|
| Status |
Public on Oct 15, 2018 |
| Title |
Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. Furthermore, through integration with RNA-seq data, we characterized genes that are altered both at epigenomic and transcriptomic levels in OA. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for MSC-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation. In conclusion, we demonstrate how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential.
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| |
|
| Overall design |
ATAC-seq libraries are genreated from oLT and iMT region cartilage of 8 OA patients
|
| |
|
| Contributor(s) |
Liu Y, Chang J |
| Citation(s) |
30341348 |
| |
| Submission date |
Dec 19, 2017 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Aki Minoda |
| E-mail(s) |
akiko.minoda@riken.jp
|
| Phone |
08021534126
|
| Organization name |
RIKEN YOKOHAMA
|
| Department |
IMS
|
| Lab |
DGT
|
| Street address |
230-0045, 1 CHOME-7-22 SUEHIROCHO
|
| City |
TSURUMI WARD YOKOHAMA |
| State/province |
KANAGAWA |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (16)
|
|
| Relations |
| BioProject |
PRJNA423060 |
| SRA |
SRP127173 |
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