Fig. 1: Genomic position of G4s and association to gene expression.

A Percentage distribution of G4 peaks in functional genomic regions according to Homer gene annotation. Percentages are normalized over the genomic abundance of each functional region. B Percentage proportion of expressed genes among the G4-containing genes (yellow). G4-depleted genes (no G4, violet) are reported as reference. One transcript per gene was considered as threshold. C Gene expression distribution expressed in transcripts per million (TPM) of all the G4-containing genes (yellow). Genes were grouped according to the functional annotation of the immunoprecipitated G4 region. G4-depleted genes (no G4, violet) are reported as reference. 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 gene category was calculated by two-sided T test (CI 95%) with respect to the no G4 group. ***p value < 0.001, **p value < 0.01, the absence of asterisks indicates that the difference is not statistically significant. Exact p values are the following: 5′UTR p = 3.3e−14, exon p = 0.0032, intergenic p = 1.2e−9, intron p < 2.22e−16, promoter-TSS p < 2.22e−16. Numerosity of each category is: 3′UTR n = 29, 5′UTR n = 49, exon n = 44, intergenic n = 729, intron n = 808, noncoding n = 36, promoter-TSS n = 1434, TTS n = 47, no G4 n = 23662. D Upper panel: percentage of G4-containing genes, in genes grouped according to their expression level (no expression, low, medium, or high) and their distance from the TSS of the closest gene (<1000 bp, between 1000–15,000 and >15,000 bp). Lower panel: detailed view of gene expression level (TPM) and density distribution of genes with folded G4s within 1000 bp from TSS in function of the G4 distance from the TSS. E Genomic view of representative regions showing the G4-ChIP peak position with respect to the TSS: G4-ChIP peaks in two gene promoters with noncoding upstream regions are displayed in the upper panels (METTL13 and SUCO); G4-ChIP peaks embedded in the coding regions of two adjacent genes with opposite transcription direction are shown in the lower panels (COMMD6 and UCHL3—left; CRTC-AS1 and BLM—right). Source data for each panel are provided or referenced in the Source data file.