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| Status |
Public on Oct 18, 2016 |
| Title |
Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Transcriptional analysis of Drosophila CNS midline cells provides a useful system for studying transcriptional regulation at the genomic level due to a well-characterized set of midline-expressed genes and in vivo-validated enhancers. To investigate how access to regulatory information is controlled during midline cell development, we performed FAIRE-seq on FACS-purified midline cells. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak (“midline-enriched”) often correspond to midline enhancers near a midline-expressed gene and provides a useful predictive tool. Analysis of a large collection of midline enhancers revealed that those with a midline-enriched peak were located near midline-expressed genes, as were about half of the midline enhancers that overlapped a midline FAIRE peak that was not statistically "midline-enriched". There is a substantial fraction of midline enhancers that do not have a midline FAIRE peak and these tend to reside in chromatin regions that are not transcriptionally active and thus, unlikely to drive midline activity in vivo. This study emphasizes the utility of combining chromatin analysis of purified cell populations with gene expression and enhancer datasets to determine an experimentally useful chromatin profile that identifies biologically relevant enhancers and genes.
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| Overall design |
We performed two FAIRE-seq replicates on purified populations of midline cells from 6-8hr embryos, two FAIRE-seq replicates from 6-8hr whole embryos, and one genomic DNA input.
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| Contributor(s) |
Pearson JC, McKay DJ, Lieb JD, Crews ST |
| Citation(s) |
27802137 |
| |
| Submission date |
Jun 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel J McKay |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of North Carolina at Chapel Hill
|
| Department |
Biology, Genetics
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| Lab |
McKay Lab
|
| Street address |
3344 Genome Sciences Building
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7100 |
| Country |
USA |
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| Platforms (2) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA326060 |
| SRA |
SRP076698 |
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