|
| Status |
Public on May 16, 2016 |
| Title |
Nucleosome positioning changes during human embryonic stem cell differentiation. |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Nucleosomes are the basic unit of chromatin. Nucleosome positioning (NP) plays a key role in transcriptional regulation and other biological processes. To better understand NP we used MNase-seq to investigate changes that occur as human embryonic stem cells (hESCs) transition to nascent mesoderm and then to smooth muscle cells (SMCs). Compared to differentiated cell derivatives, nucleosome occupancy at promoters and other notable genic sites, such as exon/intron junctions and adjacent regions, in hESCs shows a stronger correlation with transcript abundance and is less influenced by sequence content. Upon hESC differentiation, genes being silenced, but not genes being activated, display a substantial change in nucleosome occupancy at their promoters. Genome-wide, we detected a shift of NP to regions of higher G+C content as hESCs differentiate to SMCs. Notably, genomic regions with higher nucleosome occupancy harbor twice as many G↔C changes but fewer than half A↔T changes, compared to regions with lower nucleosome occupancy. Finally, our analysis indicates that the hESC genome is not rearranged and has a sequence mutation rate resembling normal human genomes. Our study reveals another unique feature of hESC chromatin, and sheds light on the relationship between nucleosome occupancy and sequence G+C content.
|
| |
|
| Overall design |
We determined genome-wide nucleosome positioning in hESCs (WA09) and two derivatives (WA09-INM and WA09-SMC) from these WA09-hESCs.
|
| |
|
| Contributor(s) |
Zhang W, Li Y, Kulik M, Tiedemann R, Robertson K, Dalton S, Zhao S |
| Citation(s) |
27088311 |
| BioProject |
PRJNA196743 |
| Submission date |
Apr 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
wenjuan zhang |
| E-mail(s) |
wenjuan@uga.edu
|
| Organization name |
University of Georgia
|
| Lab |
Shaying Zhao's Lab
|
| Street address |
120 Green street, Life Science Building, Room B304B
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
|
| Samples (4)
|
|
| This SubSeries is part of SuperSeries: |
| GSE46467 |
Nucleosome positioning changes during human embryonic stem cell differentiation |
|
| Relations |
| SRA |
SRP021182 |
Less...
More...