Single Nucleosome Epi-Polymorphisms Figure 2. Abundance and genomic distribution of Single Nucleosome Epi-Polymorphisms. (A) The fraction of nucleosomes that were called SNEP at FDR = 0.0001 was computed in every 1Kb-segment along each chromosome. Density ranged from 0 (white) to 100% (red). Grey denotes regions where nucleosomes could not be aligned. (B) Enrichment of H3K14ac SNEPs upstream Ty insertions and rDNA repeats. The fraction of BYac SNEPs among all nucleosomes was counted in 10 kb intervals upstream the rDNA region (brown triangles). The 7 fold enrichment of BYac SNEPs in the first 10 kb was significant (grey area, Chi-square test P = 0.01). Upstream regions of all Ty insertions present in BY and absent from RM were analyzed similarly (black points), and their fractions of BYac SNEPs were averaged. The 1.3 fold enrichment in the 10 kb interval directly upstream the insertions was significant (grey area, Chi-square test P = 0.014). (C) Local correlation between H3K14ac SNEPs. Ten nucleosomes were interrogated upstream and downstream each SNEP (x-axis). For each one, cases where the nucleosome was a SNEP similar to the centered one (either BYac or RMac) were counted and divided by the total number of nucleosomes interrogated at that position (brown histogram). Control values were obtained from the same procedure applied after re-assigning SNEPs to random nucleosomes (grey histogram). (D) Density of H3K14 acetylation and SNEPs relative to gene position. Every gene was divided by segmenting the coding sequence in 10 bins (average bin size of 160 bp) and its upstream and downstream regions in 100 bp bins. For every gene and every bin, log(acBY/nucBY) was averaged across replicated experiments and across all probes matching intra-nucleosomal DNA to produce the top green profile. Similarly, averaged log(acRM/nucRM) values generated the top black profile. Here acBY and acRM refer to H3K14ac ChIP-CHIP experiments on BY and RM samples, respectively, while nucBY and nucRM refer to nucleosomal mapping experiments on BY and RM samples, respectively. Note that probes matching inter-nucleosome linkers do not contribute to the profiles, which are therefore corrected for nucleosome abundance. Bottom profiles were obtained by counting the fraction of BYac SNEPs (green) and RMac SNEPs (black) among all nucleosomes that overlapped at least partially the bin, and averaging these fractions across all genes. doi:10.1371/journal.pgen.1000913.g002 PLoS Genetics | www.plosgenetics.org 4 April 2010 | Volume 6 | Issue 4 | e1000913