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| Status |
Public on Apr 28, 2014 |
| Title |
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution |
| Organisms |
Drosophila ananassae; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila yakuba; Drosophila willistoni |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. We find that the functions of a large fraction of D. melanogaster enhancers are conserved for their orthologous sequences owing to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogaster-Drosophila yakuba split about 11 million years ago without apparent adaptive selection and can contribute to changes in gene expression in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides functional insights into regulatory evolution.
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| Overall design |
STARR-seq was performed in S2 cells with paired-end sequencing in two replicates and respective inputs using genomic DNA from different Drosophila species. RNA-seq was performed in a non-stranded manner without replicates for two Drosophila species.
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| Web link |
http://starklab.org
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| Contributor(s) |
Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A |
| Citation(s) |
24908250 |
| Submission date |
Jun 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
daniel.gerlach@boehringer-ingelheim.com
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| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
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| Department |
Global Computational Biology and Digital Sciences
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| Street address |
Dr.-Boehringer-Gasse 5-11
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| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
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| Platforms (5)
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| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL13307 |
Illumina HiSeq 2000 (Drosophila yakuba) |
| GPL13309 |
Illumina HiSeq 2000 (Drosophila ananassae) |
| GPL13310 |
Illumina HiSeq 2000 (Drosophila pseudoobscura) |
| GPL14359 |
Illumina HiSeq 2000 (Drosophila willistoni) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA209379 |
| SRA |
SRP026279 |
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