Fig. 6

Stable DNA secondary structures detected in Raji cells preferentially form at the promoter-proximal regions of paused genes. Based on the traveling ratio, genes in Raji cells were classified as no Pol II (NP2, red), non-paused (NPA, green), and paused (PAU, blue). Numbers of each group of genes are listed in Table S3. a Average free energy profiles (top), in vivo secondary structure footprints (middle), and average Pol II ChIP-seq coverage profiles (bottom) are shown. Heat map representations of the same data are shown in Additional file 1: Figure S8. b Profiles of Pol II ChIP-seq (top), in vivo secondary structure footprints (middle) and the predicted free energy (bottom) at TSS ± 2 kb of human heat shock gene (HSPA1B) are shown