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

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...

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Bibliographic Details
Published in:Nature communications 2021-10, Vol.12 (1), p.6014-6014, Article 6014
Main Authors: Tu, Jing, Duan, Mengqin, Liu, Wenli, Lu, Na, Zhou, Yue, Sun, Xiao, Lu, Zuhong
Format: Article
Language:English
Subjects:
49/23
631/114/2163
631/1647/514/2254
631/61/212/2166
Deoxyribonucleic acid
DNA
DNA fingerprinting
DNA sequencing
G-Quadruplexes
Genetic Techniques
Genome, Human
Genomes
High-Throughput Nucleotide Sequencing - methods
High-Throughput Screening Assays - methods
Humanities and Social Sciences
Humans
Identification methods
multidisciplinary
Next-generation sequencing
Nucleotides
Precision Medicine
Science
Science (multidisciplinary)
Whole Genome Sequencing - methods
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Summary: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. Current methods to identify G-quadruplex structures in DNA require specialized protocols and multiple rounds of sequencing. Here, the authors develop a method to detect G-quadruplex structures in DNA based on fluctuations in sequencing quality in a standard sequencing experiment.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-021-26312-w