Alternative non-homologous end joining (Alt-NHEJ (also known as A-NHEJ or alt-EJ))

Alternative non-homologous end joining (Alt-NHEJ, also called alternative end joining or microhomology-mediated end joining) is an error-prone DNA double-strand break repair pathway that serves as a backup when classical NHEJ or homologous recombination are compromised. Unlike classical NHEJ—which uses specific proteins like Ku70/80 and Ligase IV—Alt-NHEJ relies on short regions of microhomology at the broken ends for alignment before ligation. The process often involves proteins such as poly(ADP-ribose) polymerase 1 (PARP1), XRCC1, Ligase III (LIG3), and notably DNA polymerase theta (POLQ/POLθ) which is central to MMEJ activity. Because it lacks high-fidelity sequence restoration mechanisms, Alt-NHEJ frequently results in deletions at the junction site and can promote chromosomal translocations. In cancer biology, especially tumors with defective homologous recombination pathways such as those harboring BRCA1/2 mutations, cells become highly dependent on Alt-NHEJ for survival. This dependency forms the basis for synthetic lethality exploited by PARP inhibitors—a class of drugs now standard in treating several HR-deficient cancers. Targeting POLQ is an emerging therapeutic strategy aiming at further exploiting this vulnerability. However, due to its inherently mutagenic nature—causing loss of genetic information at break sites and promoting genome rearrangements—therapeutic targeting must be approached cautiously due to risks including increased genomic instability or therapy-related secondary malignancies[3][5][6].

Other names

Alternative end-joiningalt-EJmicrohomology-mediated end joining (MMEJ; considered a major sub-pathway)A-NHEJ

Inhibition of PARP leads to synthetic lethality in HR-deficient cells by forcing reliance on Alt-NHEJ for DSB repair[6] Inhibition of POLQ/DNA polymerase theta disrupts the core machinery of Alt-NHEJ/MMEJ, leading to cell death in HR-deficient cancers[6]