Fig. 6: Loss of EAF3 leads to nucleosome changes.

a Venn diagrams showing overlaps of the indicated nucleosome sets. The sets of nucleosome changes, including changed shifts or occupancy, were calculated with that of the Δeaf3 strain versus that of WT. b Integrated analysis of RNA-seq, ChIP-seq, and MNase-seq showing the overlap of the indicated gene sets. For example, “14.7%, 773/703, P < 1.687e-04” indicates that transcription of 14.7% (773/5258) genes with forward shifted nucleosomes was up-regulated in the ∆eaf3 strain, which showed statistically significant overlaps (773/703, Observed/Expected) between two gene sets. For a and b, P-values were calculated by two-sided Fisher’s exact test. c Box plots and violin plots showing average transcriptions of the genes with down or up-regulated nucleosome occupancy in the WT and ∆eaf3 strains. d Box plots and violin plots comparing average transcriptions of genes with down-regulated nucleosome occupancy with or not Eaf3 occupancy in the WT and ∆eaf3 strains. For box-plot, the horizontal lines from top to bottom represent the maximum, first quartile, median, third quartile, and minimum of the total data, respectively. e IGV showing MNase-seq and RNA-seq of representative genes with one biological replicate in the indicated strains. Similar results were gained in other replicates. f MNase-qPCR assay was performed to verify the results of MNase-seq. Values are means ± SD from three technical replicates. For c and d, statistical significance was assessed using a two-tailed Student’s test (* P < 0.05; ** P < 0.01). The exact P-values and western blots are shown in the Source Data.