Table 2 Genome-wide 8-oxo-dG-sequencing methods.
From: 8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification
OG-Seq115 | Click-code-seq116 | CLAPS-seq117 | AP-Seq118 | enTRAP-Seq121 | ChIP-Seq122 | ||
|---|---|---|---|---|---|---|---|
Prerequisite | - 8-oxo-dG-specific in vitro oxidation- biotin conjugation | - In vitro digestion with Fpg and APE1 - Incorporation of Click-dGTP - Biotin conjugation with code sequences | - 8-oxo-dG-specific in vitro oxidation - Biotin conjugation | - In vitro digestion with OGG1 - ARP conjugation | - None | - None | - Formaldehyde treatment for crosslinking |
8-Oxo-dG isolation | Streptavidin-biotin interaction | Streptavidin-biotin interaction | Streptavidin-biotin interaction | Streptavidin-biotin interaction | Immunoprecipitation with 8-oxo-dG antibody | Affinity purification with K249Q hOGG1 protein | Immunoprecipitation with OGG1 and APE1 antibodies (acetylated active forms) |
Analysis of 8-oxo-dG distribution | Peak analysis of compiled reads | Nucleotide after code sequence | Peak analysis of compiled reads and polymerase stalling site | Peak analysis of compiled reads | Peak analysis of compiled reads | Peak analysis of compiled reads | Peak analysis of compiled reads |
Estimated resolution | ~150 bp | Single-nucleotide | Single-nucleotide | ~250 bp | ~200–800 bp | ~100–1000 bp | Size of DNA fragmentation |
Applied genome | Mouse embryonic fibroblast (MEF) | S. Cerevisiae (Yeast) | HeLa | X-ray irradiated HepG2 | MEF | A549 and HCT116 | |
Results from 8-oxo-dG sequencing | - Enriched in regulatory elements (promoter, 5′UTR and 3′UTR) | - Enriched in regions with high nucleosome occupancy | - Underrepresented in G-quadruplex and promoter | - Enriched in retrotransposons and microsatellites, open chromatin regions and G-quadruplex; Underrepresented in closed chromatin regions | - Enriched in DNA damaged regions (double strand breaks)119, promoter regions (enriched in repair proteins, G-quadruplex, CG skew, and bidirectional transcription)120 | - Enriched in open chromatin regions and regulatory elements (promoters, CpG islands, and 5′UTR) | - Located in putative quadruplex sequences (PQS) |
