Identification of G-quadruplex Clusters by High-throughput Sequencing of Whole-genome Amplified Products with a G-quadruplex Ligand

Overview

Journal Sci Rep

Specialty Science

Date 2018 Feb 17

PMID 29449667

Citations 12

Authors

Wataru Yoshida

Hiroki Saikyo

Kazuhiko Nakabayashi

Hitomi Yoshioka

Daniyah Habiballah Bay

Keisuke Iida

Tomoko Kawai

Kenichiro Hata

Kazunori Ikebukuro

Kazuo Nagasawa

Isao Karube

Affiliations

Soon will be listed here.

Abstract

G-quadruplex (G4) is a DNA secondary structure that has been found to play regulatory roles in the genome. The identification of G4-forming sequences is important to study the specific structure-function relationships of such regions. In the present study, we developed a method for identification of G4 clusters on genomic DNA 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; thus, DNA polymerase was arrested on the G4 structures stabilised by G4 ligand. We utilised the telomestatin derivative L1H1-7OTD as a G4 ligand and demonstrated that the efficiency of amplification of the G4 cluster regions was lower than that of the non-G4-forming regions. 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, suggesting that genes are regulated by G4 clusters rather than by one G4 structure.

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