Salts

In vivo maps from yeast nucleosome DNAs were prepared from log-phase cells grown in rich medium (YPD, six independent replicates) as described previously5 , as well as from cells grown in YP media supplemented with 2% galactose (three replicates) or 2.8% ethanol (four replicates) instead of glucose. The resulting DNAs were subjected to Illumina sequencing-by-synthesis. For the in vitro map, histone octamer was purified from chicken erythrocytes, assembled on purified yeast genomic DNA by salt gradient dialysis13 , digested with micrococcal nuclease and subjected to Illumina sequencing (two independent replicates). The resulting in vitro map has a lower concentration of nucleosomes along the DNA than obtained in vivo. This technical limitation was necessitated by our finding that reconstitutions at the in vivo stoichiometry on long genomic DNA resulted in insoluble chromatin that was inaccessible to micrococcal nuclease. We mapped the resulting reads to the genome and removed reads that mapped to multiple genomic locations. We extended the nucleosome reads of each experiment to the average nucleosome length in that experiment (always between 140-170 bp). For each map, we then calculated the normalized nucleosome occupancy at every base pair as the log-ratio between the number of reads that cover that base pair and the average number of reads per base pair across the genome. We then set the genomic mean in each sample to zero by subtracting the genome-wide mean from every base pair. The independent replicates for each experiment type were in excellent agreement, so we averaged the replicates within each type. The resulting tracks are termed normalized nucleosome occupancy throughout the manuscript. The detailed formulation of our sequence-based model for nucleosome positioning is given in the Methods and is similar to that described in ref. 17 , except that it was learned using only the in vitro data. For our data, results and model, see http://genie.weizmann.ac.il/pubs/nucleosomes08/, and GEO accession number GSE13622.