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| Status |
Public on Sep 17, 2015 |
| Title |
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility to MNase in D. melanogaster [RNA-seq] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Nucleosome structure and positioning play pivotal roles in gene regulation, DNA repair and other essential processes in eukaryotic cells. Nucleosomal DNA is thought to be uniformly inaccessible to DNA binding and processing factors, such as MNase. Here, we show, however, that nucleosome accessibility and sensitivity to MNase varies. Digestion of Drosophila chromatin with two distinct concentrations of MNase revealed two types of nucleosomes: sensitive and resistant. MNase-resistant nucleosome arrays are less accessible to low concentrations of MNase, whereas MNase-sensitive arrays are degraded by high concentrations. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C containing dinucleotides. In contrast, MNase-sensitive nucleosomes form on A/T rich sequences represented by transcription start and termination sites, enhancers and DNase hypersensitive sites. Lowering of cell growth temperature to ~10°C stabilizes MNase-sensitive nucleosomes suggesting that variations in sensitivity to MNase are related to either thermal fluctuations in chromatin fiber or the activity of enzymatic machinery. In the vicinity of active genes and DNase hypersensitive sites nucleosomes are organized into synchronous, periodic arrays. These patterns are likely to be caused by “phasing” nucleosomes off a potential barrier formed by DNA-bound factors and we provide an extensive biophysical framework to explain this effect.
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| Overall design |
RNA-seq S2 cells Drosophila melanogaster
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| |
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| Contributor(s) |
Chereji RV, Moshkin YM, Guryev V, Morozov AV |
| Citation(s) |
26429969 |
| Submission date |
May 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
|
| Phone |
301-435-8670
|
| Organization name |
National Institutes of Health
|
| Department |
NICHD
|
| Lab |
David J. Clark Lab
|
| Street address |
6 Center Drive, Room 2A14
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
|
| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE69336 |
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster |
|
| Relations |
| BioProject |
PRJNA285244 |
| SRA |
SRP058819 |
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