GSE132225
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
Here, we established for S. cerevisiae two orthogonal and thereby crossvalidating approaches to measure absolute nucleosome occupancy across the genome via restriction enzymes and DNA methyltransferases. We call this methods ORE (Occupancy by Restriction Enzymes)- and ODM-seq (Occupancy by DNA Methytransferases) with an average standard deviation between replicates per site of 7%. The combined high-resolution (9 bp) map shows strikingly uniform absolute occupancies. Most nucleosome positions are occupied most of the time, i.e., 96% of all nucleosomes called by chemical mapping have a mean absolute occupancy of 90 ± 6% (± SD). Depending on nucleosome calling procedures there are 56-59,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with high transcription, but with increased presence of the nucleosome evicting RSC chromatin remodeling complex and are enriched in regulatory regions upstream of gene starts. Our work finally provides a quantitative reference frame in absolute terms for future chromatin studies. Overall design: We performed ORE-seq with three different restriction enzymes (AluI, HindIII, BamHI) and and ODM-seq with two DNA methyltransferases (CpG and GpC) with different biological replicates (WT1-WT4).