Figure 2.

Transient transcription shutdown when genes are replicated

(A) Quantification of Chr-RNA-seq levels over introns at the indicated time points, as fold change to G1/S. Genes are separated based on directionality as in Figure S1J.

(B) Nascent transcription levels in early S and early/mid-S compared to G1/S as in Figure 1D for genes replicated in early S; n = 3, data represent mean ± SEM.

(C) As in (A), with genes clustered by length.

(D) Average metagene profile of Chr-RNA-seq in G1/S and early S around the TSS −1 kb/+2 kb of genes replicated in early S.

(E) Fold change in Chr-RNA-seq levels for genes with reduced nascent transcription when replicated compared to the time point before, with levels during and after replication. The analysis includes 514 genes in early/mid-S, 144 genes in mid-S, 178 genes in mid-/late S, and all 716 genes in late S/G2; paired t test analysis.

(F) As in (D) but specifically over the genes highlighted in (E).

Box whiskers plots with line at the median, Mann-Whitney t test; ns, not significant; ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001.