Fig. 3
Characterization of ectopic TSSs. a Genome browser shot of RNA-Seq signal at the Ezh2 gene showing an isoform switch in NF-YA KD (red) vs. control (blue) ESCs. A representative selection of individual RNA-Seq reads is shown beneath. Red and blue rectangles highlight the ectopic and endogenous splice sites, respectively. b Consensus sequence motif enriched within the 10 -bp region centered on canonical TSSs (top) or ectopic TSSs (bottom) of genes with promoter-proximal NF-Y binding, derived from de novo motif search. c Left: average sequence conservation in mammals, as computed using PhyloP76, of the 2-kb region centered on canonical TSS of genes with promoter-proximal NF-Y binding (gray, n = 3056), those that bind NF-Y and exhibit TSS shift (black, n = 538), or those chosen at random (purple, n = 538). Right: box plot showing PhyloP conservation score for the 1-kb region upstream of canonical TSS. *P-value = 0.01372, **P-value = 1.69E-10, ***P-value = 3.77E-12 (Wilcoxon rank-sum test, two-sided). d Box plot showing the number of CCAAT motifs within 1-kb region upstream of canonical TSS for genes with promoter-proximal NF-Y binding that exhibit TSS shifts (black) or not (gray) in NF-YA KD ESCs. *P-value = 6.67E-36 (Wilcoxon rank-sum test, two-sided). e Average sequence conservation in mammals, as computed using PhyloP76, of the 2-kb region centered on ectopic TSS of genes with promoter-proximal NF-Y binding that exhibit an ectopic TSS (n = 538). f Average fold change (log2; primary y-axis) in Start-Seq signal (blue) in NF-YA KD vs. control KD ESCs near TSSs of NF-Y-bound genes exhibiting TSS shifts (red). Also shown is the average fold change (log2; secondary y-axis) in nucleosome occupancy (red) in NF-YA KD vs. control KD ESCs. NDR nucleosome-depleted region
