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Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [RNA-Seq]

ABSTRACT: The Hippo pathway regulates metazoan growth, acting through the transcriptional co-activators Yorkie (in Drosophila) and Yap and Taz (in vertebrates). Much attention has been focused on upstream regulators of Yorkie and its homologues. In contrast, the mechanisms by which they actually promote transcription have remained poorly understood. Genome-wide chromatin binding experiments support extensive functional overlap between Yorkie and GAF. Chromatin binding identifies thousands of Yorkie sites, the majority of which are associated with elevated transcription, based on genome-wide analysis of mRNA and histone H3K4Me3 modification. Our studies establish a molecular basis for transcriptional activation by Yorkie and implicate it as a global regulator of transcriptional activity in Drosophila.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE43129 | GEO | 2013/02/07

SECONDARY ACCESSION(S): PRJNA184675

REPOSITORIES: GEO

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Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [ChIP-Seq]

2013-02-07 | GSE38594 | GEO

Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [RNA-Seq]

Project description:The Hippo pathway regulates metazoan growth, acting through the transcriptional co-activators Yorkie (in Drosophila) and Yap and Taz (in vertebrates). Much attention has been focused on upstream regulators of Yorkie and its homologues. In contrast, the mechanisms by which they actually promote transcription have remained poorly understood. Genome-wide chromatin binding experiments support extensive functional overlap between Yorkie and GAF. Chromatin binding identifies thousands of Yorkie sites, the majority of which are associated with elevated transcription, based on genome-wide analysis of mRNA and histone H3K4Me3 modification. Our studies establish a molecular basis for transcriptional activation by Yorkie and implicate it as a global regulator of transcriptional activity in Drosophila. This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Ken Irvine at HHMI/Rutgers University and Richard S. Mann at Columbia University. It contains RNA-seq data for larval wing imaginal discs.

2013-02-07 | E-GEOD-43129 | biostudies-arrayexpress

Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [ChIP-Seq]

2013-02-07 | E-GEOD-38594 | biostudies-arrayexpress

Genome-wide binding of Yki in S2 cells

2014-04-23 | GSE46305 | GEO

Genome-wide binding of Yki and GAF in embryos and wing imaginal discs

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-02-07 | GSE43130 | GEO

Genome-wide binding of Yki and GAF in embryos and wing imaginal discs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-02-07 | E-GEOD-43130 | biostudies-arrayexpress

Genome-wide analysis of Yki and Sd localization in imaginal disks of Drosophila eye by ChIP Seq

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.

2014-03-01 | GSE54601 | GEO

Genome-wide analysis of Yki and Sd localization in imaginal disks of Drosophila eye by ChIP Seq

2014-03-01 | E-GEOD-54601 | biostudies-arrayexpress

Identification of Cbt target genes in Drosophila wing imaginal discs

Project description:We performed a genome-wide ChIP analysis to find the set of target genes regulated by Cbt in Drosophila wing imaginal discs. We reported multiple transcriptional regulators and genes involved in the developlment, growth and patterning of the fruit fly.

2015-02-20 | GSE40958 | GEO

Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs.

Project description:BACKGROUND: Regeneration is the ability of an organism to rebuild a body part that has been damaged or amputated, and can be studied at the molecular level using model organisms. Drosophila imaginal discs, which are the larval primordia of adult cuticular structures, are capable of undergoing regenerative growth after transplantation and in vivo culture into the adult abdomen. RESULTS: Using expression profile analyses, we studied the regenerative behaviour of wing discs at 0, 24 and 72 hours after fragmentation and implantation into adult females. Based on expression level, we generated a catalogue of genes with putative role in wing disc regeneration, identifying four classes: 1) genes with differential expression within the first 24 hours; 2) genes with differential expression between 24 and 72 hours; 3) genes that changed significantly in expression levels between the two time periods; 4) genes with a sustained increase or decrease in their expression levels throughout regeneration. Among these genes, we identified members of the JNK and Notch signalling pathways and chromatin regulators. Through computational analysis, we recognized putative binding sites for transcription factors downstream of these pathways that are conserved in multiple Drosophilids, indicating a potential relationship between members of the different gene classes. Experimental data from genetic mutants provide evidence of a requirement of selected genes in wing disc regeneration. CONCLUSIONS: We have been able to distinguish various classes of genes involved in early and late steps of the regeneration process. Our data suggests the integration of signalling pathways in the promoters of regulated genes.

| S-EPMC2939566 | biostudies-literature

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