Precise genome-wide mapping of single nucleosomes and linkers in vivo

We develop a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in budding yeast. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, histone H1 and H2A.Z in defining the chromatin landscape. A biophysical model that neglects DNA sequence is presented and shows that steric occlusion suffices to explain the salient features of nucleosome positioning. Our study indicates that steric occlusion, and not DNA sequence, is the most important determinant of genome-wide nucleosome positioning. Permeabilized S. cerevisiae cells with cysteine substituted for histone H3Q85C were labeled on cysteines with orthophenantroline complex, which chelates a copper ion. In an oxidizing environment the derivatized residue contacts a deoxyribose CIH and cleaves DNA, and the fragments that are released are purified and subjected to paired-end Illumina sequencing.