Strand-asymmetric G-runs and G4s downstream of TSS modulate tumor suppressor gene transcription

A genome sequence is not made up of random nucleotides. Instead, it has distinctive features for evolutionary adaptation. Herein, we identified a higher frequency of continuous guanines (G-runs) located downstream of the transcription start site (TSS) in the non-template strand than that of the template strand by analyzing the genomic region around TSS (TSS ± 1 kb) across different species. G-runs are known to have the propensity to form G-quadruplex structures (G4). By integrative analysis of large-scale multi-omic datasets, predicted G4 structures in TSS downstream region (TSS-to-+300 bp) of the non-template strand were found to be associated with lower promoter DNA methylation, more accessible chromatin, and higher transcript levels. Compared to non-cancer genes, tumor-suppressor genes (TSGs) exhibited a higher G-run frequency in TSS downstream region (TSS-to-+300 bp) of the non-template strand, contributing to both their high transcript levels and resistance to tumor-specific downregulation. These results were successfully validated with independent datasets. Taken together, our study reveals an evolutionarily conserved higher G-run frequency in TSS downstream region (TSS-to-+300 bp) of the non-template strand as a beneficial genetic feature of TSGs for optimizing their function in tumor suppression.