Effect of histone H2Av depletion on temperature dependence of the Drosophila S2R+ cell transcriptome
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ABSTRACT:
PROVIDER: PRJNA668003 | ENA |
REPOSITORIES: ENA
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Project description:The histone H2A variant H2A.Z has a crucial role in the regulation of temperature-dependent gene expression in the plant Arabidopsis thaliana. To evaluate whether the Drosophila homolog histone H2Av has a similar role in the control of the transcriptional response to temperature change, we depleted this histone variant by RNA interference in S2R+ cells and analyzed the effect on the transcriptome after temperature shifts to different temperatures (14, 25 and 30°C). For control, we performed analogous experiments using treatment with lacZ dsRNA instead of His2Av dsRNA.
2021-09-13 | GSE159171 | GEO
Project description:Temperature dependence of the transcriptome in cultured Drosophila S2R+ cells
| PRJNA668006 | ENA
Project description:Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures. However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation. To assess the effects of temperature change within the readily tolerated temperature range on the transcriptome, we have performed expression profiling with S2R+ cells, which are derived from the ectothermic organism Drosophila melanogaster.
2021-09-13 | GSE159170 | GEO
Project description:Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures. However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation, including the transcriptional level. To study effects of changes in ambient temperature on chromatin accessibility, we performed ATAC-Seq with S2R+ cells, a line derived from embryos of the ectothermic organism Drosophila melanogaster. Aliquots of S2R+ cells were exposed to different temperatures (14, 25 and 29°C) within the readily tolerated range before analysis with ATAC-Seq.
2021-09-13 | GSE159221 | GEO
Project description:This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. In other experiments, we have shown that Mago is required for correct splicing of the MAP kinase gene and its depletion causes a large reduction in MAP kinase mRNA levels. MAP kinase is a large gene in heterochromatin. In this study, we find that heterochromatic genes are disproportionately down-regulated in Mago-depleted cells, and those with large introns are particularly likely to be affected. SRA accession number: SRP003001.1 Sequencing of poly(A)+ RNA from S2R+ cells treated with either lacZ (control) or mago (experimental) dsRNA
2010-10-20 | E-GEOD-23997 | biostudies-arrayexpress
Project description:Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures. However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to distinct temperatures is predicted to involve complex regulation. To assess the effects of a temperature downshift from 25 to 14°C, i.e. from the optimal temperature to the lower limit of the readily tolerated range, on the transcriptome in a time-resolved manner, we have performed expression profiling with S2R+ cells, which are derived from the ectothermic organism Drosophila melanogaster.
2021-09-13 | GSE159172 | GEO
Project description:Background H2Av is evolutionarily conserved H2A variant protein involved in the regulation of transcription. The Tip60 complex is recruited by different transcription factors to facilitate the incorporation and acetylation of H2Av, thereby influencing target gene expression by modifying the stability of the nucleosome that occludes the transcription start site. The Tip60-H2Av module is involved in various developmental processes, though its precise roles are not yet fully understood. Methods RNA interference and gene knock-out technology were used screen essential genes in regulating Notch signaling pathway. We use immunostaining method to detect the protein level of H2Av, Tip60 complex as well as Notch signaling pathway components. Chromatin immunoprecipitation assay was performed to detect the specific bind of H2Av in E(spl)-Complex and Su(H) genes. Result Here we report that H2Av is required for Notch signaling activation during Drosophila wing development. H2Av depletion disrupts the expression of Notch target genes, resulting in wing marginal defects. Unexpectedly, we find that H2Av regulates the expression of Su(H) gene which encodes the transcription factor of the Notch signaling cascade. We further demonstrate that the Tip60 complex modulates the transcription of both Notch targets and Su(H) likely through H2Av. Based on these observations, we propose a model that the Tip60-H2Av module facilitates Notch pathway activation by simultaneously promoting the expression of both the target genes and the transcription factor. Conclusion This study offers insights into the diverse roles of the Tip60-H2Av module in Notch pathway activation by identifying a novel two-tier regulatory mechanism which may also be utilized by other chromatin remodeling factors. Key words H2Av, Notch, Su(H), Drosophila, Tip60
2025-01-24 | GSE287479 | GEO
Project description:The spatiotemporal control of transcription and the maintenance of germline genome integrity depend on dynamic chromatin architecture. In Drosophila, the actin-related protein Arp6—a core subunit of the SWR1-like Domino chromatin remodeling complex—mediates the deposition of the histone variant H2Av. Previous studies have established H2Av as a key transcriptional regulator that modulates the +1 nucleosome barrier to promote RNA Polymerase II (Pol II) pause release and productive elongation. Conversely, H2Av is also integral to heterochromatin assembly and gene silencing. Here we demonstrate that Arp6 and H2Av are essential for female fertility and the global repression of transposable elements (TEs) in the Drosophila ovary. Rather than repressing TEs directly, we show that Arp6 and H2Av maintain genomic stability indirectly by driving the transcription of core PIWI-interacting RNA (piRNA) pathway genes. Depletion of either chromatin factor leads to a significant loss of piRNAs and reduced non-canonical transcription of dual-strand piRNA clusters. This defect stems from a failure to express the Rhino-Deadlock-Cutoff (RDC) complex, alongside the downregulation of multiple other piRNA biogenesis factors. Genomic profiling confirms that H2Av acts predominantly as an activating signal at host gene promoters. Upon H2Av or Arp6 depletion, genes that rely on H2Av for their expression exhibit a distinct upstream shift and more precise spatial localization of the Pol II peak at the TSS, indicating an impaired transition from transcription initiation into productive elongation. Together, our findings build upon the known transcriptional activation functions of the Arp6-H2Av axis, revealing that this established chromatin mechanism is critical for licensing piRNA-mediated genome defense and ensuring germline maintenance.
