Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA139533 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In vivo genomic binding sites for the Drosophila CTCF Insulator
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Project description:Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptome-wide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Drosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridinylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridinylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The three mRNAs most enriched for Psi encode highly-expressed yolk proteins (YP1, YP2, YP3). By comparing the pseudouridine profiles in the RluA-2 mutant and the w1118 control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.
2022-12-13 | GSE213312 | GEO
Project description:Genome-wide analysis of dFOXO binding sites in Drosophila
| PRJNA191574 | ENA
Project description:Long non-coding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed CHART, a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly-crosslinked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from fly and human. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage-compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the MSL-complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to ChIP for proteins. Examination of the binding sites of roX2 ncRNA from S2 cells using two different elution strategies compared with a sense control or input control. Processed data file 'roX2.2.peaks.bed' (for roX2 CHART RNase eluted, combined replicates) linked below as supplementary file.
2011-12-07 | E-GEOD-28180 | biostudies-arrayexpress
Project description:Mapping binding sites of SIN3 isoforms across the Drosophila genome.
| PRJNA293235 | ENA
Project description:The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX sites are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a non-productive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a low-diffusion chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of similar components.
2021-06-23 | PXD023747 | Pride
Project description:Genome-wide Tinman binding sites in early and late Drosophila embryos
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Project description:Chromosomal High Affinity Binding Sites for the Drosophila Dosage Compensation Complex.
| PRJNA113583 | ENA