Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

Abstract

8-Oxo-7,8-dihydro-2′-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. Here, we developed a single-nucleotide resolution OG-sequencing method, named CLAPS-seq (Chemical Labeling And Polymerase Stalling Sequencing), to measure the genome-wide distribution of both exogenous and endogenous OGs with high specificity. Our data identified decreased OG occurrence at G-quadruplexes (G4s), in association with underrepresentation of OGs in promoters which have high GC content. Furthermore, we discovered that potential quadruplex sequences (PQSs) were hotspots of OGs, implying a role of non-G4-PQSs in OG-mediated oxidative stress response.

Structure-driven effects on genomic DNA damage propensity at G-quadruplex sites

“…Overall, the above observations agree with the general mapping of 8oxoG sites at around PQSs, showing the surprising outcome of having lower propensity to 8oxoG damage in G4s (57). However, in our design, we could look at the differential effects of G4 structures at varying G4 stability levels.…”

“…We also exemplified a damage type, 8oxoG, where the structural changes influence damageability through the alterations and coherence in electronic delocalisation effects, shedding light on and unifying the seemingly contradictory results in past considerations (13,57). Overall, our results outline the multifaceted nature of genomic G4 sites, and enable the demonstration of the linked structure-driven effects on 9 types (including 4 subtypes of UV damage cross links and 3 types of strand-invariant DNA fragmentation) of DNA damage phenomena.…”

“…The genome-wide distribution of both 8-oxoguanine (8oxoG) oxidative DNA damage data (Figure 2B) were taken from (57), as accessed through the GEO repository under the accession identifier GSE181312. We investigated the dataset of 8oxoG-mapped naked genomic DNA, with the damages induced by KBrO3 treatment.…”

“…Recently, there has been a number of important contributions by Fleming and Burrows, demonstrating the possibility of fine interplay between the ROS damage at non-B DNA structures in modulating gene regulation, while investigating the consequence of 8oxoG formation at G4 and Z-DNA sites (13,14). With the very recent publication of the seminal work by Hu and co-workers (57), first time depositing a nucleotide resolution genomic profile of 8oxoG damage for human, here we have a chance to investigate the purified and strength-differential structural effects at G4 sites on the predisposition to this type of damage, by operating on human genome G4 and 8oxoG datasets, all measured for naked genomic DNA. 8oxoG damage brings an example of a structure-driven electronic effect that deviates once more from the other observations from all our investigated damage types (Figure 3D).…”

Concordance of hydrogen peroxide–induced 8-oxo-guanine patterns with two cancer mutation signatures of upper GI tract tumors

“…Nick-sequencing (nick-seq) has been used for mapping oxidative DNA damage in Escherichia coli ( 34 ). 8-oxo-G can be further oxidized and chemically labeled with biotin, which produces a polymerase stop signal ( 35 ). However, to our knowledge, there is currently no straightforward enzyme-based method to map oxidized DNA bases genome-wide and at single-base resolution in mammalian cells.…”