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| Status |
Public on Feb 01, 2010 |
| Title |
S. pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from S. cerevisiae |
| Platform organisms |
Schizosaccharomyces pombe; Saccharomyces cerevisiae |
| Sample organism |
Schizosaccharomyces pombe |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
Expression profiling by array
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| Summary |
Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome-wide. Using this resource we found surprising differences compared to the nucleosome organization in the distantly related yeast Saccharomyces cerevisiae [the cerevisiae data has been published by others (PMID: 17873876) and the raw data is deposited at ArrayExpress(E-MEXP-1172)]. DNA sequence guides nucleosome positioning differently, e.g., poly(dA:dT) elements are not enriched in S. pombe nucleosome-depleted regions (NDRs). Regular nucleosomal arrays emanate more asymmetrically, i.e., mainly co-directionally with transcription, from promoter NDRs, but promoters harbouring the histone variant H2A.Z show regular arrays also upstream. Regular nucleosome phasing in S. pombe has a very short repeat length of 154 base pairs, and requires a remodeler, Mit1, conserved in humans but not found in S. cerevisiae. Nucleosome positioning mechanisms are evidently not universal but evolutionarily plastic.
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| Overall design |
For GSM401392-400: Nucleosomal DNA vs. Genomic Input DNA in wildtype, Mit1 mutant and Fft3 mutant S. pombe.
For GSM468642-6: Wildtype and Mit1 mutant S. pombe total RNA. 3 biological replicates for wildtype and 2 for mutant have been collected.
For GSM468647-8: Nucleosomal DNA vs. Genomic Input DNA in wildtype, Mit1 mutant, Fft3 and Tup11/12 mutant S. pombe.
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| Contributor(s) |
Lantermann A, Straub T, Strålfors A, Yuan GC, Ekwall K, Korber P |
| Citation(s) |
20118936 |
| |
| Submission date |
May 11, 2009 |
| Last update date |
Feb 21, 2017 |
| Contact name |
Tobias Straub |
| E-mail(s) |
tstraub@med.uni-muenchen.de
|
| Organization name |
LMU Munich
|
| Department |
Biomedical Center, Bioinformatics
|
| Street address |
Großhadener Str. 9
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platforms (2) |
| GPL2529 |
[Yeast_2] Affymetrix Yeast Genome 2.0 Array |
| GPL7715 |
[Sp20b_M] Affymetrix S. pombe Tiling 1.0FR Array |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA115405 |
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