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| Status |
Public on Feb 01, 2020 |
| Title |
MNase-seq analysis in human breast cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Nucleosomes are the most basic units of chromatin and are regulators of genome integrity and gene expression. The fundamental mechanism how nucleosomes are dynamically regulated is one of the main questions in chromatin organization; most of the study has, however, focused on its positioning. Here we performed HiLo-MNase-seq, which involves limit and partial digestion of chromatin by micrococcal nuclease (MNase) to identify the positioning of nucleosome array along with the kinetics of MNase digestion. We identified a subset of unique nucleosomes with fast digestion kinetics at the transcription factor binding sites that have been characterized as nucleosome depleted regions (NDRs). By inhibiting RNA polymerase II, we also showed that those nucleosomes changed its sensitivity to MNase in a context-dependent manner. These findings implicated a self-reinforcing regulatory network involving nucleosomes, Pol II, and transcription factors for fine-tuning of gene expression.
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| |
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| Overall design |
MNase-seq experiment was performed in human breast cancer cells, MCF-7. Two biological replicates were prepared.
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| Contributor(s) |
Shimbo T, Sara GA, Wade PA |
| Citation missing |
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| Submission date |
Feb 03, 2016 |
| Last update date |
Feb 02, 2020 |
| Contact name |
Takashi Shimbo |
| E-mail(s) |
shimbot@niehs.nih.gov
|
| Organization name |
NIH/NIEHS
|
| Street address |
111 TW Alexander Dr.
|
| City |
RTP |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA310726 |
| SRA |
SRP069236 |
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