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| Status |
Public on Jan 21, 2022 |
| Title |
GLI transcriptional repression is inert prior to HH pathway activation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: Most Hedgehog responsive gene expression is mediated through GLI de-repression. Additionally GLI -repression is proposed to play roles in limb pre-patterning before HH pathway activation. This study evaluates if GLI repression is established prior to HH pathway activation.
Methods: To determine if GLI-repression is established prior to pathway activation, we used genomic approaches to study GLI-mediated repression using the mouse developing limb as a model. We identified pre-HH (E9.25, 21-23S) and post-HH (E10.5, 32-25S) GLI3 binding regions using CUT&RUN for endogenous FLAG-tagged GLI3 proteins. Using a combination of ChIP-seq, CUT&RUN, CUT&Tag, ATAC-seq and RNA-seq, we tested whether loss of Gli3 prior to HH signaling was able to de-repress genes and enhancers, as it does after HH signaling.
Results: Prior to HH signaling, GLI3 binds to poised, accessible regions with histone deacetylase (HDAC) proteins, similar to post-HH signaling. Despite GLI3 binding to most regions as it does in the post-HH limb, loss of Gli3 is unable to prematurely active target genes or enhancers. Furthermore, we find that GLI3-dependent chromatin compaction does not occur until roughly 10 hours after HH signaling would have normally been induced. Collectively, these results support that GLI repressor proteins are inert prior to HH pathway activation.
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| Overall design |
ChIP-seq, CUT&RUN, CUT&Tag, ATAC-seq and RNA-seq on pre-HH (E9.25, 21-23S) and post-HH (E10.5, 32-25S) forelimb buds.
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| Contributor(s) |
Lex RK, Zhou W, Ji H, Vokes SA |
| Citation(s) |
35145123, 37805104 |
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| Submission date |
Jun 24, 2021 |
| Last update date |
Jan 24, 2025 |
| Contact name |
Steven A. Vokes |
| E-mail(s) |
svokes@austin.utexas.edu
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| Organization name |
University of Texas at Austin
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| Department |
Molecular Biosciences
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| Street address |
2500 Speedway, STOP A5000
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| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78757 |
| Country |
USA |
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| Platforms (4)
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| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (67)
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| Relations |
| BioProject |
PRJNA741224 |
| SRA |
SRP325496 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE178838_RAW.tar |
10.4 Gb |
(http)(custom) |
TAR (of BIGWIG, BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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