Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Profiling of Islet, Lim3, Hb9 and Eve genomic binding in Drosophila with DamID

ABSTRACT: While developmental processes such as axon pathfinding and synapse formation have been characterized in detail, comparatively less is known of the intrinsic developmental mechanisms that regulate transcription of ion channel genes in embryonic neurons. Early decisions, including motoneuron axon targeting, are orchestrated by a cohort of transcription factors that act together in a combinatorial manner. These transcription factors include Even-skipped (Eve), Islet, Lim3 and Hb9. The perdurance of these factors in late embryonic neurons is, however, indicative that they might also regulate additional aspects of neuron development, including the acquisition of electrical properties. We have shown that Eve binds and regulates both voltage- and ligand-gated currents in motoneurons (Pym et al., 2006). We have also shown that Islet is sufficient to repress a Shaker-mediated A-type K(+) current, most likely due to a direct transcriptional effect (Wolfram et al., 2012). Finally, we have shown that Islet and Lim3 act in a combinatorial fashion to regulate Shaker-mediated A-type K(+) current (Wolfram et al., 2014). 3 biological relicates were performed for Islet, Lim3 and Hb9 (with one dye-swap). 2 biological relicates were performed for Eve.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Tony Southall

PROVIDER: E-GEOD-53446 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The transcription factors islet and Lim3 combinatorially regulate ion channel gene expression.

Wolfram Verena V Southall Tony D TD Günay Cengiz C Prinz Astrid A AA Brand Andrea H AH Baines Richard A RA

The Journal of neuroscience : the official journal of the Society for Neuroscience 20140201 7

Expression of appropriate ion channels is essential to allow developing neurons to form functional networks. Our previous studies have identified LIM-homeodomain (HD) transcription factors (TFs), expressed by developing neurons, that are specifically able to regulate ion channel gene expression. In this study, we use the technique of DNA adenine methyltransferase identification (DamID) to identify putative gene targets of four such TFs that are differentially expressed in Drosophila motoneurons. ...[more]

PMID: 24523544

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Project description:Cell-type specific transcriptional profiling is key to understanding cell fate specification and function. In order to achieve this it has been necessary, to date, to isolate specific cell types from complex tissues. We have developed 'TaDa', a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation or affinity purification. The method is simple, sensitive, highly reproducible and is in principle transferable to any model system. Here we show that TaDa can be used to identify transcribed genes in a cell-type specific manner. We profile the genome-wide binding of RNA polymerase II (Pol II) in adjacent, clonally related neural stem cells in intact Drosophila brains. Our data reveal the activity of non-canonical metabolic pathways in proliferating neuroepithelial cells, and highlight a possible role for the retinal determination gene regulatory network in patterning neural stem cell fates. We also identify temporal differences in the activity of signalling pathways that control neuroepithelial cell fate by profiling Pol II occupancy at two different stages of brain development. Using RNA Pol II TaDa to profile, in a cell-type specific manner, the transcriptional state of neuroepithelial cells at two stages of larval brain development. Closely related asymmetrically dividing neural stem cells (neuroblasts) were also profiled, in order to compare the transcriptomes of two different types of neural stem cells. 3 biological relicates were performed for 3rd instar neuroepithelial cells (with one dye-swap). 2 biological relicates were performed for 3rd instar neuroblasts (with dye-swap). 2 biological relicates were performed for 1st instar neuroepithelial cells (with dye-swap). As additional supporting evidence for the Pol II TaDa technique, 2 biological relicates were performed for 3rd instar salivary glands (with dye-swap) in order to compare with previous Pol II-ChIP data for this tissue [PMID 22821985].

Dataset Information

Profiling of Islet, Lim3, Hb9 and Eve genomic binding in Drosophila with DamID

Publications

The transcription factors islet and Lim3 combinatorially regulate ion channel gene expression.

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