Transcriptome analysis of the developing Drosophila ovary
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE109258 | GEO | 2018/04/16
REPOSITORIES: GEO
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Project description:We use single cell RNA sequencing approach to identify and characterize all cell types in developing Drosophila ovaries at late third instar larval stage (LL3).
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Project description:Transcriptome analysis of the developing Drosophila ovary
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Project description:Here we perform transcriptional profiling of late third instar larval ovaries and gonadal fatbody from Drosophila melanogaster w1118 flies. We designed this experiment to investigate the effect of protease treatment on dissected ovaries. We profiled ovaries without protease treatment with some fatbody still attached, fatbody alone dissected from around the ovaries, ovaries cleaned of fatbody using a papain/collagenase cocktail, and ovaries dissociated using a papain/collagenase cocktail. We then constructed polyA+ libraries and performed 50 bp stranded single end RNA-Seq.
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Project description:Alternative transcription initiation, which refers to the transcription of a gene from different transcription start sites (TSSs), is prevalent in mammalian systems and has important biological functions. Although transcriptional regulation has been extensively studied, the mechanism that selects one TSS over others in a gene remains elusive. We discovered Piwi, an RNA-binding protein, regulated TSS usage of genes and identified 87 genes with significantly altered TSS usage (ATU) in piwi-deficient Drosophila ovaries using the cap-analysis gene expression sequencing (CAGE-seq) method. This regulation occurs in both germline and somatic cells in ovaries as well as in cultured ovarian somatic cells (OSCs). Correspondingly, RNA Pol II initiation and elongation at TSSs of ATU genes were affected in germline-piwi-knockdown ovaries and piwi-knockdown OSCs. We identified a FACT complex component, Ssrp, which is essential for mRNA elongation, as a novel interactor of Piwi in the nucleus. Temporally controlled knockdown of ssrp affected TSS usage of ATU genes whereas overexpression of ssrp partially rescued the TSS usage of ATU genes in piwi mutant ovaries. Thus, Piwi may interact with Ssrp to regulate TSS usage in Drosophila ovaries by affecting Pol II initiation and elongation.
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Project description:Alternative transcription initiation, which refers to the transcription of a gene from different transcription start sites (TSSs), is prevalent in mammalian systems and has important biological functions. Although transcriptional regulation has been extensively studied, the mechanism that selects one TSS over others in a gene remains elusive. We discovered Piwi, an RNA-binding protein, regulated TSS usage of genes and identified 87 genes with significantly altered TSS usage (ATU) in piwi-deficient Drosophila ovaries using the cap-analysis gene expression sequencing (CAGE-seq) method. This regulation occurs in both germline and somatic cells in ovaries as well as in cultured ovarian somatic cells (OSCs). Correspondingly, RNA Pol II initiation and elongation at TSSs of ATU genes were affected in germline-piwi-knockdown ovaries and piwi-knockdown OSCs. We identified a FACT complex component, Ssrp, which is essential for mRNA elongation, as a novel interactor of Piwi in the nucleus. Temporally controlled knockdown of ssrp affected TSS usage of ATU genes whereas overexpression of ssrp partially rescued the TSS usage of ATU genes in piwi mutant ovaries. Thus, Piwi may interact with Ssrp to regulate TSS usage in Drosophila ovaries by affecting Pol II initiation and elongation.
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Project description:Alternative transcription initiation, which refers to the transcription of a gene from different transcription start sites (TSSs), is prevalent in mammalian systems and has important biological functions. Although transcriptional regulation has been extensively studied, the mechanism that selects one TSS over others in a gene remains elusive. We discovered Piwi, an RNA-binding protein, regulated TSS usage of genes and identified 87 genes with significantly altered TSS usage (ATU) in piwi-deficient Drosophila ovaries using the cap-analysis gene expression sequencing (CAGE-seq) method. This regulation occurs in both germline and somatic cells in ovaries as well as in cultured ovarian somatic cells (OSCs). Correspondingly, RNA Pol II initiation and elongation at TSSs of ATU genes were affected in germline-piwi-knockdown ovaries and piwi-knockdown OSCs. We identified a FACT complex component, Ssrp, which is essential for mRNA elongation, as a novel interactor of Piwi in the nucleus. Temporally controlled knockdown of ssrp affected TSS usage of ATU genes whereas overexpression of ssrp partially rescued the TSS usage of ATU genes in piwi mutant ovaries. Thus, Piwi may interact with Ssrp to regulate TSS usage in Drosophila ovaries by affecting Pol II initiation and elongation.
