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Status |
Public on Sep 12, 2013 |
Title |
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 2) |
Organisms |
Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in blastoderm embryos of four species, which sample much of the diversity in the 40 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, measured by mRNA-seq, to the genome-wide binding, measured by ChIP-seq, of four transcription factors involved in early anterior-posterior patterning. We found that mRNA levels are much better conserved than individual transcription factor binding events, and that changes in a gene’s expression were poorly explained by changes in adjacent transcription factor binding. However highly bound sites, sites in regions bound by multiple factors and sites near genes are conserved more frequently than other binding, suggesting that a considerable amount of transcription factor binding is weakly or non-functional and not subject to purifying selection
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Overall design |
Comparison of the evolution of gene expression and regulatory TF binding in early Drosophila embryos.
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Contributor(s) |
Paris M, Kaplan T, Li X, Villalta JE, Lott SE, Eisen MB |
Citation missing |
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Submission date |
Sep 11, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Mathilde PARIS |
E-mail(s) |
thildeparis@gmail.com
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Organization name |
CNRS
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Department |
Institut de Genomique Fonctionnelle de Lyon
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Street address |
32-34 avenue Tony Garnier
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City |
Lyon |
ZIP/Postal code |
69006 |
Country |
France |
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Platforms (3) |
GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
GPL17715 |
Illumina Genome Analyzer II (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis) |
GPL17717 |
Illumina HiSeq 2000 (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis) |
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Samples (16)
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This SubSeries is part of SuperSeries: |
GSE50773 |
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression |
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Relations |
BioProject |
PRJNA218869 |
SRA |
SRP029885 |