# Nonhomologous end joining—the importance of end tethering and beyond

**Authors:** Shan Zha, Geunil Yi

PMC · DOI: 10.1101/gad.353407.125 · Genes & Development · 2026-04-01

## TL;DR

This review explains how the NHEJ pathway repairs DNA breaks through five phases, emphasizing the role of protein bridges in stabilizing DNA ends.

## Contribution

The paper provides a detailed molecular and structural analysis of the five phases of NHEJ, focusing on end tethering and protein interactions.

## Key findings

- NHEJ operates through five distinct phases involving dynamic protein bridges.
- End tethering is supported by multiple overlapping machineries anchored on Ku.
- Structural insights reveal how NHEJ contributes to genome stability and lymphocyte development.

## Abstract

In this review, Zha and Yi dissect the molecular and structural mechanisms underlying the five discrete phases of nonhomologous end joining (NHEJ); namely, end sensing, end protection, end tethering, end processing, and end ligation. They highlight how the dynamic network of protein bridges (i.e., Ku–protein interactions) stabilizes DNA ends and enables the assembly of NHEJ machinery to facilitate the repair of DNA double-strand breaks independent of sequence complementarity.

The nonhomologous end joining (NHEJ) pathway is a major mechanism for repairing DNA double-strand breaks (DSBs), essential for lymphocyte development and for maintaining genome stability in postmitotic cells, including neurons. Under pathological conditions, NHEJ is also responsible for most oncogenic translocations and the repair of DSBs induced by chemotherapy/radiation. Advances in structural biology and single-molecule imaging have captured NHEJ at various stages of the reaction, revealing a modular, dynamic organization with built-in redundancy and resilience. Here, we describe NHEJ in five phases (end sensing, end protection, end tethering, end processing, and end ligation), highlighting their molecular features and transitions and how structural insights explain genetic interactions and physiological consequences, including lymphocyte development. Unlike other DSB repair mechanisms, NHEJ operates with minimal or no sequence complementarity, relying instead on protein assemblies to bridge and stabilize the two DNA ends. This review highlights the unique end-tethering phase, supported by at least five known overlapping machineries, all anchored on Ku.

## Linked entities

- **Proteins:** ku (non-homologous end joining protein Ku)

