Conserved G-Quadruplex-Forming Sequences in Mammalian TERT Promoters and Their Effect on Mutation Frequency

SIMPLE SUMMARY: Guanine-rich genomic DNA sequences are known to be able to fold into noncanonical G-quadruplex (G4) polymorphic structures. G4s play important physiological roles in DNA replication, repair, mutagenesis, regulation of gene expression, etc. G4-forming DNA sequences (G4 motifs) predominate in the regulatory elements (promoters) of human oncogenes, which indicate G4 involvement in cancer progression. The object of our study was the search for G4 motifs located in the promoter regions of the telomerase reverse transcriptase (TERT) oncogene, the product of which is responsible for the immortalization of cancer cells. Using a combination of known and newly developed bioinformatics approaches, we identified G4 motifs in the TERT promoter regions of 141 mammalian species belonging to 20 orders, 5 of which, including primates and predators, contain more than 10 species. Comparison of their location in the TERT promoters, degree of conservation, and mutability potential revealed that the G4 motifs of the TERT promoters across the mammalian class are evolutionarily conserved and are therefore biologically significant. The obtained data support our hypothesis that G4s can interfere with DNA repair pathways and affect the evolutionary adaptation of organisms and species. ABSTRACT: Somatic mutations in the promoter region of the human telomerase reverse transcriptase (hTERT) gene have been identified in many types of cancer. The hTERT promoter is known to be enriched with sequences that enable the formation of G-quadruplex (G4) structures, whose presence is associated with elevated mutagenicity and genome instability. Here, we used a bioinformatics tool (QGRS mapper) to search for G4-forming sequences (G4 motifs) in the 1000 bp TERT promoter regions of 141 mammalian species belonging to 20 orders, 5 of which, including primates and predators, contain more than 10 species. Groups of conserved G4 motifs and single-nucleotide variants within these groups were discovered using a block alignment approach (based on the Nucleotide PanGenome explorer). It has been shown that: (i) G4 motifs are predominantly located in the region proximal to the transcription start site (up to 400 bp) and are over-represented on the non-coding strand of the TERT promoters, (ii) 11 to 22% of the G4 motifs found are evolutionarily conserved across the related organisms, and (iii) a statistically significant higher frequency of nucleotide substitutions in the conserved G4 motifs compared to the surrounding regions was confirmed only for the order Primates. These data support the assumption that G4s can interfere with the DNA repair process and affect the evolutionary adaptation of organisms and species.