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| Status |
Public on Dec 19, 2017 |
| Title |
Drosophila simulans embryonic development RAMPAGE time series |
| Organism |
Drosophila simulans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Multicellular development is largely determined by transcriptional regulatory programs that orchestrate the expression of thousands of protein-coding and noncoding genes. To decipher the genomic regulatory code that specifies these programs, and to investigate globally the developmental relevance of noncoding transcription, we profiled genome-wide promoter activity throughout embryonic development in 5 Drosophila species. We show that core promoters, generally not thought to play a significant regulatory role, in fact impart broad restrictions on the developmental timing of gene expression on a genome-wide scale. We propose a hierarchical model of transcriptional regulation during development in which core promoters define broad windows of opportunity for expression, by defining a limited range of transcription factors from which they are able to receive regulatory inputs. This two-tiered mechanism globally orchestrates developmental gene expression, including noncoding transcription on a scale that defies our current understanding of ontogenesis. Indeed, noncoding transcripts are far more prevalent than ever reported before, with ~4,000 long noncoding RNAs expressed during embryogenesis. Over 1,500 are functionally conserved throughout the melanogaster subgroup, and hundreds are under strong purifying selection. Overall, this work introduces a hierarchical model for the developmental regulation of transcription, and reveals the central role of noncoding transcription in animal development.
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| Overall design |
22 Samples of Drosophila simulans
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| Contributor(s) |
Batut PJ, Gingeras TR |
| Citation(s) |
29260710 |
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| Submission date |
Oct 28, 2016 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Philippe Batut |
| E-mail(s) |
[email protected]
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| Phone |
516-422-4122
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| Organization name |
CSHL
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| Lab |
Gingeras
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| Street address |
500 Sunnyside Blvd.
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| City |
Woodbury |
| State/province |
NY |
| ZIP/Postal code |
11797 |
| Country |
USA |
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| Platforms (1) |
| GPL13306 |
Illumina HiSeq 2000 (Drosophila simulans) |
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| Samples (22)
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| This SubSeries is part of SuperSeries: |
| GSE89335 |
Drosophila species embryonic development RAMPAGE time series |
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| Relations |
| BioProject |
PRJNA351832 |
| SRA |
SRP092332 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89302_Dsim_Gene_Expression.txt.gz |
757.3 Kb |
(ftp)(http) |
TXT |
| GSE89302_Dsim_Gene_Expression_Aligned.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE89302_Dsim_RAMPAGE_TSC.bed.gz |
328.2 Kb |
(ftp)(http) |
BED |
| GSE89302_Dsim_TSC_Expression.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE89302_RAW.tar |
23.6 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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