Nonhomologous End Joining Mechanisms in Double-Strand Break Repair

Nonhomologous end joining (NHEJ) is the principal pathway for repairing DNA double-strand breaks (DSBs) throughout the cell cycle, acting rapidly to preserve genomic integrity when a sister chromatid is not available. The process begins with the Ku70/80 heterodimer binding to DNA ends and recruiting the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form a synaptic complex. This assembly tethers the two broken ends in close proximity. If DNA termini are incompatible, specialised nucleases such as Artemis trim damaged bases and polymerases add or remove nucleotides to generate ligatable ends. Ultimately, the XRCC4–Ligase IV complex, often aided by XRCC4-like factor (XLF) and paralogues such as PAXX, seals the break. Fidelity is ensured by a short-range synaptic arrangement that favours direct ligation of compatible ends before processing, while accessory factors modulate dynamic assembly and disassembly of the repair machinery. NHEJ underpins diverse biological processes, from lymphocyte V(D)J recombination to telomere maintenance, and its modulation has implications for cancer therapy, genome editing and resistance to genotoxic stress.

Research from Nature Portfolio

Recent studies have elucidated structural bases for NHEJ fidelity. High-resolution analysis of Ligase IV within the short-range synaptic complex reveals that a single Ligase IV molecule bridges both DNA ends immediately upon synapsis, prioritising direct ligation of compatible termini and suppressing error-prone processing. Conformational snapshots of the DNA-PK holoenzyme obtained by cryo-EM define an intermediate and an active state, showing how ligand binding and helical repeat movements activate kinase function and coordinate autophosphorylation. These insights clarify how DNA-PKcs switches between end-bridging and signalling modes without disrupting the core ligation apparatus. Together, these structural advances define the choreography of enzyme and DNA interactions that ensure both speed and precision in NHEJ.

Nonhomologous End Joining Mechanisms in Double-Strand Break Repair publication trend

The graph below shows the total number of articles in nonhomologous end joining mechanisms in double-strand break repair across all publications each year (not limited to Nature Index journals).

Technical terms

Double-strand break (DSB): A lesion in which both strands of the DNA helix are severed.

Synaptic complex: A protein–DNA assembly that juxtaposes the two DNA ends prior to processing and ligation.

DNA-PKcs: The catalytic subunit of DNA-dependent protein kinase that, together with Ku70/80, orchestrates NHEJ.

Ku heterodimer: A ring-shaped protein complex (Ku70 and Ku80) that recognises and binds DNA termini.

XRCC4–Ligase IV: A core ligation complex essential for sealing DNA ends in NHEJ.

Accessory factors (XLF, PAXX): Proteins that stabilise synapsis and promote efficient end joining by bridging or scaffolding NHEJ components.

References

1. Structural role for DNA Ligase IV in promoting the fidelity of non-homologous end joining. Nature Communications (2024).
2. Human DNA-dependent protein kinase activation mechanism. Nature Structural & Molecular Biology (2023).
3. DNA-PK controls Apollo’s access to leading-end telomeres. Nucleic Acids Research (2024).
4. PAXX binding to the NHEJ machinery explains functional redundancy with XLF. Science Advances (2023).
5. GCN5 mediates DNA-PKcs crotonylation for DNA double-strand break repair and determining cancer radiosensitivity. British Journal of Cancer (2024).