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Project description:Alternative transcription initiation, which refers to the transcription of a gene from different transcription start sites (TSSs), is prevalent in mammalian systems and has important biological functions. Although transcriptional regulation has been extensively studied, the mechanism that selects one TSS over others in a gene remains elusive. We discovered Piwi, an RNA-binding protein, regulated TSS usage of genes and identified 87 genes with significantly altered TSS usage (ATU) in piwi-deficient Drosophila ovaries using the cap-analysis gene expression sequencing (CAGE-seq) method. This regulation occurs in both germline and somatic cells in ovaries as well as in cultured ovarian somatic cells (OSCs). Correspondingly, RNA Pol II initiation and elongation at TSSs of ATU genes were affected in germline-piwi-knockdown ovaries and piwi-knockdown OSCs. We identified a FACT complex component, Ssrp, which is essential for mRNA elongation, as a novel interactor of Piwi in the nucleus. Temporally controlled knockdown of ssrp affected TSS usage of ATU genes whereas overexpression of ssrp partially rescued the TSS usage of ATU genes in piwi mutant ovaries. Thus, Piwi may interact with Ssrp to regulate TSS usage in Drosophila ovaries by affecting Pol II initiation and elongation.
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Project description:The gene-regulatory mechanisms behind the female germline piRNA pathway in ovaries of metazoan species remain largely unexplored. Here, using the Drosophila model and combinations of RNA-seq, ATAC-seq, and single-cell approaches, we reveal the transcription factors that regulate the female germline piRNA pathway in animal ovaries.
2024-12-23 | GSE233245 | GEO
Project description:The gene-regulatory mechanisms behind the female germline piRNA pathway in ovaries of metazoan species remain largely unexplored. Here, using the Drosophila model and combinations of RNA-seq, ATAC-seq, and single-cell approaches, we reveal the transcription factors that regulate the female germline piRNA pathway in animal ovaries.
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Project description:Insulators delimit independent transcriptional domains within genomes by constraining enhancer and silencer action. These transcriptional effects depend upon DNA recognition by insulator binding proteins that recruit partners that protect against inappropriate long range modulation of non-target promoters. Insulator binding proteins are broadly expressed during development, with largely constitutive binding to thousands of genomic sites. Yet, tissue-specific transcriptional changes result from the loss of individual insulator binding proteins. To understand the molecular basis for such effects, we are studying the classic Drosophila insulator protein Suppressor of Hairy-wing [Su(Hw)]. Genetic studies show that loss of this broadly expressed insulator protein prevents oocyte development. To determine the basis for the block in oogenesis, we coupled transcriptional analyses in su(Hw) mutant ovaries with genome-wide definition of Su(Hw) binding in this tissue. These studies identified 71 direct targets of Su(Hw) regulation, with nearly 70% of these genes showing increased RNA accumulation when Su(Hw) is lost. Surprisingly, derepressed Su(Hw) target genes correspond to genes normally highly expressed in neural tissues, suggesting that Su(Hw) has a critical role in silencing neural genes in the ovary. Support for this postulate was obtained by genetic studies. We found that oocyte production was restored in su(Hw) mutant females that carry a deletion of one allele of the elav family RNA binding protein 9 (Rbp9) gene. These su(Hw) null oocytes can be fertilized, with evidence that embryos lacking Su(Hw) show compromised development. Our studies extend the known transcriptional activities of Su(Hw), indicating that Su(Hw) can function as an insulator, activator and repressor, the latter function being essential for oogenesis. These findings highlight that insulator proteins are versatile transcriptional regulatory proteins, suggesting that tissue specific contributions to transcription result from direct regulation of individual genes. Ovaries for RNA isolation were dissected from 4-6 hour old virgin females of wild type, su(Hw)f/v (fertile), su(Hw)2/v (sterile) and su(Hw)Pb/2 (sterile) Drosophila melanogaster. At this stage of development, ovaries only contain egg chamber stages 1-8. Loss of Su(Hw) causes apoptosis at stage 9. Thus, the experimental design compares transcriptionl changes in the ovary prior to induction nof apoptosis in su(Hw) mutants.
2012-09-01 | E-GEOD-36528 | biostudies-arrayexpress