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| Status |
Public on Jul 01, 2015 |
| Title |
Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of chromatin organization and transcriptional activity to determine Sox9’s direct regulatory actions in normal developing chondrocytes. Sox9-associated regions resolve into two distinct regulatory categories. Class I regions closely associate with transcriptional start sites (TSSs). Their targets reflect general regulators of basal cell activities that Sox9 engages indirectly though a likely association with the basal transcriptional complex. In contrast, Class II regions outside of the local TSS domains highlight evolutionarily conserved, active enhancers directing expression of chondrocyte specific target genes, though DNA binding of Sox9-dimers at target sites with sub-optimal binding affinity. The level of associated chondrocyte gene expression correlates with the number of enhancer modules around the target gene and grouping into super-enhancer clusters. Comparison of Sox9 programs between neural crest and mesoderm-derived chondrocytes points to similar modes of chondrocyte specification in distinct chondrocyte lineages. These data provide the first insight into mammalian Sox family actions at the genome scale in the vivo setting. The resulting enhancer sets provide a key resource for further dissection of the regulatory programs of mammalian chondrogenesis.
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| Overall design |
Incorportation of ChIP-seq data of Sox9 and histone modification marks for chromatin status together with micorarray gene expression profiling in neonatal mice chondrocytes to uncover Sox9 regulatory system. Overexpression of Sox9 with a control of EGFP in human fibroblasts to identify the direct targets of Sox9 regulatory system
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| |
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| Contributor(s) |
He X, Ohba S, Hojo H, McMahon AP |
| Citation(s) |
26146088 |
| |
| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinjun He |
| E-mail(s) |
xinjun.he@med.usc.edu
|
| Phone |
323-442-8077
|
| Organization name |
University of Southern California
|
| Department |
BROAD CIRM Center
|
| Street address |
1425 San Pablo St
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (13)
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| This SubSeries is part of SuperSeries: |
| GSE69111 |
Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte |
|
| Relations |
| BioProject |
PRJNA284581 |
| SRA |
SRP058566 |
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