Fig. 2: Relationship between G4s and open chromatin.

A Genomic view showing input and G4 IP samples (blue tracks), ATAC-seq (purple track), and RNA-seq (gray track) peaks in the promoter of representative genes: CDK4 (upper panel), SMU1 (mid panel), and ESR1 as negative control gene (lower panel). B Venn diagram displaying the intersection between peak regions corresponding to IP G4s (light blue) and open chromatin regions (violet) mapped by ATAC-seq in promoters. C Percentage proportion of expressed genes grouped according to the presence of G4s and open chromatin signal in their promoter region. One transcript per gene was considered as expression threshold. D Expression distribution of all genes grouped according to the presence of ChIP-seq G4s and ATAC-seq signals in their promoter region. Gene expression is reported as TPM (transcript per million). In C and D, the presence and absence of G4 and ATAC-seq signals are indicated below the graphs. The box plots central line represents the median, the bottom, and upper bounds of the box represent the 25th and 75th percentile, respectively, and the whiskers represent the lowest and highest score, excluding outliers. The significance level of each category was calculated by two-sided T test (CI 95%) with respect to the G4:ATAC −/− group. ***p value < 0.001. Exact p values are <2.22e−16 for both G4:ATAC +/+ and −/+ categories. Numerosity of each category is the following: G4:ATAC +/+ n = 1351, −/+ n = 8893, −/− n = 16204. Source data for each panel are provided or referenced in the Source data file.