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| Status |
Public on Jun 23, 2023 |
| Title |
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ATAC-seq INTACT] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
While enhancers are often regulated at the level of accessibility by pioneer factors, promoters tend to be constitutively accessible and poised for activation by paused Pol II — thus are often not considered as sites of developmental regulation. Here we show that the accessibility of promoters and the acquisition of paused Pol II can also be subject to developmental regulation by pioneer factors. We show that Lola-I, a Drosophila zinc finger transcription factor, is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene expression. Lola-I mediates this function by binding to the edges of the promoter nucleosomes, which leads to their depletion, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers, providing further evidence that promoters and enhancers display unexpectedly similar characteristics.
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| |
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| Overall design |
scRNA-seq, RNA-seq, ChIP-seq, ATAC-seq or MNase-seq was performed in Drosphila embryos.
|
| Web link |
https://www.nature.com/articles/s41467-023-41408-1
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| |
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| Contributor(s) |
Ramalingam V, Zeitlinger J |
| Citation(s) |
37735176 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| DP2 OD004561 |
Investigating Developmental Potential Based on Genome-wide Chromatin Status |
STOWERS INSTITUTE FOR MEDICAL RESEARCH |
Julia Zeitlinger |
|
| |
| Submission date |
Apr 15, 2022 |
| Last update date |
Sep 22, 2023 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
|
| Samples (16)
|
| GSM6045681 |
ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep1 |
| GSM6045682 |
ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep2 |
| GSM6045683 |
ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep3 |
| GSM6045684 |
ATAC-seq in wildtype INTACT Epidermis 14-17hrs embryo Rep1 |
| GSM6045685 |
ATAC-seq in wildtype INTACT Epidermis 14-17hrs embryo Rep2 |
| GSM6045686 |
ATAC-seq in wildtype INTACT Muscle 14-17hrs embryo Rep1 |
| GSM6045687 |
ATAC-seq in wildtype INTACT Muscle 14-17hrs embryo Rep2 |
| GSM6045688 |
ATAC-seq in wildtype INTACT Neuron 14-17hrs embryo Rep1 |
| GSM6045689 |
ATAC-seq in wildtype INTACT Neuron 14-17hrs embryo Rep2 |
| GSM6045690 |
ATAC-seq in wildtype INTACT Trachea 14-17hrs embryo Rep1 |
| GSM6045691 |
ATAC-seq in wildtype INTACT Trachea 14-17hrs embryo Rep2 |
| GSM6045692 |
ATAC-seq in wildtype INTACT Trachea 14-17hrs embryo Rep3 |
| GSM6045693 |
ATAC-seq in Lola-I mutant ORC4 Gut 14-17hrs embryo Rep1 |
| GSM6045694 |
ATAC-seq in Lola-I mutant ORC4 Gut 14-17hrs embryo Rep2 |
| GSM6045695 |
ATAC-seq in Lola-I mutant ORC4 Trachea 14-17hrs embryo Rep1 |
| GSM6045696 |
ATAC-seq in Lola-I mutant ORC4 Trachea 14-17hrs embryo Rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE200875 |
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development |
|
| Relations |
| BioProject |
PRJNA827114 |
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