Figure 4: Set1 and Jhd2 co-regulate nucleosomal occupancy and histone turnover at their shared target genes.

(a,b) Heat maps for nucleosome occupancy ratios (Δnucleosome occupancy) between jhd2Δ and WT or between set1Δ and WT at genes either co-repressed (a) or co-activated (b) by Set1 and Jhd2. Red, gain in nucleosome occupancy; blue, loss in nucleosome occupancy. Genes in rows are organized into six groups using k-means clustering. Columns represent 50 bp windows over ±800 bp regions relative to the TSS (0). Windows overlapping neighbouring genes were excluded. Total reads for mononucleosomal DNA in WT show the native state of nucleosome occupancy (leftmost panel). Asterisk, NDR; black arrow, the well-positioned +1 nucleosome. (c) Western blots showing RITE. WT, set1Δ and jhd2Δ strains expressing histone H3 tagged with V5-LoxP-HygMX-LoxP-2Flag cassette were grown overnight in YPD medium and then grown to saturation followed by addition of β-estradiol to induce tag switch. Saturated cultures were re-inoculated into fresh medium to release cells into the cell cycle in the presence of β-estradiol. Cells were arrested in G1 using α-factor. Cells before addition of β-estradiol (pre) and β-estradiol-treated G1 cells (post) were collected for whole-cell lysate preparation and detection of old (V5) and new (Flag) histone H3. The levels of H3K4me1, H3K4me2, H3K4me3 and total histone H3 in the indicated strains are shown. 2Flag, two copies of Flag tag; asterisk, truncated H3. See Supplementary Fig. 22 for full-length image of blots. (d) The average mean profile for histone H3 turnover across 800 bp region upstream (−) or downstream (+) of the TSSs (0) at all yeast genes. (e,f) Mean profiles for histone H3 turnover across regions (as described for d) at genes co-repressed (e) or co-activated (f) by Set1 and Jhd2 in WT, set1Δ and jhd2Δ strains.