Fig. 6. Main repair pathways for trapped topoisomerases in humans.

a | Overall scheme for conversion of topoisomerase DNA–protein crosslinks (TOP-DPCs) into protein-free DNA breaks²⁰¹. Association of TOP-DPCs with replication or transcription complexes and phase of the cell cycle (S phase versus G1 phase) are likely determinants of pathway choice. Debulking of TOP-DPCs by the three ubiquitin–proteasome pathways includes the conserved SUMO-targeted ubiquitin ligase (STUbL) pathway, in which RNF4 is the human E3 ubiquitin ligase for TOP1-DPCs, TOP2A-DPCs and TOP2B-DPCs²⁴⁹; the TRIM41 E3 ligase pathway for crosslinks between TOP3B and DNA or RNA²; and the cullin pathway for TOP1-DPCs^365,366 (step 1). Non-proteasomal TOP-DPC proteolytic pathways²⁴⁵. The proteases Spartan (SPRTN), GCNA (also known as ACRC), FAM111A and DDI debulk TOP1-DPCs and TOP2-DPCs (step 2). Non-proteolytic pathway for TOP2, driven by SUMO E3 ligase ZNF451 (ref.²⁵⁹) (step 3). Nucleic-acid excision pathways for TOP1 and/or TOP2 include excision by the endonucleases MRE11, CtIP and XPF–ERCC1, or excision by tyrosyl-DNA phosphodiesterase 1 (TDP1) and TDP2 (step 4). b | TDP1 is activated by poly(ADP-ribose) polymerase 1 (PARP1)^268,269,275, and upon cleaving DNA leaves a 3′-phosphate that is further processed by polynucleotide kinase phosphatase (not shown). TDP2 leaves a 5′-phosphate that can be directly ligated or extended by DNA polymerases (not shown). Both TDP1 and TDP2 require debulking of TOP-DPCs to gain access to the tyrosyl–DNA links. Additional excision pathways involve endonucleases. c | Differential roles of non-homologous end joining (NHEJ) and homology-directed repair (HDR) in repair of TOP1-induced single-ended DNA double-strand breaks (seDSBs) and TOP2-DPC-induced DSBs. Whereas seDSB repair by NHEJ is toxic²²², possibly by inducing large deletions owing to illegitimate end joining of distant seDSBs (Fig. 5b), NHEJ is crucial for repair of TOP2-DPCs. TOP1cc, TOP1 cleavage complex.