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| Status |
Public on Aug 04, 2006 |
| Title |
Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by genome tiling array
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| Summary |
Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence specific transcription factor distributed in a broad nuclear gradient in the precellular embryo.Previous studies have identified as many as 70 protein-coding genes and one microRNA gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30 protein-coding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5' exons were identified for at least 10 of the ~100 protein-coding genes that were missed in earlier annotations. As many as 9 intergenic, uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and miR-9a. We discuss the potential functions of these newly identified genes, and suggest that intronic enhancers are a common feature of the DV gene network.
Keywords: gene expression, dorsal-ventral pattern genes, tiling array
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| Overall design |
3 samples where analyzed (Tollrm9/Tollrm10, pipe386/pipe664, Toll10B/+), 3 technical replicates
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| Contributor(s) |
Biemar F, Manak J, Nix D, Levine M |
| Citation(s) |
16908844 |
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| Submission date |
Aug 02, 2006 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Frederic Biemar |
| E-mail(s) |
fbiemar@berkeley.edu
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| Phone |
510-642-5007
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| Organization name |
UC Berkeley
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| Department |
Molecular & Cell Biology
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| Lab |
Levine Lab
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| Street address |
142 LSA
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3200 |
| Country |
USA |
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| Platforms (1) |
| GPL3923 |
Affymetrix Drosophila Melanogaster Antisense Tiling Array |
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| Samples (6)
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| GSM124762 |
Total RNA from Drosophila Embryo at 2-4 hrs: 10B_pipe |
| GSM124763 |
Total RNA from Drosophila Embryo at 2-4 hrs: 10B_rm9 |
| GSM124764 |
Total RNA from Drosophila Embryo at 2-4 hrs: pipe_10B |
| GSM124765 |
Total RNA from Drosophila Embryo at 2-4 hrs: pipe_rm9 |
| GSM124766 |
Total RNA from Drosophila Embryo at 2-4 hrs: rm9_10B |
| GSM124767 |
Total RNA from Drosophila Embryo at 2-4 hrs: rm9_pipe |
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| Relations |
| BioProject |
PRJNA96097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE5434_RAW.tar |
1.3 Gb |
(http)(custom) |
TAR (of CEL, TXT) |
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