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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Tag-seq in eye-antennal and wing imaginal discs of D.melanogaster, D.yakuba, and D.virilis; RNA-seq in wild-type and glass mutant D.melanogaster eye-antennal imaginal discs.

ABSTRACT: In this study we use Tag-sequencing in eye-antennal and wing imaginal discs across Drosophila species to determine a set of conserved eye-specific developmental genes. Next, we perform motif discovery analysis using the tool i-cisTarget, to depict the core gene developmental network underlying compound eye photoreceptor. The Glass position weight matrix appears as the most highly overrepresented motif, thus positioning Glass as a master regulator in compound eye photoreceptor development. Differential gene expression analysis by RNA-seq in D.melanogaster wild-type eye-antennal versus glass mutant [gl 60j] shows that the majority of our predicted Glass targets show strong downregulation in the glass mutant. This SuperSeries is composed of the following subset Series: GSE39781: RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster GSE39782: Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Stein Aerts

PROVIDER: E-GEOD-39784 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

Project description:The aim of this study is to identify a set of eye-specific genes across Drosophila species. Species are used as replicates to remove biological noise and identify a core set of conserved eye-developmental genes. We analyze this conserved core using the motif discovery tool i-cisTarget, and identify master regulators of retinal determination, including the Zinc Finger transcription factor Glass. Six samples were analyzed by Illumina Digital Gene Expression (DGE) using the NlaIII restriction enzyme, namely two different tissues (eye-antennal discs and wing discs) for each of the three species under study.

2012-09-21 | E-GEOD-39782 | biostudies-arrayexpress

RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster

Project description:The aim of this data set is to perform a differential expression analysis between wild type eye-antennal imaginal disc and discs that are homozygous glass mutant gl[60j]. This data set is used to validate Glass target gene predictions identified by i-cisTarget on a set of conserved eye-specific genes. RNA-seq was performed in eye-antennal imaginal discs of two D.melanogaster wild-type strains (Canton S and strain RAL-208 (Jordan et al. 2007, Ayroles et al. 2009)), representing two biological replicates; and in glass mutant (gl[60j]) discs for two technical replicates.

2012-09-21 | E-GEOD-39781 | biostudies-arrayexpress

Tag-seq in eye-antennal and wing imaginal discs of D.melanogaster, D.yakuba, and D.virilis; RNA-seq in wild-type and glass mutant D.melanogaster eye-antennal imaginal discs.

Project description:In this study we use Tag-sequencing in eye-antennal and wing imaginal discs across Drosophila species to determine a set of conserved eye-specific developmental genes. Next, we perform motif discovery analysis using the tool i-cisTarget, to depict the core gene developmental network underlying compound eye photoreceptor. The Glass position weight matrix appears as the most highly overrepresented motif, thus positioning Glass as a master regulator in compound eye photoreceptor development. Differential gene expression analysis by RNA-seq in D.melanogaster wild-type eye-antennal versus glass mutant [gl 60j] shows that the majority of our predicted Glass targets show strong downregulation in the glass mutant. This SuperSeries is composed of the SubSeries listed below.

2012-09-21 | GSE39784 | GEO

RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster

2012-09-21 | GSE39781 | GEO

The BTB-zinc finger transcription factor Abrupt acts as an epithelial oncogene in Drosophila through maintaining a progenitor-like cell state

