Fig. 1

Bidirectional transcription initiates around DHSs but is not a specific mark of active enhancers. a–c The fold-change in transcription frequency (fraction of loci with evidence of transcription initiation) for sites with transcription initiation signal in 25-bp consecutive windows around DHS midpoints (x = 0) relative to the mean transcription frequency in the flanking regions: 500 to 1000 bp from the DHS midpoint. Total bidirectional transcription initiation across DHSs in Gm12878 cells as measured by GRO-cap is shown by the solid lines while stable bidirectional transcription initiation as measured by CAGE is shown by the dashed lines. Purple lines consider transcription initiation from the forward strand and green lines show transcription initiation from the reverse strand. In all panels, only DHSs that do not overlap annotated promoters were included. d–f Heatmaps of GRO-cap signal as measured by log2(Forward/Reverse) RPM and DNase hypersensitivity as measured by RPM around DHS midpoints for the same chromatin state annotations described in a–c. Rows are ranked by the DNase hypersensitivity signal (RPM). The height of each heatmap corresponds to the total number of DHSs which generated the plot as shown on the y-axis so that shading density is directly comparable between plots