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Series GSE16040 Query DataSets for GSE16040
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
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.
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.
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
Organization name LMU Munich
Department Biomedical Center, Bioinformatics
Street address Großhadener Str. 9
City Martinsried
ZIP/Postal code 82152
Country Germany
Platforms (2)
GPL2529 [Yeast_2] Affymetrix Yeast Genome 2.0 Array
GPL7715 [Sp20b_M] Affymetrix S. pombe Tiling 1.0FR Array
Samples (16)
GSM401392 nucleosomes_WT_1
GSM401393 nucleosomes_WT_2
GSM401394 nucleosomes_WT_3
BioProject PRJNA115405

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16040_RAW.tar 706.8 Mb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file
Processed data included within Sample table

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