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| Status |
Public on Aug 20, 2010 |
| Title |
High-throughput sequencing reveals a simple model of nucleosome energetics |
| Organisms |
Escherichia coli; Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a secondary role. Furthermore, similar sequence signatures are exhibited by control experiments in which genomic DNA is either sonicated or digested with micrococcal nuclease in the absence of nucleosomes, making it possible that current predictions based on highthroughput nucleosome positioning maps are biased by experimental artifacts.
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| Overall design |
Included are raw (eland) and mapped (wig) reads. The mapped reads are provided in eland and wiggle formats, and the raw reads are included in the eland file.
This series includes only Mnase control data. The sonicated control is part of this already published accession, as is a in vitro nucleosome map:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15188
We also studied data (in vitro and in vivo maps as well as a model) from
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13622
and from:
http://www.ncbi.nlm.nih.gov/sra/?term=SRA001023
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| Contributor(s) |
Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV |
| Citation(s) |
21084631 |
| |
| Submission date |
Aug 19, 2010 |
| Last update date |
Jun 11, 2013 |
| Contact name |
George Locke |
| E-mail(s) |
glocke@physics.rutgers.edu
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| Phone |
(732) 445-3156
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| Fax |
(732) 445-5958
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| URL |
http://nucleosome.rutgers.edu/
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| Organization name |
Rutgers University
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| Department |
Physics
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| Street address |
136 Frelinghuysen Rd
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| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
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| Platforms (1) |
| GPL10839 |
Illumina Genome Analyzer (Escherichia coli; Saccharomyces cerevisiae) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA130885 |