## Full-text entities

- **Genes:** Cyren (cell cycle regulator of NHEJ) [NCBI Gene 78412] {aka 3110062M04Rik, Mri}, Nbn (nibrin) [NCBI Gene 27354] {aka Nbs1}, Mre11a (MRE11A homolog A, double strand break repair nuclease) [NCBI Gene 17535] {aka Mre11, Mre11b}, Trp53 (transformation related protein 53) [NCBI Gene 22059] {aka Tp53, bbl, bfy, bhy, p44, p53}, Rbbp8 (retinoblastoma binding protein 8, endonuclease) [NCBI Gene 225182] {aka 9930104E21Rik, CtIP, RBBP-8, RIM, SAE2}, Dntt (deoxynucleotidyltransferase, terminal) [NCBI Gene 21673] {aka Tdt}, Prkdc (protein kinase, DNA activated, catalytic polypeptide) [NCBI Gene 19090] {aka DNA-PKcs, DNAPDcs, DNAPK, DNPK1, DOXNPH, HYRC1}, Aplf (aprataxin and PNKP like factor) [NCBI Gene 72103] {aka 2010301N04Rik}, Xrcc6 (X-ray repair cross complementing 6) [NCBI Gene 14375] {aka 70kDa, G22p1, Ku70}, Xrcc5 (X-ray repair complementing 5) [NCBI Gene 22596] {aka CTC85, CTCBF, Ku80, Ku86, Kup80}, PAXX (PAXX non-homologous end joining factor) [NCBI Gene 286257] {aka C9orf142, XLS}, Trp53bp1 (transformation related protein 53 binding protein 1) [NCBI Gene 27223] {aka 53BP1, Tp53bp1, m53BP1, p53BP1}, Mdc1 (mediator of DNA damage checkpoint 1) [NCBI Gene 240087] {aka 6820401C03, Nfbd1, mKIAA0170}, Polm (polymerase (DNA directed), mu) [NCBI Gene 54125] {aka B230309I03Rik, Tdt-N}, Paxx (non-homologous end joining factor) [NCBI Gene 227622] {aka D930050G13Rik}, Atr (ataxia telangiectasia and Rad3 related) [NCBI Gene 245000], Rnf168 (ring finger protein 168) [NCBI Gene 70238] {aka 3110001H15Rik}, H2ax (H2A.X variant histone) [NCBI Gene 15270] {aka H2A.X, H2afx, Hist5-2ax, gammaH2ax}, Pnkp (polynucleotide kinase 3'- phosphatase) [NCBI Gene 59047] {aka 1810009G08Rik, PNK}, Atm (ataxia telangiectasia mutated) [NCBI Gene 11920] {aka C030026E19Rik}, Xrcc4 (X-ray repair complementing 4) [NCBI Gene 108138] {aka 2310057B22Rik}, WRN (WRN RecQ like helicase) [NCBI Gene 7486] {aka RECQ3, RECQL2, RECQL3}, Lig4 (ligase IV, DNA, ATP-dependent) [NCBI Gene 319583] {aka 5830471N16Rik, tiny}, Nhej1 (non-homologous end joining factor 1) [NCBI Gene 75570] {aka 1700029B21Rik, XLF, cernunnos}, Lig1 (ligase I, DNA, ATP-dependent) [NCBI Gene 16881] {aka LigI}, LIG4 (DNA ligase 4) [NCBI Gene 3981] {aka LIG4S}, Wrn (Werner syndrome RecQ like helicase) [NCBI Gene 22427], Lig3 (ligase III, DNA, ATP-dependent) [NCBI Gene 16882] {aka D11Wsu78e}, NHEJ1 (non-homologous end joining factor 1) [NCBI Gene 79840] {aka IMD124, MCOPCB13, XLF}, PRKDC (protein kinase, DNA-activated, catalytic subunit) [NCBI Gene 5591] {aka DNA-PKC, DNA-PKcs, DNAPK, DNAPKc, DNPK1, HYRC}, Apo (anterior polar opacity) [NCBI Gene 104237], XRCC4 (X-ray repair cross complementing 4) [NCBI Gene 7518] {aka SSMED, hXRCC4}, DCLRE1C (DNA cross-link repair 1C) [NCBI Gene 64421] {aka A-SCID, DCLREC1C, RS-SCID, SCIDA, SNM1C}, APLF (aprataxin and PNKP like factor) [NCBI Gene 200558] {aka APFL, C2orf13, PALF, Xip1, ZCCHH1}, Poll (polymerase (DNA directed), lambda) [NCBI Gene 56626] {aka 1110003P06Rik}, XRCC6 (X-ray repair cross complementing 6) [NCBI Gene 2547] {aka CTC75, CTCBF, G22P1, KU70, ML8, TLAA}, Myc (Myc proto-oncogene, bHLH transcription factor) [NCBI Gene 17869] {aka Myc2, Niard, Nird, bHLHe39}, ATM (ATM serine/threonine kinase) [NCBI Gene 472] {aka AT1, ATA, ATC, ATD, ATDC, ATE}, DNTT (DNA nucleotidylexotransferase) [NCBI Gene 1791] {aka TDT}, Mtor (mechanistic target of rapamycin kinase) [NCBI Gene 56717] {aka 2610315D21Rik, FRAP, FRAP2, Frap1, RAFT1, RAPT1}, Rad50 (RAD50 double strand break repair protein) [NCBI Gene 19360] {aka Mrell, Rad50l}, XRCC5 (X-ray repair cross complementing 5) [NCBI Gene 7520] {aka KARP-1, KARP1, KU80, KUB2, Ku86, NFIV}, ERCC6L2 (ERCC excision repair 6 like 2) [NCBI Gene 375748] {aka BMFS2, C9orf102, HEBO, RAD26L, SR278}, Trav6-3 (T cell receptor alpha variable 6-3) [NCBI Gene 328483] {aka Gm13948, Gm193, Gm4, TCR}, Igh (immunoglobulin heavy chain complex) [NCBI Gene 111507], Terf2 (telomeric repeat binding factor 2) [NCBI Gene 21750] {aka TRF2}, Rnf8 (ring finger protein 8) [NCBI Gene 58230] {aka 3830404E21Rik, AIP37, laXp180}, CYREN (cell cycle regulator of NHEJ) [NCBI Gene 78996] {aka C7orf49, CYREN-1, CYREN-2, MRI, MRI-2}, Sh2d1a (SH2 domain containing 1A) [NCBI Gene 20400] {aka Gm686, SAP}, Ercc6l2 (excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2) [NCBI Gene 76251] {aka 0610007P08Rik, 1700019D06Rik, 9330134C04Rik, Rad26l, Sr278}, Terf2ip (telomeric repeat binding factor 2, interacting protein) [NCBI Gene 57321] {aka Rap1}, Exo1 (exonuclease 1) [NCBI Gene 26909] {aka 5730442G03Rik, Msa}
- **Diseases:** NHEJ (MESH:D003643), XLF deficiency (MESH:C565168), oncogenic (MESH:D000074723), primary immunodeficiency (MESH:D000081207), neurological complications (MESH:D002493), Artemis deficiency (MESH:D007153), microcephaly (MESH:D008831), immune deficiency (MESH:D007154), tumor (MESH:D009369), B-T- severe combined immunodeficiency (MESH:D016511), autoimmune (MESH:D001327), neuronal apoptosis (MESH:D065703), growth retardation (MESH:D006130), B-cell lymphomas (MESH:D016393), embryonic lethality (MESH:D020964)
- **Chemicals:** I-SceI (-), ATP (MESH:D000255)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932]
- **Mutations:** D3922A, L3062R

## Full text

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## Figures

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## References

200 references — full list in the complete paper: https://tomesphere.com/paper/PMC13041557/full.md

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Source: https://tomesphere.com/paper/PMC13041557