Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA352382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4885910.fastq.gz | Fastqsanger.gz | |||
| SRR4885920.fastq.gz | Fastqsanger.gz | |||
| SRR4885930.fastq.gz | Fastqsanger.gz | |||
| SRR4885911.fastq.gz | Fastqsanger.gz | |||
| SRR4885921.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq analysis of MZD-overexpressed Drosophila embryos
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Project description:Purpose: Study how maternal Pioneer Transcription factor CLAMP affects sex-specifc splicing during initial embryonic development by regulating occupancy of spliceosome component Maleless (MLE), a RNA helicase on chromatin Method: Cut and Run (CUT&RUN) DNA libraries (Uyehara and McKay 2019) using anti-MLE antibody were generated from male embryos at 0-2 Hr pre-MZT and 2-4 hr post-MZT stages in presence and absence of maternal CLAMP. Maternal CLAMP was depleted by driving UAS-CLAMPRNAi in the ovaries using MTD-GAL4 maternal triple driver. As a control UAS-GFPRNAI was driven using the MTD-GAL4. Embryos were sexed using the meiotic drive system that produces sperm with only Y chromosomes (Reider et al 2017), resulting in progeny of only male genotypes. Results: We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZTand 2-4 Hr post-MZT embryonic stages in males. In 0-2 Hr and 2-4 Hr old control embryos 28,279 and 24,910 MLE peaks were detected. After depletion of maternal CLAMP, 41.97% of 0-2 Hr peaks (22183 remaining, 6096 lost) and 59.1% of 2-4 Hr peaks (15735 remaining, 9175 lost) are lost. We also found loss of maternal CLAMP resulted in 26% and 35.25% new MLE peaks at 0-2 hr pre-MZT and 2-4 Hr post-MZT embryonic stages. Our motif search shows presence of putative motifs for MLE binding on chromatin which needs further validation. Conclusion: This is the first study showing genome-wide MLE occupancy in sexed embryos during 0-2 hr pre-MZT and 2-4 hr post-MZT stages. We show that the maternally deposited transcription factor CLAMP affects MLE occupancy on chromatin in early embryos. Thus, we conclude that maternal transcription factors can affect spliceosome function by regulating occupancy of their components on chromatin.
2022-05-01 | GSE174781 | GEO
Project description:ELAV ChIP-seq in Drosophila melanogaster embryos
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Project description:RIP-Chip of BRAT and PUM from 0-3 hour Drosophila melanogaster embryos
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Project description:Alternative polyadenylation (APA) has been implicated in a variety of developmental and disease processes, such as stem cell differentiation and cancer. A particularly dramatic form of APA has been documented in the developing nervous system of flies and mammals, whereby a variety of neurogenic genes undergo coordinate extension of their 3’ UTRs. In Drosophila, the RNA-binding protein ELAV inhibits RNA processing at proximal polyadenylation (poly(A)) sites, thereby fostering the formation of 3’ extensions that can reach 12 kb in length. Here, we present evidence that paused Pol II plays an important role in the selective recruitment of ELAV to elongated genes. Replacing native promoters of elongated genes with heterologous promoters blocks normal 3’ extension in the nervous system, while native promoters can induce 3’ extension in ectopic tissues expressing ELAV. Computational analyses suggest that the promoter regions of elongated genes tend to contain paused Pol II and associated cis-regulatory elements such as GAGA. ELAV ChIP-Seq assays indicate pervasive binding to the promoter regions of extended genes. Our study provides the first evidence for a regulatory link between promoter-proximal pausing and APA. ELAV ChIP-Seq assays were conducted with nuclei obtained from 6-8 hr and 10-12 hr embryos
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Project description:We used single-embryo metabolomics to characterize early developmental metabolism in Drosophila. We employed a multi-omics approach where samples were collected, homogenized in 80% methanol and the soluble fraction recover to perform targeted metabolomic whle RNA-seq was performed on the insoluble fraction to accurately stage each embryo. Then, this RNA-based staging was used to place single embryo metabolomes across the developmental trajectory. Thus, we are able to construct a highly detailed metabolomic map of embryonic development. Importantly, we validated our single-embryo metabolomics results in pools of 10 embryos. The data provide a continuous timeline of metabolite levels (and gene expression) during early development (0-3 hours) in Drosophila melanogaster. We used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males/DGRP_352, females/DGRP_737). RNA-seq data related to this dataset can be accessed at GEO under accession number GSE263568.
2024-05-14 | MSV000094752 | MassIVE
Project description:RNA-seq analysis of Drosophila melanogaster embryos infected and uninfected with male-killing Spiroplasma
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Project description:Nucleus is a highly structured organelle and contains many functional compartments. While the structural basis for this complex spatial organization of compartments is unknown, a major component of this organization is likely to be the non-chromatin scaffolding called nuclear matrix (NuMat). Experimental evidence over the past decades indicates that most of the nuclear functions are at least transiently associated with the NuMat although the components of NuMat itself are poorly known. Here, we report NuMat proteome analysis from Drosophila melanogaster embryos and discuss its links with nuclear architecture and functions. In the NuMat proteome, we find structural proteins, chaperones related, DNA/RNA binding, chromatin remodeling and transcription factors. This complexity of NuMat proteome is an indicator of its structural and functional significance. Comparison of the 2D profile of NuMat proteome from different developmental stages of Drosophila embryos shows that less than half of the NuMat proteome is constant and rest of the proteins are stage specific dynamic components. This NuMat dynamics suggests a possible functional link between NuMat and the embryonic development. Finally, we also show that a subset of NuMat proteins remain associated with the mitotic chromosomes implicating their role in mitosis and possibly the epigenetic cellular memory. NuMat proteome analysis provides tools and opens up ways to understand nuclear organization and function.
2011-05-05 | PRD000255 | Pride
Project description:RIP-Chip of endogenous Staufen and GFP-tagged Staufen from 0-3 hour Drosophila embryos
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