGA-Timer, time-series RNA-seq data are modeled by a pattern recognition method and the onset of ZGA can be estimated in multiple species. ZGA-Timer outperforms current foldchange-based approaches. Furthermore, we investigate the epigenetic modifications and find that accessible chromatin predominately contributes to the regulation of ZGA genes. Moreover, ZGA genes show significant enrichment in housekeeping genes and cancer driver genes. Together, our ZGA-Timer framework provides a new approach to further understand the ZGA process.
2021-05-18 | GSE174530 | GEO
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:Upon fertilization, maternal factors direct development in a transcriptionally silent embryo. At the maternal-to-zygotic transition (MZT), a universal step in animal development, unknown maternal factors trigger zygotic genome activation (ZGA). In zebrafish, ZGA is required for gastrulation and clearance of maternal mRNAs, which is achieved in part by the conserved microRNA miR-430. However, the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog, Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors, thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre-MZT embryo revealed that nanog, sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog, SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation, and a failure to activate >75% of zygotic genes. Furthermore, we found that Nanog binds the miR-430 locus and together with Pou5f1 and SoxB1 initiate miR-430 expression and activity. Our results demonstrate that maternal Nanog, Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR-430 expression. Wild type and loss-of-function total mRNA sequencing of embryonic transcriptomes pre- and post-MZT; ribosome profiling pre-MZT
2013-09-22 | E-GEOD-47558 | biostudies-arrayexpress
Project description:The epigenome plays critical roles in controlling gene expression and development. However, how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here, we show parental-to-zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly, this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4-cell stage, and zygotic enhancers are not activated until around zygotic genome activation (ZGA). By contrast, many promoters remain hypomethylated and, unexpectedly, acquire de novo histone acetylation as early as at the 4-cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally, such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus, these data revealed widespread enhancer dememorization and promoter priming during parental-to-zygotic transition.
2018-10-25 | GSE114954 | GEO
Project description:We generated NUP133 WT and KO podocytes to model human hereditary SRNS in vitro. A subtype of SRNS is caused by monogenetic mutations of the nuclear pore complex including NUP133. Immortalized human podocytes were genome edited applying the CRISPR/Cas9 technique and two independent NUP133 sgRNAs. Two monoclonal cell backgrounds were used to create two matching sets of NUP133 WT and KO cells (WT-1 versus KO-1 and WT-2 versus KO-2). Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis was performed in duplicate for each cell line. NUP133 KO podocytes exhibit vast transcriptional changes compared to WT cells.
2022-04-07 | GSE189703 | GEO