|
| Status |
Public on Apr 19, 2021 |
| Title |
Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors [ATAC-seq] |
| Organism |
Gallus gallus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.
|
| |
|
| Overall design |
We used ATAC-seq to profile the open chromatin regions in early embryonic chick retinal tissue
|
| |
|
| Contributor(s) |
Lonfat N, Wang S, Lee C, Garcia M, Choi J, Park PJ, Cepko C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jun 03, 2020 |
| Last update date |
Apr 20, 2021 |
| Contact name |
CHANGHEE LEE |
| E-mail(s) |
chlee@genetics.med.harvard.edu
|
| Phone |
617-432-6534
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Clifford Tabin
|
| Street address |
77 AVENUE LOUIS PASTEUR
|
| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19787 |
Illumina NextSeq 500 (Gallus gallus) |
|
| Samples (5)
|
|
| This SubSeries is part of SuperSeries: |
| GSE151948 |
Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors |
|
| Relations |
| BioProject |
PRJNA637029 |
| SRA |
SRP265798 |
Less...
More...