Figure 3: Replisome interactions differ between core and variable genes
A: Gene expression in quartiles separated by gene type. NET-seq reads in the first 500bp of each ORF for cells in YPD were used to rank all genes by expression (Churchman and Weissman, 2011); genes were then separated into 4 expression quartiles of 1,663 genes. Within the 3 higher quartiles, genes were separated into TFIID and CR regulated sets based on (Donczew et al., 2020), unassigned genes were discarded. n= (left to right) 1189, 366, 1414, 131, 1364, 96, 1664.  B: TrAEL-seq metaplots of cells growing on YPD for TFIID and CR genes in quartiles described in A, as well as the unstratified lowest quartile. In each case, TrAEL-seq reads representing forks moving head-on or co-directional to the direction of transcription are considered separately. Metaplots are calculated in 20 bp bins over the transcriptional start site (TSS) to transcriptional end site (TES), and for 10kb regions either side. Bins from multi-copy regions (mitochondrial DNA, ribosomal DNA, CUP1 ,ENA , telomeres and sub-telomeres, Ty elements and LTRs) were excluded. Data is an average of 4 wild-type datasets, shaded region shows standard deviation across datasets. C: Metaplot as in B but for 30kb either side of TSS/TES. D: Plot of the distance from TSS to nearest ARS for each gene separated by categories in B. Random distribution represents distance from 2000 random sites to nearest ARS. Whiskers indicate 10-90%. Analysis by one-way ANOVA, *** = p<0.0001, ns = not significant p>0.05.