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

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.

High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation

“…Similarly, rG4-seq, which is a variant of G4-seq, has enabled transcriptome-wide identification of RNA G-quadruplexes [ 57 ]. Recently, a novel method called G4-miner was used for genome-wide profiling of G-quadruplexes from standard whole-genome sequencing based on deviations in sequencing quality, with drop in sequencing quality at G-quadruplex structures [ 58 ]. Antibodies with high affinity for G-quadruplexes have been used for G4 ChIP-seq experiments to demonstrate genome-wide G-quadruplex structure formation in human cells [ 1 , 59 ].…”

Methodological advances of bioanalysis and biochemical targeting of intracellular G‐quadruplexes

“…Recently, the G4‐Miner method was reported to be used to detect genomic G4s through a novel principle. [ 95 ] In the standard whole‐genome sequencing process of Illumina sequencing, the reaction buffer without K + cannot lead to the formation of stable G4s, but the existing unstable G4s can still cause abnormal fluctuations of the Phred quality scores. Through capturing the subtle changes in the sequencing quality of these sites with computational algorithm, the G4 structures can be directly predicted.…”

“…Positive detection rate is low. [95] Detecting RNA G4s in cellular transcriptome rG4-seq Identifying the formation and stability of RNA G4s.…”

Polymorphic and Higher-Order G-Quadruplexes as Possible Transcription Regulators: Novel Perspectives for Future Anticancer Therapeutic Applications

“…This general output suggested that G4s might be involved in biological processes other than telomere maintenance. Consistently, bioinformatic analyses have highlighted the fact that putative G4-forming sequences are enriched at other genomic loci besides telomeres [ 5 , 6 ]. More recently, the results from several ChIP-Seq, CUT&Tag, and related sequencing studies in cells have supported this evidence as well [ 7 , 8 ].…”