Figure 1. The DNA damage response: integration of repair and cell cycle checkpoints.

Endogenous DNA damage is shown in blue boxes, environmental in green boxes and therapeutically induced in purple boxes. ROS (reactive oxygen species), IR (irradiation) TMZ (temozolomide) and other DNA methylating agents and TopI (topoisomerase I poisons) result in damaged bases and SSBs. BER/SSBR (base excision repair/single strand break repair) repair these lesions by removing damaged bases by glycosylase and endonuclease action to produce a SSB. PARP binds to and is activated by the nick to recruit the SSB repair proteins XRCC1, PolB and Ligase 1 or 3 to fill the gap and join the ends, for short patch repair with the additional requirement for PNPK, PCNA and FEN1 for long patch repair. HDL (Helix distorting lesions) caused by UV photoproducts, bulky adducts, e.g. from tobacco smoke and platinum therapy are repaired by NER (nucleotide excision repair) which can be global or transcription-coupled and involves several proteins including TFIIH XPG and XPF-ERCC1 to remove 25–30 nt, re-filling the gap using the complementary strand as a template by DNA pol δ, ε or κ and ligation by Lig 1 or 3. TopII (topoisomerase II poisons) along with ROS and IR cause DSBs that are repaired in GI exclusively by NHEJ (non-homologous end-joining) which involves the recognition, stabilisation and synapsis of the break by DNA-dependent protein kinase DNA-PK, a heterodimeric complex of KU70 and Ku80 and the catalytic subunit, DNA-PKcs, modest end resection, limited by 53BP1, and end ligation by Ligase 4 and XRCC4-XLF. DSBs signal via ATM and CHK2, primarily but not exclusively via p53, to G1 cell cycle arrest. ICL (interstrand cross-links) induced endogenously and environmentally by, e.g. acrolein and therapeutically by CisPt (cis- or carboplatin) are repaired by the FA (Fanconi anaemia) pathway when the replication fork encounters the lesion. The ICL is recognised by FANCM then recruitment of the core FA proteins for fork stabilisation, nucleases to excise the lesion then translesional and/or homologous recombination DNA synthesis. Several FA components are in common with NER (FANCM/ERCC1/XPF family) and HRR (homologous recombination repair), including BRCA2/FANCD1, PALB2/FANCN, RAD51C/FANCO. Oncogene activation and dNTP depletion and unrepaired (SSL) single strand lesions result in RS (replication stress) that can cause stalled/collapsed replication forks are repaired by HRR. Similarly DSBs are repaired by HRR during S phase. HRR involves end-resection involving MRN and CtIP, promoted by BRCA1, to produce single strand overhangs, BRCA2 recruits RAD51 to allow invasion of the complementary chromatid template for faithful DNA synthesis across the break. The process is completed by resolution of Holliday junctions by helicases and synthesis-dependent strand annealing. NER, FA, stalled replication forks and resected DSBs all result in SS DNA, which activate ATR, that activates CHK1, and WEE1 ultimately resulting in increased inactivating phosphorylation of the S and G2/M cyclin dependent kinases CDK2 and CDK1 causing S-phase and G2/M cell cycle arrest. There is cross-talk between ATR/CHK1/WEE1 and FA/HRR and ATM/CHK2 and NHEJ to ensure co-ordination between repair and cell cycle arrest.