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| Status |
Public on Oct 31, 2018 |
| Title |
Genome-wide chromatin accessibility and transcriptome profiling shows that minimal epigenome changes lead to coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice (RNA-seq) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Danforth’s short tail (Sd) mice provide an excellent model for investigating the underlying etiology of human caudal birth defects, which affect 1 in 10,000 live births. Sd animals exhibit aberrant axial skeleton, urogenital, and gastrointestinal development similar to human caudal syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. Previous studies have shown that the Sd mutation results from an endogenous retroviral (ERV) insertion upstream of the Ptf1a gene causing its ectopic expression at E9. Though the genetic lesion has been determined, the resulting epigenomic and transcriptomic changes driving the phenotype have not been investigated. Here, we performed ATAC-seq experiments on isolated E9.5 tailbud tissue revealing localized changes in chromatin accessibility in Sd/Sd mutant embryos. Interestingly, chromatin changes were localized to a small genomic sequence overlapping a Ptf1a enhancer region, which is conserved in both mouse and humans. Furthermore, mRNA-Seq experiments revealed increased transcription of Ptf1a target genes and, importantly, the downregulation of the hedgehog pathway genes. Reduced Sonic hedgehog signaling (Shh) was confirmed by both in-situ hybridization and immunofluorescence experiments indicating that the Sd mutation may result, in part, from downregulated Shh signaling. Taken together these data indicate that human caudal dysgenesis disorders may result from dysregulation of hedgehog signaling pathways. Thus it will be important to investigate how epigenome and transcriptome alterations result in hedgehog pathway disruption.
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| Overall design |
RNA-seq was performed on DNA isolated from the tailbuds of E9.5 WT and homozygous Danforth mutant mice (n = 3 per group). Tailbuds from 2 mice were pooled when necessary to ensure sufficient input material.
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| Contributor(s) |
Orchard P, White JS, Thomas PE, Mychalowych A, Kiseleva A, Hensley J, Allen B, Parker SC, Keegan CE |
| Citation(s) |
30380057 |
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| Submission date |
Jan 05, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Stephen C.J. Parker |
| Organization name |
University of Michigan
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| Street address |
100 Washtenaw Avenue
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE108804 |
Genome-wide chromatin accessibility and transcriptome profiling shows that minimal epigenome changes lead to coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice |
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| Relations |
| BioProject |
PRJNA428787 |
| SRA |
SRP128168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108803_RAW.tar |
186.9 Mb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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