Fig. 5

TT-seq identifies FACT-dependent regulation of non-coding RNAs. A IGV genome browser tracks showing nascent transcription (TT-seq) over the Nanog gene and three Nanog superenhancers following 24-h IAA treatment to deplete SPT16, along with published H3K27ac ChIP-seq data. Three individually scaled windows are shown to highlight eRNA transcription from the superenhancers (shaded red) and Nanog gene (shaded blue). Merged replicates are shown as a single track (TT-seq: n = 3, H3K27ac ChIP-seq: n = 1; ChIP-seq from GSE32218) [83,84,85]. B Volcano plot of differentially transcribed putative eRNAs (analyzed with DESeq2). Putative eRNAs were called by transcription from a TSS-distal DHS marked by either H3K4me1 or H3K27ac. Red points are significantly changed ncRNAs (adj. p < 0.05, log₂ fold change > 0.75). Dark blue points are significantly changed by adjusted p-value but below the fold change cutoff, while light blue points are significantly changed by log₂ fold change but below the adjusted p-value cutoff. Labeled arrows denote closest genes to the indicated ncRNA. C Pathway analysis of nearest genes to differentially expressed putative eRNAs following 24-h IAA treatment to deplete SPT16. Y-axis indicates pathway enrichment ranking. Q-value was calculated from p-values by the Benjamini–Hochberg procedure. D As in B, but for differentially expressed PROMPTs. E As in C, but for the genes nearest differentially expressed PROMPTs