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| Status |
Public on Jan 21, 2020 |
| Title |
Genome-wide maps of chromatin accessibility in response to Hh signaling in mouse embryonic forelimb buds |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: The response to Hedgehog signaling in the limb is driven by GLI bound enhancers and the majority of Hh targets in the developing limb bud are regulated solely by the activity of GLI-repressor. Currently, we do not have a comprehensive understanding of how GLI bound enhancers respond to Hedgehog signaling. The goal of this study is to identify how GLI bound enhancers are regulated by Hedgehog signaling and specifically by GLI-repressor.
Methods: ATAC-seq was done in embryonic day 10.5 posterior limb buds from control and Shh-null embryos to identify GLI enhancers that change chromatin accessibility in response to Hedgehog signaling.
Results: We found that Hedgehog signaling regulates the chromatin accessibility of a subset of GLI binding regions. This subset of GLI bound enhancers has reduced accessibility in the absence of Hedgehog signaling and largely overlaps with GLI enhancers that also have reduced H3K27ac in the absence of Hedgehog signaling.
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| Overall design |
ATAC-sequencing in Shh-/- and WT control posterior E10.5 forelimb buds. Two biological replicates were done for each ATAC experiment.
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| Contributor(s) |
Lex RK, Zhou W, Ji H, Vokes SA |
| Citation(s) |
31989924, 35145123 |
| |
| Submission date |
Dec 08, 2017 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Rachel Lex |
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Vokes
|
| Street address |
2500 Speedway
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78704 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE108880 |
GLI transcriptional repression regulates enhancer activity and chromatin accessibility for Hedgehog target genes |
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| Relations |
| BioProject |
PRJNA421774 |
| SRA |
SRP126433 |
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