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| Status |
Public on Oct 02, 2018 |
| Title |
ATAC-seq and RNA-seq from mouse mandible during distraction osteogenesis |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
During development and tissue regeneration, changes in chromatin structure driven by master transcription factors lead to stimulus-responsive transcriptional programs. A thorough understanding of how stem cells in the skeleton interpret mechanical stimuli and enact regeneration will also shed light on how mechanical forces are transduced in other embryonic and regenerative processes. Here we employ a rigorous mandibular distraction model in mice that is genetically dissectable, allowing for detailed examination of the fundamental principles regulating de novo bone formation. Using lineage tracing, we show that regions of new bone are clonally derived, indicating a stem/progenitor cell origin in regeneration. We go on to profile the distraction-specific response of skeletal stem cells (d-SSC) within the facial skeleton and track their downstream progenitors, revealing that this lineage gives rise to the regenerate. Using the assay for transposase accessible chromatin (ATAC-seq), we show that these stem cell populations have a distinct pattern of chromatin accessibility during distraction, including within the FAK pathway. Inhibiting the FAK pathway blocks bone formation and reverts the chromatin accessibility profile back to that of a fractured bone with suboptimal healing. Mechanotransduction and FAK-responsiveness in skeletal stem cells activates regulatory elements and retrotransposons normally active only in primitive neural crest cells; this reversion of chromatin state may allow robust developmental tissue growth that facilitates regeneration.
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| Overall design |
ATAC-seq was performed on skeletal stem and progenitor cells from the mouse mandible during bone regeneration in the context of bone lengthening (distraction osteogenesis) or fracture and compared to these cell types in an uninjured, homeostatic state. RNA-seq was performed in distracted and fractured SSCs, pre-bone cartilage and stromal progenitors (BCSPs), and osteogenic progenitors (OPs) during a timecourse from POD5 to POD15.
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| Contributor(s) |
Carter AC, Ransom RC, Chang HY, Longaker MT |
| Citation(s) |
30356216 |
| |
| Submission date |
Oct 02, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Howard Chang |
| E-mail(s) |
howchang@stanford.edu
|
| Phone |
650-725-7022
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Y. Chang
|
| Street address |
CCSR 2130, 269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (51)
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| Relations |
| BioProject |
PRJNA412798 |
| SRA |
SRP119221 |
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