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Series GSE113574 Query DataSets for GSE113574
Status Public on Jul 11, 2018
Title Dll and Sp1 ChIP-seq data from Drosophila third instar leg imaginal discs
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design Triplicate pools of 100 yw and 100 recombineered Sp1-GFP (BAC) L3 wandering larvae were used to perform independent chromatin IPs. The Sp1-GFP (BAC) is a GFP-tagged Sp1 in BAC clone CH321-64M02 inserted in landing site VK00033 (gift from Dr. Rebecca Spokony). All 6 leg discs from each larva were used as material for each IP. Chromatin from the yw larvae pools was immuno-precipitated with goat anti-Dll antibody (sc-15858, Santa Cruz Biotechnology, 1.5 µg/ml for IP) while chromatin from the Sp1-GFP larvae pools was immuno-precipitated with rabbit anti-GFP antibody (ab290, Abcam, 1∶300 dilution for IP). DNA from non-immunoprecipitated 10% chromatin input was isolated from each pool as reference control.
 
Contributor(s) Richard M, Roumen V
Citation(s) 30142157
Submission date Apr 24, 2018
Last update date Jan 23, 2019
Contact name Matthew Slattery
Organization name University of Minnesota Medical School
Street address 1035 University Drive, SMed 219
City Duluth
State/province MINNESOTA
ZIP/Postal code 55812
Country USA
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (8)
GSM3109245 Leg.Dll.Input
GSM3109246 Leg.Dll.ChIP1
GSM3109247 Leg.Dll.ChIP2
Relations
BioProject PRJNA453135
SRA SRP142446

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113574_Leg.Dll.p2q4.peaks.txt.gz 119.1 Kb (ftp)(http) TXT
GSE113574_Leg.Sp1.p2q4.peaks.txt.gz 92.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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