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.