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| Status |
Public on Nov 12, 2013 |
| Title |
Chemical map of S. pombe reveals species-specific features in nucleosome positioning |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Other
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| Summary |
Knowing the exact positions of nucleosomes not only advances our understanding of their role in gene regulation, but also the mechanisms that underlie between-species variation in chromatin structure. We have generated a chemical map of nucleosomes in vivo in Schizosaccharomyces pombe at base pair resolution. This new map reveals that S.pombe genome shares a similar periodic linker length distribution with Saccharomyces cerevisiae, but with major distinctions in nucleosomal/linker DNA sequence features. In S.pombe, A/T rich sequences are enriched in the nucleosome core region, particularly +/-20 bp of dyad, while they are disfavored in S.cerevisiae nucleosomes. The poly (dA-dT) tracts only slightly affect the nucleosome occupancy in S.pombe; and they possess preferential rotational positions within the nucleosome core with significant enrichment in the 10-30 bp region from the dyad for longer tracts. S.pombe does not have well-defined nucleosome free region immediately upstream of most transcription start sites (TSS), instead the -1 nucleosome is positioned with regular distance to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. The nucleosomes around TSS show more pronounced bidirectional phasing when the intergenic distance is relatively short, and the downstream nucleosome positioning is strongly correlated with DNA sequence features. We discovered that heterochromatin regions tend to have sparse nucleosome positioning, mixed with both well-positioned and fuzzy nucleosomes. The S.pombe map suggests that some of nucleosome positioning codes, formerly thought to be intrinsic, may largely depend on species-specific extrinsic factors including linker histone, chromatin remodelers and other DNA-binding proteins.
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| Overall design |
2 samples were analyzed with high throughput paired-end parallel sequencing. Both samples were created using the same chemical mapping protocol
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| Contributor(s) |
Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Widom J, Uhlenbeck OC, Holmgren RA, Widom J, Wang J |
| Citation(s) |
24277842 |
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| Submission date |
May 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ji-Ping Wang |
| E-mail(s) |
jzwang@northwestern.edu
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| Organization name |
Northwestern University
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| Street address |
2006 Sheridan Road
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| City |
Evanston |
| ZIP/Postal code |
60208 |
| Country |
USA |
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| Platforms (2) |
| GPL17165 |
AB SOLiD 4 System (Schizosaccharomyces pombe) |
| GPL17205 |
AB SOLiD 5500 (Schizosaccharomyces pombe) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA205487 |
| SRA |
SRP023196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46975_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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