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Genome-wide differences in RNA expression in Drosophila melanogaster leg imaginal discs based on time and presence/absence of broad-based gene regulation

ABSTRACT: Genome-wide differences in RNA expression in Drosophila melanogaster leg imaginal discs based on time and presence/absence of broad-based gene regulation

PROVIDER: PRJNA589047 | ENA |

REPOSITORIES: ENA

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Genome-wide differences in RNA expression in Drosophila melanogaster leg imaginal discs based on time and presence/absence of broad-based gene regulation

Project description:We report on changes in gene expression resulting from the ecdysone-directed broad-based transcriptional regulatory hierarchy in Drosophila melanogaster leg imaginal discs by comparing expression in white1118 third-instar larvae (-18 hrs relative to pupariation) and white prepupae (0 hrs) to examine the transcriptional effects of the late larval ecdysone pulse, as well comparing expression in white1118 and broad5 white prepupal leg imaginal discs to examine the transcriptional effects of the early ecdysone responder, broad. Using this approach, we were able to identify critical leg disc elongation genes that are differentially regulated in broad mutants

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Project description:Animal limb development relies on the establishment of organizing centers, which govern limb outgrowth and patterning by regulating the spatial and temporal expression of secreted signaling molecules. On a molecular level the establishment of organizing centers occurs via cis regulatory modules (CRMs), also known as transcriptional enhancers, that integrate upstream temporal and spatial inputs. We elucidated the mechanism that governs the establishment of an Epidermal Growth Factor Receptor (EGFR) organizing center (EOC) during leg development in Drosophila melanogaster. We find that EGFR activation occurs by sequential activation of the EGFR ligand Vein (Vn) and the EGFR ligand-processing protease Rhomboid (Rho), each through single CRMs. These CRMs integrate in a distinct manner inputs from the Wingless (Wg) and Decapentaplegic (Dpp) signaling pathways, and from the leg selector transcription factors Distal-less (Dll) and Sp1. Elimination of the vn (vnE) and rho (rhoE) EOC enhancers eliminates the expression of these genes in the center of the leg imaginal discs, respectively. A vnE rhoE double deficiency, but not single deletions, demonstrates an absolute requirement of these CRMs for specifying the most distal, but not more proximal, leg fates. In addition, the cis-regulatory logic of vnE and rhoE transcends the leg EOC developmental program, because genomic regions with similar inputs, based on predicted and genome-wide binding by the transcription factors that establish the EOC, faithfully predicts novel CRMs active in the distal leg. The combinatorial input of Wg, Dpp, Dll and Sp1 at these CRMs reveals a molecular signature for coordinating gene expression in the Drosophila leg that might be analogous to many other multi-cellular systems.

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Project description:The Hox genes are responsible for generating morphological diversity along the anterior-posterior axis during animal development. The Drosophila Hox gene Ultrabithorax (Ubx), for example, is required for specifying the identity of the third thoracic (T3) segment of the adult, which includes the dorsal haltere, an appendage required for flight, and the ventral T3 leg. Ubx mutants show homeotic transformations of the T3 leg towards the identity of the T2 leg and the haltere towards the wing. All Hox genes, including Ubx, encode homeodomain containing transcription factors, raising the question of what target genes Ubx regulates to generate these adult structures. To address this question, we carried out whole genome ChIP-chip studies to identify all of the Ubx bound regions in the haltere and T3 leg imaginal discs, which are the precursors to these adult structures. In addition, we used ChIP-chip to identify the sites bound by the Hox cofactor, Homothorax (Hth). 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 Richard S. Mann at Columbia University. It contains ChIP-chip data on Affymetrix Drosophila Tiling 2.0R arrays for multiple transcription factor antibodies in multiple Drosophila tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Haltere or leg imaginal discs ChIPped for Ubx or Hth vs. input DNA from corresponding imaginal discs. For each combination of tissue and antibody, ChIP experiments have been performed and hybridized on Affymetrix Drosophila Tiling 2.0R arrays. At least 3 biological replicates for the ChIP sample have been hybridized.

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Genome-wide binding of Sd and Yki in imaginal discs

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