Figure 3.
TSSs of transcribed genes remain under-replicated throughout S phase
(A) Average metagene profile of BrdU-seq levels normalized to input DNA in early S at TSSs ±2.5 kb for all genes, transcribed genes, or not transcribed genes.
(B) As for (A) for genes replicated in early S according to Figure S1D, separated in four groups by gene length or transcription levels.
(C) As for (A) for transcribed and not transcribed genes in all five fractions of the Repli-seq.
(D) As for (A) for genes >100 kb replicated in early S in all time points.
(E) BrdU incorporation at TSSs and in the gene body for the indicated genes in all time points. Schematic of gene structure with gene length, exons as orange boxes, and introns as red lines; primer positions are specified by the red boxes above; nascent transcription levels at TSSs and gene body are shown as fold change compared to G1/S for SMURF1 first time points shown in Figure 2B; n = 3, data represent mean ± SEM, Student’s t test.
(F) Relative enrichment of BrdU-seq levels of all time points compared to the levels in early S for genes >100 kb replicated in early S.
(G) As for (B), with genes separated based on their P3R2 levels as from Figure S3F. ∗p < 0.05; ∗∗p < 0.01.