Fig. 3

Characterization of yeast promoters. a Heat map of the nucleosome dyad distribution at yeast promoters. Each row represents a 2-kb window focused on the NDR centers of yeast genes, which are sorted according to the NDR width. b Zoomed-in view of a 500-bp region around the NDR center, including only the +1 and –1 nucleosomes of all yeast genes. The high resolution of the nucleosome positioning data allows the identification in the ensemble of cells of alternative rotational positions (parallel sigmoidal stripes corresponding to +1 and –1 nucleosomes), which differ by multiples of the helical twist. c NDRs are flanked by H2A.Z-containing nucleosomes (data from [61]). NDRs are generally bound by TATA-binding protein (d) (TBP, data from [62]), Reb1 (e) (data from [63]), remodelers RSC, Snf2, and ISW1 (f-h) (data from [64]). NDRs are accessible to DNase I (i) (data from [65]) and transposase Tn5 (j) (data from [66]). k In rsc8-depleted cells, nucleosomes +1 and –1 shift by a multiple of the helical twist, maintaining the same rotational setting. Heat maps showing the average G/C content of the preferred dyad locations. MNase-seq data from [58]