S. pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from S. cerevisiae

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. 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.