Figure 1

A consensus of consensus nucleosome calls defines the nucleosome reference map. (a) Screen shot of six consensus nucleosome calls (vertical bars) in which each is a consensus of positions from six datasets (five datasets for positions 1 and 4). Shown is chromosome 11 (loci 90200 to 91200). Narrower peaks have a stronger consensus. The trace indicates the probability landscape for a reference nucleosome. (b) Bar graph of the number of datasets contributing to the set of reference nucleosome positions (including hypothetical positions). (c) Illustration of the types of nucleosomes in the yeast genome, and their specifications. (d) Bar graph indicating nucleosome occupancy level throughout the genome at quartile intervals. (e) Browser screen shot of consensus nucleosome positions from 128000 to 130600 at chromosome 1. Any location can be queried online [21]. The top track, indicated as 'RNA', provides coordinates of different types of RNA transcripts as color-coded by the legend immediately under it. The 'Reference' track provides the location and the positional number of the reference nucleosome calls. The darkness of the box indicates the mode-normalized nucleosomal occupancy: light gray, < 5% (that is, in NFRs); intermediate gray, 5 to 50% (that is, in nucleosome-depleted regions); dark gray, 50 to 100%; black, 100%. The remaining six sets of tracks represent the individual consensus calls from datasets 1 to 6 (see Materials and methods). Within each set, additional nucleosome subsets are shown (for example, H2A.Z nucleosomes, nucleosomes from heat-shocked cells, and nucleosomes from an isw2 deletion strain). One nucleosome may have multiple names (for example, '+1,-1') when it is associated with more than one gene (exemplified in red boxes). Asterisks indicate this nucleosome is the terminal one to its associated gene (that is, the last one at the 3' end of the gene). (f) Smoothed frequency distribution of all linker lengths and only those found at the 5' end of genes.