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Status |
Public on Dec 19, 2017 |
Title |
Drosophila erecta embryonic development RAMPAGE time series |
Organism |
Drosophila erecta |
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 |
23 Samples of Drosophila erecta
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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) |
batut@cshl.edu
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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) |
GPL19321 |
Illumina HiSeq 2000 (Drosophila erecta) |
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Samples (23)
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This SubSeries is part of SuperSeries: |
GSE89335 |
Drosophila species embryonic development RAMPAGE time series |
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Relations |
BioProject |
PRJNA351835 |
SRA |
SRP092333 |
Supplementary file |
Size |
Download |
File type/resource |
GSE89304_Dere_Gene_Expression.txt.gz |
845.4 Kb |
(ftp)(http) |
TXT |
GSE89304_Dere_Gene_Expression_Aligned.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
GSE89304_Dere_RAMPAGE_TSC.bed.gz |
305.4 Kb |
(ftp)(http) |
BED |
GSE89304_Dere_TSC_Expression.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
GSE89304_RAW.tar |
25.4 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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