Fig. 5: NELF directly binds to nascent eRNAs in vivo.
From: Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF
a Example track showing one of the activity-induced genes, Fosb (Blue shaded at its promoter) and its nearby enhancer (Yellow shaded area) along with ChIP- (H3K27ac, NELF-E, and NELF-A), eCLIP-, GRO-, and mRNA-seq data. b, c The coverage profiles of the crosslinking sites (green line) from eCLIP-seq and NELF ChIP-seq coverage profiles (red line) present up to 600 bp downstream from the TSSs as defined by ENCODE annotation of pre-mRNAs (9028) (b) and from the de novo defined 5′-ends (TSSs) of intergenic eRNAs (1226) (c) at different time points after KCl stimulation (0 and 30 min). NELF peak (~60–70 bp downstream of the TSSs) portions (thin red box) from ChIP-seq data are also shown. The 607 overlapping eRNAs out of 1226 eRNAs were selected after transcript calling with GRO-seq (KCl 30 min). A total of 7242 annotated pre-mRNAs having one or more crosslinking sites out of 9028 pre-mRNAs (b) and a total of 240 eRNAs having crosslinking sites out of 607 eRNAs (c) were used for these analyzes. See also the figure legend of Supplementary Fig. 8a, b. d, e The coverage profiles of eCLIP-seq (green line) from the normalized number of crosslinking sites considering the expression level from GRO-seq and Exo-seq coverage profiles (purple line) for a total of 7242 annotated pre-mRNAs having crosslinking sites out of 9028 pre-mRNAs (d) and a total of 240 eRNAs having crosslinking sites out of 607 eRNAs (e) at KCl stimulation (0 and 30 min). NELF peak (~60–70 bp downstream of the TSSs) portions (thin red box) from ChIP-seq data were also shown. f–i Pie charts that show the proportion of crosslinking sites present in three distance windows (1–200, 201–400, or 401–600 nucleotides) for the total annotated (9028) (f) or KCl-up/NELF-bound (548) (h) pre-mRNAs, and the total intergenic (1226) (g) or KCl-up/NELF-bound (144) (i) eRNAs at different time points after KCl stimulation. P values were determined by Chi-squared. j ChIP-seq analysis of the NELF-E protein. The pie chart shows the genomic distribution of annotated NELF-E peaks. 5′UTR 5′ untranslated region, 3′UTR 3′ untranslated region, CDS coding sequence, TSS transcription start site, TTS transcription termination site. Source data for (b–j) are provided in a Source Data file.
