Fig. 2

Highly stable DNA secondary structures preferentially form at the promoter-proximal regions of paused genes. a Box plots show the mean free energy at the TSS ± 250 nt in two cell lines: H1-hESC (left) and HeLa-S3 (right). Based on the traveling ratio, genes were classified as no Pol II (NP2, red), non-paused (NPA, green), and paused (PAU, blue). Numbers of each group of genes in each cell line (shown in Table S3) are depicted in pie charts. *p < 2.2 × 10^− 16, t-test (Additional file 1: Table S4). b Average free energy profiles (solid line) and average Pol II ChIP-seq coverage profiles (dotted line) are shown in two cell lines: H1-hESC (top) and HeLa-S3 (bottom). Paused, non-paused, and no Pol II genes are shown in blue, green, and red, respectively. The Mfold analysis was used here, and the ViennaRNA anlysis is shown in Additional file 1: Figure S2D