|
| Status |
Public on Oct 21, 2012 |
| Title |
Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription factors to sites with either low (e.g. Myc, Klf4, Zfx) or high (e.g. Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome depleted regions around transcription start and termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to their CpG-content or histone methylation marks. Throughout the genome nucleosome occupancy was dependent on the presence of certain histone methylation or acetylation modifications. In addition, the average nucleosome-repeat length increased during differentiation by 5-7 base pairs, with local variations for specific genomic regions. Our results reveal regulatory mechanisms of cell differentiation acting through nucleosome repositioning.
|
| |
|
| Overall design |
We have determined genome-wide nucleosome position maps in mouse embryonic stem cells (ESCs), neural progenitor cells (NPCs) derived from these ESCs by retinoic acid induced differentiation as well as mouse embryonic fibroblasts (MEFs) from the corresponding mouse strain
|
| |
|
| Contributor(s) |
Teif VB, Rippe K |
| Citation(s) |
23085715 |
| Submission date |
Sep 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Vladimir B Teif |
| E-mail(s) |
vteif@essex.ac.uk
|
| Organization name |
University of Essex
|
| Department |
School of Life Sciences
|
| Street address |
Wivenhoe Park
|
| City |
Colchester |
| ZIP/Postal code |
CO4 3SQ |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (3) |
|
| This SubSeries is part of SuperSeries: |
| GSE40896 |
Genome-wide nucleosome positioning during embryonic stem cell development |
|
| Relations |
| SRA |
SRP015795 |
| BioProject |
PRJNA175501 |
