Figure 5: Co-regulation of nucleosomal occupancy and transcription by Set1 and Jhd2 at candidate target genes.

(a–c) Changes to H3K4 methylation levels, nucleosomal occupancy and transcripts at SER3, CHA1 and PHO5 genes in jhd2Δ or set1Δ are shown. The normal nucleosomal, H3K4 methylation, Jhd2 and Set1 occupancies at target genes are also shown: reads for mononucleosomal DNA in WT shows native chromatin organization (brown). Reads for H3K4 monomethyl (me1, magenta), H3K4 dimethyl (me2, cyan) and H3K4 trimethyl (me3, green) marks in WT shows their distribution over candidate target genes. Enrichment values (qpois) for Jhd2 (black) and Set1 (pink) in WT show their occupancy at the indicated genes. Fold-change in the levels of H3K4me1, H3K4me2 and H3K4me3 marks in jhd2Δ or set1Δ relative to that in WT are shown. Fold-change in H3K4 methylation in set1Δ relative to WT was calculated using published datasets⁴². Increase or decrease in a given H3K4 methyl mark in the mutant is shown in red or blue, respectively. Mononucleosomal DNA from WT were subtracted from those obtained from jhd2Δ or set1Δ and visualized using a genome browser. Gain or loss in nucleosome occupancy in the mutant is represented in red or blue, respectively. RNA-seq reads showing transcript levels for the three target genes in WT, jhd2Δ or set1Δ strains are shown (orange). Teal arrow indicates SRG1, a gene coding for regulatory non-coding RNA involved in SER3 regulation³⁴. In c, schematic diagram at top shows the nucleosome organization at PHO5. Circles, well-positioned promoter nucleosomes; black arrow, TSS; and pink box, the Pho4 binding site, determined using published datasets^69,70. Grape coloured arrow and dotted line indicate decrease in nucleosomal occupancy at the Pho4 binding site. (d) The average mean profile for histone H3 turnover across 800 bp region upstream (−) or downstream (+) of the TSSs (0) at all 236 yeast ribosome biogenesis or Ribi genes in WT, set1Δ and jhd2Δ are shown.