Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Drosophila Johnston organ genes

ABSTRACT: Hemizygous ato[1]/Df(3R)p[13] null mutants lack Johnston organ (JO) in their 2nd antennal segment. We screened for genes that are expressed in JO by comparing the 2nd antennal segment transcriptomes between ato[1]/Df(3R)p[13] mutants and balanced Df(3R)p[13]/TM3 and ato[1]/TM3 controls. To assess transcriptomes, we isolated the 2nd antennal segments of ~50 flies per strain and extracted their total RNA. Because about half of the JO cells are sensory neurons, we also isolated RNA from the brains of ato[1]/TM3 controls to delineate neuronal JO genes. cRNA was hybridized to Affymetrix Drosophila Genome 2.0 arrays. For each experiment, three biological replicates were run.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Martin Gopfert

PROVIDER: E-MEXP-3609 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Drosophila auditory organ genes and genetic hearing defects.

Senthilan Pingkalai R PR Piepenbrock David D Ovezmyradov Guvanch G Nadrowski Björn B Bechstedt Susanne S Pauls Stephanie S Winkler Margret M Möbius Wiebke W Howard Jonathon J Göpfert Martin C MC

Cell 20120801 5

The Drosophila auditory organ shares equivalent transduction mechanisms with vertebrate hair cells, and both are specified by atonal family genes. Using a whole-organ knockout strategy based on atonal, we have identified 274 Drosophila auditory organ genes. Only four of these genes had previously been associated with fly hearing, yet one in five of the genes that we identified has a human cognate that is implicated in hearing disorders. Mutant analysis of 42 genes shows that more than half of th ...[more]

PMID: 22939627

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Project description:Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes. FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs

Dataset Information

Drosophila Johnston organ genes

Publications

Drosophila auditory organ genes and genetic hearing defects.

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