Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing

Jing Tu (), Mengqin Duan, Wenli Liu, Na Lu, Yue Zhou, Xiao Sun and Zuhong Lu ()
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Jing Tu: Southeast University
Mengqin Duan: Southeast University
Wenli Liu: Southeast University
Na Lu: Southeast University
Yue Zhou: Southeast University
Xiao Sun: Southeast University
Zuhong Lu: Southeast University

Nature Communications, 2021, vol. 12, issue 1, 1-9

Abstract: Abstract We present a user-friendly and transferable genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. In the human genome, 736,689 G4 structures were identified, of which 45.9% of all predicted canonical G4-forming sequences were characterized. Over 89% of the detected canonical G4s were also identified by combining polymerase stop assays with next-generation sequencing. Testing using public datasets of 6 species demonstrated that the present method is widely applicable. The detection rates of predicted canonical quadruplexes ranged from 32% to 58%. Because single nucleotide variations (SNVs) influence the formation of G4 structures and have individual differences, the given method is available to identify and characterize G4s genome-wide for specific individuals.

Date: 2021
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DOI: 10.1038/s41467-021-26312-w

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