Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

ABSTRACT: Control of metazoan embryogenesis shifts from maternal to zygotic gene products as the zygotic genome becomes transcriptionally activated. In Drosophila, zygotic genome activation (ZGA) begins with a minor wave, but technical challenges have hampered the identification of early transcripts or obscured the onset of their transcription. Here, we develop an approach to isolate transcribed mRNAs and apply it over the course of the minor wave and the start of the major wave of Drosophila ZGA. Our results increase known genes of the minor wave by 10 fold and show that this wave is continuous and gradual. Transposable-element mRNAs are also produced, but discontinuously. Genes in the early and middle part of the minor wave are short with few if any introns, and their transcripts are frequently aborted and tend to have retained introns, suggesting that inefficient splicing as well as rapid cell divisions constrain the lengths of early transcripts.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE125575 | GEO | 2019/05/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos [RNA-Seq]

Project description:Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a critical factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through co-phase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF–HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

2024-11-15 | GSE253714 | GEO

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos [ChIP-Seq]

2024-11-15 | GSE253709 | GEO

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos [ATAC-seq]

2024-11-15 | GSE253704 | GEO

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos

Project description:Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through cophase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF-HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

2024-11-14 | GSE253765 | GEO

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos (response) [RNA-seq]

2024-11-15 | GSE275419 | GEO

Metabolic control of histone acetylation for precise and timely regulation of minor ZGA in early mammalian embryos

Project description:We report that oxidized nicotinamide adenine dinucleotide (NAD+) is indispensable for mouse pre-implantation development. NAD+ could avoids excessive minor zygotic gene activation (ZGA) by cooperating with SIRT1 to remove zygotic H3K27ac. In human, NAD+ supplement can promote the removal of zygotic H3K27ac and benefit pre-implantation development. Our findings demonstrate that precise and timely regulation of minor ZGA is controlled by metabolic dynamics, and enhance our understanding of the metabolism of mammalian early embryos.

2022-10-05 | GSE185653 | GEO

A family of double-homeodomain transcription factors promotes zygotic genome activation in placental mammals [RNA-seq]

Project description:In metazoans, the fertilized embryo is transcriptionally mostly silent for a few cell divisions, until release of a first major wave of embryonic transcripts by so-called zygotic genome activation (ZGA). Maternally provided ZGA-triggering factors have been identified in Drosophila melanogaster and Danio rerio but their mammalian homologues are still undefined. Here, we reveal that DUX family transcription factors are key to this process in human and mouse. First, human Dux4 and murine Dux are expressed prior to ZGA in both species. Second, both orthologues bind to and activate the promoters of ZGA genes. Third, Dux knockdown hinders the progression of mouse embryos beyond the 2-cell stage. Fourth, it prevents the cycling of mouse embryonic stem (ES) cells through a 2-cell-like state whereas, conversely, Dux overexpression induces the accumulation of these ZGA genes-expressing ES cells. We conclude that DUX proteins are master regulators of mammalian ZGA.

2017-03-23 | GSE94324 | GEO

A family of double-homeodomain transcription factors promotes zygotic genome activation in placental mammals [ChIP-seq_d2]

2017-03-23 | GSE94323 | GEO

A family of double-homeodomain transcription factors promotes zygotic genome activation in placental mammals [ChIP-seq_d1]

2017-03-23 | GSE94322 | GEO

Repeat elements activating lncRNAs drives zygotic genome activation

Project description:Vertebrate life begins with fertilization, then the zygote genome is activated after transient silencing, termed zygotic genome activation (ZGA). The mechanism of how ZGA initiates is far from clear although it underlay the mystery of totipotency and start of life. The specific property of the minor ZGA implied the possible critical role of ncRNA in the initiation of ZGA. Here we delineated the expression profile of the lncRNAs in the mouse early embryo development and elucidated their critical role in the minor ZGA. LncRNAs showed closer correlation with minor ZGA, they activated earlier than the protein coding genes (PCGs) and suppressed quickly after ZGA. H3K9me3 enrichment prior the ZGA could explain the suspended expression of major ZGA PCGs albeit they possess the PolII pre-configuration. The PolII enriched MuERV-L was found around the TSS of the minor ZGA lncRNAs, and they were responsible for the activation of the minor ZGA lncRNAs and the subsequent embryo development. Our work suggested the MuERV-L mediated minor ZGA lncRNA activation as a critical driver between the epigenetic reprogramming triggered by fertilization and the embryo developmental program, thus provided clues for understanding totipotency and starting of life.

2024-01-01 | GSE213407 | GEO

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