Identification of G-quadruplex clusters on human genomic DNA

We identified 9,651 G-quadruplex clusters on human genomic DNA. The paper has been published in Scientific Reports.1

G-quadruplex (G4) is a non-canonical DNA structure that has been found in several regulatory regions, such as telomeres, CpG islands and promoters. The identification of G4-forming sequences is important in elucidating the function of G4 structures on genomic DNA. In this study, a method for identifying G4 clusters on genomic DNA was developed by high-throughput sequencing of genomic DNA amplified via whole-genome amplification (WGA) in the presence of a G4 ligand. The G4 ligand specifically bound to G4 structures on genomic DNA to inhibit DNA replication at the G4 clusters by WGA. By high-throughput sequencing of the WGA products, 9,651 G4 clusters were identified on human genomic DNA. Among these clusters, 3,766 G4 clusters contained at least one transcriptional start site and 95 G4 clusters have been found in oncogenes or tumor suppressor genes. These results suggest that the G4 clusters would be novel cancer drug targets.

Fig. 1 Scheme of identification of G-quadruplex clusters on human genomic DNA.

1. Yoshida W., Saikyo H., Nakabayashi K., Yoshioka H., Bay D.H., Iida K., Kawai T., Hata K., Ikebukuro K., Nagasawa K., Karube I.
Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand.
Scientific Reports (2018)8, 3116, DOI: 10.1038/s41598-018-21514-7,
https://www.nature.com/articles/s41598-018-21514-7