Expression data from Control and Yorkie overexpression pupal eye discs
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE26700 | GEO | 2011/12/20
SECONDARY ACCESSION(S): PRJNA136153
REPOSITORIES: GEO
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Project description:To probe mechanistic determinants of Yki function in mitochondrial biogenesis, we conducted a genome-wide microarray experiment, and specifically compared expression patterns of genes from control (GMR gal4) and Yorkie over-expressing (GMR gal4; UAS yki) pupal eye discs. The above mentioned genotypes were grown at 29 deg C and at about 40 hrs after pupariation, the pupal eye discs were dissected. RNA was extracted from the pupal eye discs, purified and used to generate microarray probes that were hybridized to the Drosophila genome 2 arrays (Affymetrix). The Gene Chip Operating system (Affymetrix) and dCHIP program (Harvard University) were used to generate pairwise comparisons between the transcription profiles of control and Yorkie over-expressing discs.
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2014-03-01 | E-GEOD-54600 | biostudies-arrayexpress
Project description:To identify novel regulators of the Hippo pathway, we performed affinity purification-mass spectrometry (AP-MS) using Drosophila embryos overexpressing Yki-EGFP with a ubiquitous driver da-GAL4, as well as cultured S2 cells expressing Yki-SBP. We identified the core Hippo pathway components, multiple Hippo pathway regulators and functional groups, and several putative Yki interactors including Bonus (Bon). To identify additional cofactors that are recruited by Bon, we performed AP-MS using Bon-SBP expressed in Drosophila S2 cells. Further genetic tests revealed the involvement of Bon interactors, HDAC1, Su(var)2-10, and Hrb27C, in the Drosophila eye specification that is regulated by the Yki-Bon complex.
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2011-08-31 | E-GEOD-25267 | biostudies-arrayexpress
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2011-09-01 | GSE25267 | GEO
Project description:As miRs are one of the crucial regulators of various cellular processes, our interest was to see whether any change in their expression occurs under Ago-1 overexpression. miRNA microarray analysis was carried out using total RNA extracted from control (GMR-GAL4), Ago-1 overexpressed (UAS Ago-1/GMR GAL4) and Ago-1 mutant (Ago-1^72/ Ago-1^45) adult eye. Several miRNAs were upregulated and several showed down regulation. miRs, which has shown significant fold change in there expression, were selected for further study.
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Project description:Purpose: Feeding larvae of fly models of polyQ and other neurodegenerative disorders on AR or RS supplemented food substantially suppressed neurodegeneration. With a view to gain further insight into the suppression of polyQ pathology by AR or RS, we expressed the UAS-127Q transgene using the predominantly eye-specific GMR-GAL4 driver and examined the transcriptomic changes in wild type and 127Q-expressing eye discs following feeding on AR or RS. In order to find out reason underlying the suppression of neurodegeneration by feeding of AR and RS, we checked difference in gene expression between eye discs expressing GMR-GAL4>UAS-127Q and wild type. Method: Eye disc RNA profiles of wandering late third instar larvae of GMR-GAL4>UAS-127Q and wild type larvae, reared on normal food or food supplemented with AR or RS since after hatching, were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 51bp pair-end reads, 12 samples per lane and each sample run across 2 lanes of flowcell (Flowcell ID: C7K52ACXX).This resulted in a sequencing depth of 19-25 million reads. The resulting sequencing fastq files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to merge with Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 19-25 million sequence reads per sample to the Drosophila melanogaster genome (dm6) and identified 15,904 transcripts with cufflink workflow in each genotypes studied. The GMR-GAL4 driven UAS-127Q expression in eye discs reared on AR supplemented food resulted in 259 differential expression, with 147 genes being down-regulated and 112 up-regulated, when compared with those reared on normal food, however, when larvae from same genotype reared on RS supplemented food resulted in 1641 DEGs, with 846 genes being down-regulated and 795 up-regulated compared with larvae reared on normal food. In eye disc of wild type larvae reared on AR supplemented food resulted in 680 DEGs, with 470 genes being down-regulated and 205 up-regulated compared with those reared on normal food. Larvae from wild type reared on RS supplemented food resulted in 427 DEGs, with 264 genes being down-regulated and 163 up-regulated compared with those reared on normal food. Compared to only GMR-GAL4>UAS-127Q and wild type larval eye discs reared on normal food, total of 1691, with 799 gene were up-regulated while 892 were down-regulated. Conclusion: The present results not only re-inforce earlier findings from our lab that the Ayurvedic Amalaki Rasayana and Rasa-Sindoor are potent suppressors of neurodegeneration but also provide direct evidence that these general health-promoting formulations significantly alter expression of many genes in protein-aggregation-clearance pathways and thus eliminate the cause of proteinopathy so that cell death is inhibited while other normal cellular activities continue. These formulations, which have been used in Ayurvedic practice for thousands of years as health-promoting as well as curative supplements, do not have any side-effects. Therefore, we believe that these Ayurvedic formulations have a good potential to ameliorate the sufferings of polyQ and other neurodegenerative disorders.
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Project description:Throughout Metazoa, developmental processes are controlled by a surprisingly limited number of conserved signaling pathways. Precisely how these signaling cassettes were assembled in early animal evolution remains poorly understood, as do the molecular transitions that potentiated the acquisition of their myriad developmental functions. Here we analyze the molecular evolution of the proto-oncogene YAP/Yorkie, a key effector of the Hippo signaling pathway that controls organ size in both Drosophila and mammals. Based on heterologous functional analysis of evolutionarily distant Yap/Yorkie orthologs, we demonstrate that a structurally distinct interaction interface between Yap/Yorkie and its partner TEAD/Scalloped became fixed in the eumetazoan common ancestor. We then combine transcriptional profiling of tissues expressing phylogenetically diverse forms of Yap/Yorkie with ChIP-seq validation in order to identify a common downstream gene expression program underlying the control of tissue growth in Drosophila. Intriguingly, a subset of the newly-identified Yorkie target genes are also induced by Yap in mammalian tissues, thus revealing a conserved Yap-dependent gene expression signature likely to mediate organ size control throughout bilaterian animals. Combined, these experiments provide new mechanistic insights while revealing the ancient evolutionary history of Hippo signaling. We sought to determine Yki and Sd target genes in Drosophila by immunoprecipitation of Yki, sd and RNA polymerase II. Chromatin immunoprecipitation of Yki, sd, and RNA polymerase II from eye disks was performed.
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