Fig. 6

High rates of initiation disrupt the transcription factor landscape. A Nucleosome positioning heatmaps of the NDT80 locus, which has two Ume6 binding sites in the promoter region (vertical solid red lines). The vertical dashed red line marks the TSS and each row represents one timepoint, from G1 to 60 from top to bottom. Yellow corresponds to a high density of MNase-seq reads corresponding to nucleosome peaks, while blue corresponds to nucleosome depleted regions. B Average nucleosome profiles for the 89 URS1 locations identified in promoters of cluster 1 genes in G1 and at 25 min. The profiles are centered on the URS1 sequence (the Ume6 binding site - dotted line). C Sub-nucleosomal MNase-seq read coverage around the GAL1-10 promoter in G1. D Sub-nucleosomal MNase-seq reads of the NDT80 locus 5 min after release from G1 phase. Y-axis shows the sub-nucleosomal read coverage in this genomic region. Top track shows the location of genes. Peak annotated to the Ume6 binding site is highlighted. E Each sub-nucleosomal MNase-seq peak was assigned to a known TF binding site from [43]. For each TF, the ratio of peaks that change in the SSDDCS strain over total number of peaks for that TF (x-axis “TF binding changes”) was plotted against the ratio of the differential TF peaks that are in the promoters of genes that are DE or non-DE in the SSDDCS strain (y-axis “TF effect on gene expression”). The size of the points is proportional to the total number of sub-nucleosomal peaks identified for each TF. The dashed lines mark the ratios when considering all sub-nucleosomal peaks. F In wild type cells, nascent DNA is loaded with old and new nucleosomes (yellow) in competition with TFs (blue) as the replication fork progresses. Post-replicative chromatin matures via a variety of mechanisms. In the SSDDCS strain, which drives global early replication, lots of concurrent replication forks increase the rate of nascent DNA production, altering the balance of competition between nucleosomes and TFs, leading to aberrant chromatin organization and TF positioning. This increased S-phase rate provides a window of opportunity to change the pattern of gene expression in a single cell cycle