Figure 6: Set1 and Jhd2 co-regulate chromatin structure and nucleosomal turnover genome-wide during transcriptional regulation in yeast.
(a) Nucleosome occupancy ratios (Δnucleosome occupancy) between jhd2Δ and control WT across all yeast genes are shown as a heat map, where gain or loss in nucleosome occupancy are in red and blue, respectively. Genes in rows are organized into six k-means clusters. Columns represent 50 bp windows over ±800 bp regions relative to the TSS. Relative positions for −1, +1 and other coding regions nucleosome are indicated at the bottom. Windows overlapping neighbouring genes were excluded. (b) Heat map for Δnucleosome occupancy between set1Δ and WT across all yeast genes. Heat map details are as described for a. (c) Native nucleosome occupancy for genes in the six k-means clusters generated from reads obtained in WT are shown. Nucleosome occupancy above global mean is in brown. (d,e) Heat maps for Set1 and Jhd2 occupancy within the six clusters are shown. (f) Heat map for Rpb3 occupancy within the six k-means clusters, using published data51, is shown. Pol2 subunit occupancy above global mean is in green (Supplementary Fig. 14b). (g) The average mean profile for histone H3 turnover across 800 bp region upstream (−) or downstream (+) of the TSSs (0) at all yeast genes in WT, set1Δ and jhd2Δ are shown.
