Fig. 2

SPT16 is enriched at sites occupied by master regulators of pluripotency. A SPT16-V5 CUT&RUN data visualized over transcription start sites and sorted by nascent transcription in control samples (TT-seq data; see Fig. 3). Averaged replicates are shown as heatmaps ± 2 kb from the TSS (n = 3 for untagged, n = 2 for each V5-tagged clone). No 1º refers to negative control experiments where no primary antibody is added, but pA/G-MNase is still added to assess background cutting. B IGV genome browser track for CUT&RUN data at the Nanog (top) and Sox2 (bottom) loci. Averaged replicates are shown as a single track (n = 3 for untagged and n = 2 for each V5-tagged clone). C Proportion of peaks called from V5-enriched CUT&RUN corresponding to gene bodies (blue), repetitive regions (red), intergenic regions (teal), promoters (purple, defined as 1 kb upstream of annotated TSSs), and other regions (green). D Pathway analysis of SPT16-V5 CUT&RUN peaks overlapping mRNA loci (genic and promoter regions). Q-values were calculated from p-values by the Benjamini–Hochberg procedure. E The three most significantly enriched sequence motifs of all SPT16-V5 CUT&RUN peaks (n = 4) identified using HOMER [74]