Project description:The capacity of tumor cells to maintain continual overgrowth potential has been linked to the commandeering of normal self-renewal pathways. Using an epithelial cancer model in Drosophila we carried out an overexpression screen for oncogenes capable of cooperating with the loss of the epithelial apico-basal cell polarity regulator, scribbled, and identified the cell fate regulator, Abrupt, a BTB-zinc finger protein. Abrupt overexpression alone is insufficient to transform cells, but in cooperation with scrib loss of function, Abrupt promotes the formation of massive tumors in the eye/antennal disc. The steroid hormone receptor coactivator, Taiman (SRC3/AIB1), is known to associate with Abrupt, and Taiman overexpression also drives tumor formation in cooperation with the loss of Scribbled. Expression arrays and ChIP-Seq indicates that Abrupt overexpression represses a large number of genes, including steroid hormone-response genes and multiple cell fate regulators, thereby maintaining cells within an epithelial progenitor-like state. The progenitor-like state is characterised by the failure to express the conserved Eyes absent/Dachshund regulatory complex in the eye disc, and in the antennal disc by the failure to express cell fate regulators that define the temporal elaboration of the appendage along the proximo-distal axis downstream of Distalless. Loss of scribbled promotes cooperation with Abrupt through impaired Hippo signaling, which is required and sufficient for cooperative overgrowth with Abrupt, and JNK signaling, which is required for tumor cell migration/invasion but not overgrowth. These results thus identify a novel cooperating oncogene, mammalian family members of which are also known oncogenes, and demonstrate that epithelial tumors in Drosophila can be characterised by the maintenance of a progenitor-like state. ChIP-Seq of Abrupt, ChIP-Seq of Abrupt (scrib-), Input, Input (scrib-)

2013-08-15 | E-GEOD-42928 | biostudies-arrayexpress

Binding site turnover produces pervasive quantitative changes in TF binding between closely related Drosophila species

Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.

2010-02-18 | E-GEOD-20369 | biostudies-arrayexpress

Genome-wide comparative ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer

Project description:This data consists of RNA-seq data of whole animal white pre pupa of four Drosophila species: Drosophila melanogaster, Drosophila simulans, Drosophila yakuba, and Drosophila pseudoobscura. The processed RPKM values are calculated following the method in Garber et al 2011 Nature Methods paper. Examination of H3K27me3 in 4 Drosophila species and its correlation with gene expression levels in the same development stage relevant ChIP-seq data can be found in GSE25663, GSE25668

2013-08-17 | E-GEOD-49945 | biostudies-arrayexpress

ChIP-Seq of six Drosophila species with anti-Drosophila melanogaster Twist and anti-Snail antibodies using different library fragment sizes

Project description:The binding patterns of some transcription factors have been shown to diverge substantially between closely related species. Here, we show that the binding pattern of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at developmental enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their cooperative binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. We predict that conservation, dynamic occupancy, and combinatorial regulation will be generally true for developmental enhancers.

2010-12-07 | E-MTAB-376 | biostudies-arrayexpress

Dachshund ChIP-seq in Drosophila Melanogaster 3rd instar imaginal eye discs

Project description:The patterning of Drosophila retina occurs both very fast and with high precision. This process is driven by the dynamic changes in signalling activity of the conserved Hedgehog (Hh) pathway, which coordinates cell fate determination, cell cycle and tissue morphogenesis. Here we show that during Drosophila retinogenesis, the retinal determination gene dachshund (dac) is not only a target of the Hh signaling pathway, but is also a modulator of its activity. Using developmental genetics techniques, we demonstrate that dac enhances Hh signaling by promoting the accumulation of the Gli transcription factor Cubitus interruptus (Ci) parallel to or downstream of fused. In the absence of dac, all Hh-mediated events associated to the morphogenetic furrow are delayed. One of the consequences is that, posterior to the furrow, dac- cells cannot activate a Roadkill-Cullin3 negative feedback loop that attenuates Hh signaling and which is necessary for retinal cells to continue normal differentiation. Therefore, dac is part of an essential positive feedback loop in the Hh pathway, guaranteeing the speed and the accuracy of Drosophila retinogenesis. ChIP-seq against Dachshund vs input ChIP-seq. Eye-antennal imaginal discs are dissected from Grh-GFP (Bloomington stock 42269) 3rd instar larvae and fixed with formaldehyde. Chromatin is prepared and sonicated until fragments reach an average size of 500 bp. Chromatin is immunoprecipitated with an anti-GFP Ab (ab290, Abcam) and the immunocomplexes are recovered with protein A/G magnetic beads (Millipore).

2016-07-01 | E-GEOD-82151 | biostudies-arrayexpress

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

Project description:Background: Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions. Results: We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs. Conclusions: This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism. RNA-Immunoprecipitation sequencing of RNA-Sm protein complexes.

2013-12-01 | E-GEOD-35842 | biostudies-arrayexpress

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