Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic Profiling of Early Drosophila Embryogenesis Reveals Similarities in Replication Checkpoint and Histone mRNA Processing Mutants

ABSTRACT: In higher eukaryotes, maternally provided gene products drive the initial stages of embryogenesis until the zygotic transcriptional program takes over, a developmental process called the midblastula transition (MBT). In addition to zygotic genome activation, the MBT involves alterations in cell-cycle length and the implementation DNA damage/replication checkpoints that serve to monitor genome integrity. Previous work has shown that mutations affecting histone mRNA metabolism or DNA replication checkpoint factors severely impact developmental progression through the MBT, prompting us to characterize and contrast the transcriptomic impact of these genetic perturbations. In this study, we define gene expression profiles that mark early embryogenesis in Drosophila through transcriptomic analyses of developmentally staged (early syncytial vs late blastoderm) and biochemically fractionated (nuclear vs cytoplasmic) wild-type embryo. We then compare the transcriptomic profiles of loss-of-function mutants of the dChk1/Grapes replication checkpoint kinase and the Stem Loop Binding Protein (SLBP), a key regulator of replication-dependent histone mRNAs. Our analysis of RNA spatial and temporal distribution during embryogenesis offers new insights into the dynamics of early embryogenesis. Moreover, we find that grp and slbp mutant embryos display profound and highly similar defects in gene expression, most strikingly in zygotic genome activation, compromising the transition from a maternal to a zygotic regulation of development.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE89001 | GEO | 2017/01/20

SECONDARY ACCESSION(S): PRJNA349484

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The Spatiotemporal Control of Zygotic Genome Activation

Project description:One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the midblastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal, and BMP signaling together generate most of the spatiotemporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.

2019-05-14 | GSE122551 | GEO

Histone concentration times the cell cycle and transcription in early development.

Project description:This study measures transcriptomic differences due to overexpression (via Slbp RNAi) or knockdown (via abo mutation) of histones in precisely staged Drosophila melanogaster embryos spanning the maternal to zygotic transition.

2019-08-30 | GSE136631 | GEO

Different transcriptional strategies for zygotic genome activation in Drosophila [MNase-Seq]

Project description:During animal development, a fertilized egg is initially under the control of maternal products and only starts zygotic transcription after several cell divisions. In animals such as Xenopus, zebrafish and Drosophila, a massive increase in zygotic transcription occurs during the mid-blastula transition (MBT), when cells shift from rapid, synchronous cell divisions without gap phases to prolonged asynchronous divisions. Before MBT, only a few so-called pre-MBT genes are expressed. How transcription is set up during these early stages is poorly understood. For example, paused RNA Polymerase (Pol II) is frequently found at developmental control genes in mammalian embryonic stem cells and Drosophila embryos but when Pol II pausing is first established in the embryo is unknown. We have analyzed the genome-wide Pol II occupancy during the maternal-to-zygotic transition in hand-staged Drosophila embryos. The results show that massive Pol II recruitment and pausing is established during MBT. The ~100 genes that are transcribed before MBT are particularly short, consistent with a need for rapid transcription during these early cell divisions. Remarkably, most of these genes are transcribed without Pol II pausing and this correlates with a TATA-enriched promoter type. This suggests that distinct strategies are used for activation in the early Drosophila embryo and this may reflect general dynamic properties of promoters used throughout development. Mnase-seq in staged Drosophila embryos

2013-07-26 | E-GEOD-41686 | biostudies-arrayexpress

Ikk2 regulates cytokinesis during vertebrate development (Trancriptome profiling from the wild-type and Ikk2 maternal-zygotic mutant zebrafish)

Project description:Purpose: The Ikk2 maternal-zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition (MBT) and after MBT may provide a clean strategy to identify the NFkB target genes. Methods: Zebrafish lines were maintained under standard laboratory procedures. Results: Using an optimized data analysis workflow, we identified 54,276 transcripts in the embryos at 2 hours postfertilization (hpf) and 4 hpf. RNA-seq data confirmed lack of expression of a number of genes in the mutant both prior to and after the MBT, including genes linked to angiogenesis, skin development, cytokinesis, innate immunity and cytoskeletonT, and 4 of these were validated with qRT–PCR. M. add here if required. Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2, with two biologic replicates, generated by RNA-seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA-seq based transcriptome characterization improves analysis of NFkB regulated genes.

2017-08-21 | GSE90971 | GEO

Different transcriptional strategies for zygotic genome activation in Drosophila [ChIP-Seq]

2013-07-26 | E-GEOD-41700 | biostudies-arrayexpress

Marking of the genome by H3K4 methylation prior to embryonic gene activation

Project description:Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization. Very little is known on how the zygotic genome is programmed for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff.

2011-12-02 | GSE27314 | GEO

Profiling DNA Replication Timing in Zebrafish Embryos Reveals Dynamic Regulation During Development

Project description:The temporal order of DNA replication is modified during differentiation, but when a replication timing program is established and what alterations occur in vivo during embryogenesis are not known. Here we used zebrafish embryos to generate genome-wide, high-resolution replication timing maps throughout development. Unexpectedly, a non-random and defined replication timing program was evident in the rapid cell cycles before the midblastula transition. The majority of the genome undergoes dynamic shifts in replication timing throughout development as the timing program is decompressed, with many abrupt timing changes occurring during lineage specification. Strikingly, the long arm of chromosome 4 undergoes a developmentally regulated switch to late replication, reminiscent of mammalian X chromosome inactivation. This analysis also revealed a strong relationship between early replication and epigenetic marks at enhancers. Collectively, these data reveal the major changes in replication timing that occur during zebrafish embryogenesis, and demonstrate its dynamic regulation during vertebrate development.

2017-04-13 | GSE85713 | GEO

A global change in RNA Polymerase II pausing during the Drosophila midblastula transition [MNase-seq]

2013-07-26 | GSE41686 | GEO

A global change in RNA Polymerase II pausing during the Drosophila midblastula transition [ChIP-seq]

2013-07-26 | GSE41700 | GEO

High-resolution analysis of gene activity during the Xenopus mid-blastula transition

Project description:The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization

2014-03-27 | E-GEOD-56242 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data