|
| Status |
Public on Dec 10, 2014 |
| Title |
Enhancer-core promoter specificity separates developmental and housekeeping regulation |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
|
| Summary |
Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters – one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genes’ core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.
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| Overall design |
STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.
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| Contributor(s) |
Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A |
| Citation(s) |
25517091 |
| Submission date |
May 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Stark |
| Organization name |
Research Institute for Molecular Pathology (IMP), Vienna Biocenter VBC
|
| Street address |
Dr Bohr-Gasse 7
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platforms (2) |
| GPL11203 |
Illumina Genome Analyzer IIx (Drosophila melanogaster) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (39)
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| Relations |
| BioProject |
PRJNA248308 |
| SRA |
SRP042166 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57876_DSCP_BAC_S2.peaks.txt.gz |
7.2 Kb |
(ftp)(http) |
TXT |
| GSE57876_NipB_BAC_S2.peaks.txt.gz |
8.4 Kb |
(ftp)(http) |
TXT |
| GSE57876_NipB_S2_rep2.peaks.txt.gz |
103.9 Kb |
(ftp)(http) |
TXT |
| GSE57876_RpS12_BAC_S2.peaks.txt.gz |
5.1 Kb |
(ftp)(http) |
TXT |
| GSE57876_X16_BAC_S2.peaks.txt.gz |
4.5 Kb |
(ftp)(http) |
TXT |
| GSE57876_X16_S2_rep2.peaks.txt.gz |
77.1 Kb |
(ftp)(http) |
TXT |
| GSE57876_dCP_OSC_merged.peaks.txt.gz |
63.4 Kb |
(ftp)(http) |
TXT |
| GSE57876_dCP_S2_merged.peaks.txt.gz |
63.8 Kb |
(ftp)(http) |
TXT |
| GSE57876_eEF1delta_BAC_S2.peaks.txt.gz |
6.0 Kb |
(ftp)(http) |
TXT |
| GSE57876_eEF1delta_S2_rep1.peaks.txt.gz |
86.0 Kb |
(ftp)(http) |
TXT |
| GSE57876_eve_BAC_S2.peaks.txt.gz |
5.5 Kb |
(ftp)(http) |
TXT |
| GSE57876_evelong_BAC_S2.peaks.txt.gz |
5.0 Kb |
(ftp)(http) |
TXT |
| GSE57876_hkCP_OSC_merged.peaks.txt.gz |
83.0 Kb |
(ftp)(http) |
TXT |
| GSE57876_hkCP_S2_merged.peaks.txt.gz |
86.0 Kb |
(ftp)(http) |
TXT |
| GSE57876_hsp70_BAC_S2.peaks.txt.gz |
4.1 Kb |
(ftp)(http) |
TXT |
| GSE57876_pnr_BAC_S2.peaks.txt.gz |
3.6 Kb |
(ftp)(http) |
TXT |
| GSE57876_pnr_S2.peaks.txt.gz |
53.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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