 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 15, 2024 |
| Title |
A fine kinetic balance of interactions directs transcription factor hubs to genes [RNA-Seq] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding events. Despite their ubiquity, such microenvironments have been difficult to study in endogenous contexts due to technical limitations. Here, we overcome these limitations and investigate how hubs drive TF occupancy at their targets. Using a DNA binding perturbation to a hub-forming TF, Zelda, in Drosophila embryos, we find that hub properties, including the stability and frequencies of associations to targets, are key determinants of TF occupancy. Our data suggest that hub targeting is driven not just by specific DNA motif recognition, but also by a fine-tuned kinetic balance of interactions between TFs and their co-binding partners.
|
| |
|
| Overall design |
WT embryos were compared to embryos with the 5th Zinc Finger of Zelda deleted
|
| |
|
| Contributor(s) |
Mukherjee A, Fallacaro S, Ratchasanmuang P, Zinski J, Boka A, Shankta K, Mir M |
| Citation(s) |
38659757 |
| |
| Submission date |
Apr 15, 2024 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Mustafa Mir |
| E-mail(s) |
MIRM@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3501 Civic Center Boulevard, CTRB 9030
|
| City |
philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
|
| Samples (18)
|
| GSM8208540 |
WT,day2,rep4 |
| GSM8208541 |
WT,day2,rep5 |
| GSM8208542 |
WT,day2,rep6 |
| GSM8208543 |
Zf5,day2,rep1 |
| GSM8208544 |
Zf5,day2,rep2 |
| GSM8208545 |
Zf5,day2,rep3 |
| GSM8208546 |
Zf5,day2,rep4 |
| GSM8208547 |
Zf5,day2,rep5 |
| GSM8208548 |
Zf5,day2,rep6 |
| GSM8208549 |
Zf5,day1,rep1 |
| GSM8208550 |
Zf5,day1,rep2 |
| GSM8208551 |
Zf5,day1,rep3 |
| GSM8208552 |
WT,day1,rep1 |
| GSM8208553 |
WT,day1,rep2 |
| GSM8208554 |
WT,day1,rep3 |
|
| This SubSeries is part of SuperSeries: |
| GSE264096 |
A fine kinetic balance of interactions directs transcription factor hubs to genes |
|
| Relations |
| BioProject |
PRJNA1100525 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE263997_RAW.tar |
2.4 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...