MNase-seq.

MNase-seq experiments were carried out as previously described (25). In brief, isolated nuclei were digested with MNase to mononucleosomes. Paired-end sequencing libraries were prepared (Illumina). Paired reads (50 nucleotides [nt]) were mapped to the reference genome (SacCer2) using Bowtie-2 (133,–135). For analysis of nucleosome occupancy (coverage) at tDNAs, both across the genome and on chromosome III, tDNAs were aligned on their start sites or at the deletion points. Data sets were normalized to their genomic average (i.e., 1) using only DNA fragments in the 120- to 180-bp range. In one experiment, mononucleosomal DNA was gel purified, but not in the replicate, in which short fragments (<120 bp) derived from digestion of the TFIIIB-TFIIIC complex at tDNAs (97) were observed.