2026-05-18 | GSE330545 | GEO
Project description:The spatiotemporal control of transcription and the maintenance of germline genome integrity depend on dynamic chromatin architecture. In Drosophila, the actin-related protein Arp6—a core subunit of the SWR1-like Domino chromatin remodeling complex—mediates the deposition of the histone variant H2Av. Previous studies have established H2Av as a key transcriptional regulator that modulates the +1 nucleosome barrier to promote RNA Polymerase II (Pol II) pause release and productive elongation. Conversely, H2Av is also integral to heterochromatin assembly and gene silencing. Here we demonstrate that Arp6 and H2Av are essential for female fertility and the global repression of transposable elements (TEs) in the Drosophila ovary. Rather than repressing TEs directly, we show that Arp6 and H2Av maintain genomic stability indirectly by driving the transcription of core PIWI-interacting RNA (piRNA) pathway genes. Depletion of either chromatin factor leads to a significant loss of piRNAs and reduced non-canonical transcription of dual-strand piRNA clusters. This defect stems from a failure to express the Rhino-Deadlock-Cutoff (RDC) complex, alongside the downregulation of multiple other piRNA biogenesis factors. Genomic profiling confirms that H2Av acts predominantly as an activating signal at host gene promoters. Upon H2Av or Arp6 depletion, genes that rely on H2Av for their expression exhibit a distinct upstream shift and more precise spatial localization of the Pol II peak at the TSS, indicating an impaired transition from transcription initiation into productive elongation. Together, our findings build upon the known transcriptional activation functions of the Arp6-H2Av axis, revealing that this established chromatin mechanism is critical for licensing piRNA-mediated genome defense and ensuring germline maintenance.
2026-05-18 | GSE330543 | GEO
Project description:The spatiotemporal control of transcription and the maintenance of germline genome integrity depend on dynamic chromatin architecture. In Drosophila, the actin-related protein Arp6—a core subunit of the SWR1-like Domino chromatin remodeling complex—mediates the deposition of the histone variant H2Av. Previous studies have established H2Av as a key transcriptional regulator that modulates the +1 nucleosome barrier to promote RNA Polymerase II (Pol II) pause release and productive elongation. Conversely, H2Av is also integral to heterochromatin assembly and gene silencing. Here we demonstrate that Arp6 and H2Av are essential for female fertility and the global repression of transposable elements (TEs) in the Drosophila ovary. Rather than repressing TEs directly, we show that Arp6 and H2Av maintain genomic stability indirectly by driving the transcription of core PIWI-interacting RNA (piRNA) pathway genes. Depletion of either chromatin factor leads to a significant loss of piRNAs and reduced non-canonical transcription of dual-strand piRNA clusters. This defect stems from a failure to express the Rhino-Deadlock-Cutoff (RDC) complex, alongside the downregulation of multiple other piRNA biogenesis factors. Genomic profiling confirms that H2Av acts predominantly as an activating signal at host gene promoters. Upon H2Av or Arp6 depletion, genes that rely on H2Av for their expression exhibit a distinct upstream shift and more precise spatial localization of the Pol II peak at the TSS, indicating an impaired transition from transcription initiation into productive elongation. Together, our findings build upon the known transcriptional activation functions of the Arp6-H2Av axis, revealing that this established chromatin mechanism is critical for licensing piRNA-mediated genome defense and ensuring germline maintenance.
2026-05-18 | GSE330555 | GEO