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| Status |
Public on Aug 04, 2017 |
| Title |
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic |
| Organisms |
Drosophila melanogaster; Drosophila simulans; Drosophila melanogaster x Drosophila simulans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns in Drosophila melanogaster × D. simulans hybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially-varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. Combined with mathematical modeling and regulatory locus editing, we determine the SNP responsible for the allele-specific expression observed in the gene hunchback.
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| Overall design |
Embryonic mRNA profiles of mid-stage 5 hybrid and parental embryos were generated using RNA-seq
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| Contributor(s) |
Combs PA, Fraser HB |
| Citation(s) |
30383747 |
|
Peter A. Combs and Hunter B. Fraser. Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. bioRxiv 175059, 2017. DOI:10.1101/175059
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| Submission date |
Aug 03, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Peter Acuña Combs |
| E-mail(s) |
pcombs@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biology
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| Lab |
Hunter Fraser
|
| Street address |
Gilbert Rm 309, 371 Serra Mall
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (4)
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| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
| GPL23863 |
Illumina HiSeq 2500 (Drosophila melanogaster x Drosophila simulans) |
| GPL23864 |
Illumina NextSeq 500 (Drosophila melanogaster x Drosophila simulans) |
| GPL23865 |
Illumina NextSeq 500 (Drosophila simulans) |
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| Samples (186)
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| Relations |
| BioProject |
PRJNA397062 |
| SRA |
SRP114787 |
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