Table 3.
DNA modifications and damage amenable to Nick-seq mapping
| DNA modification | Base excision enzymea | Additional processingb | Reference |
|---|---|---|---|
| DNA repair intermediates (abasic sites, strand-breaks) | None | Endo IV (NEB) | (15) |
| Bulky adducts formed by benzo[a]pyrene, acrolein, aflatoxin, et al. | UvrABC | None | (43) |
| 8-Oxoguanine, formamidopyrimidine | FPG, hOGG1 (NEB) | None | (44) |
| UV photodimers (TT, TC, CC) | T4 Endo V (NEB) | Endo IV (NEB) for 3′-UA | (45) |
| 1,N6-Ethenoadenine, hypoxanthine | hAAG (NEB) | Endo IV (NEB) for AP | (45) |
| Uracil | UDG (NEB) | Endo IV (NEB) for AP | (45) |
| A:8-oxoG mispair | MutY (RD) | None | (45) |
| Thymine glycol, 5-hydroxyuracil, 6-dihydroxythymine, 5-hydroxycytosine, urea | Endo III (NEB) | Endo IV (NEB) for AP | (46) |
| T:G mispair | TDG (RD) | Endo IV (NEB) for AP | (45) |
| N3-Methylcytosine, N1-methyladenine, N3-methyladenine, N7‐methylguanine | AlkC, AlkD | Endo IV (NEB) for AP | (47) |
| Hypoxanthine, xanthine | E. coli EndoV (NEB) | Endo IV (NEB) for AP | (48) |
| Single-strand nicking endonucleases | >20 types (NEB) | None | (49) |
| 5-Methylcytosine | TET, TDG | Endo IV (NEB) for AP | (50) |
| 5-Methylcytosine | DEMETER, ROS1, DML2 and DML3 | Endo IV (NEB) for AP | (51) |
| 5-Methylcytosine | Bisulfite seq + TDG (RD) | Endo IV (NEB) for AP | (52) |
| 5-Hydroxymethyl-cytosine | TET/bisulfite seq. + TDG (RD) | Endo IV (NEB) for AP | (52) |
| DNase I footprinting | DNase I (NEB) | None | (53) |
aEnzyme suppliers in parentheses: NEB, New England Biolabs; RD, R&D Systems; other abbreviations: TDG, thymine DNA glycosylase; Endo, endonuclease; UDG, uracil DNA glycosylase.
bProcessing to remove 3′-α, β-unsaturated aldehydes (3′-UA) or abasic (AP) sites for Nick-seq library preparation (46).