Cancer Biology Wiki · DNA damage & repair

DNA double-strand break repair

A double-strand break severs both strands of DNA. Cells repair it through different pathways, chiefly homologous recombination and non-homologous end joining, and the choice between them depends on context.

Álvaro Esteban PérezDNA damage & repairUpdated

01 / The lesion

What is a DNA double-strand break?

A double-strand break (DSB) cuts both strands of the DNA double helix, splitting the molecule in two. [1] Repairing it accurately needs an undamaged homologous sequence as a template for both broken strands. [2]

The lesion itself has its own molecular entry (entry under review). This page is about how cells repair it.

A broken DNA molecule (top) beside an intact copy, the sister chromatid (bottom). A sister chromatid exists only after DNA replication, which is one reason the cell-cycle stage shapes how a break is repaired. Schematic; frame from the homologous recombination mechanism.

02 / Why it matters

Why double-strand breaks are dangerous

Double-strand breaks are among the most toxic DNA lesions, and they must be repaired to keep chromosomes intact. [1][3] A break that is not repaired can lead to genomic instability or cell death. A break that is repaired wrongly can join the wrong DNA ends together, producing chromosomal translocations of the kind that commonly underlie oncogenic transformation. [4]

03 / Origins

Where double-strand breaks come from

Some breaks come from outside the cell, such as ionising radiation or drugs that inhibit topoisomerases, such as etoposide. [1] Others arise during normal DNA replication, when a replication fork encounters another lesion. [5][3] Broken forks are a special case: their repair follows rules of pathway choice that appear to differ from those at a conventional break. [6]

Cells also make some breaks on purpose. In developing lymphocytes, V(D)J recombination cuts and rejoins antibody and T-cell receptor genes. The RAG enzymes leave hairpin-sealed ends, which must be opened before the ends can be joined. [1][7]

04 / First responders

Sensing the break

Cells have systems that detect DNA damage, signal that it is there and coordinate its repair. [5] At a double-strand break, the MRN complex is thought to recruit the kinase ATM to the break and activate it. [2] The chromatin flanking the break is marked by phosphorylation of the histone H2AX, carried out by ATM, ATR or DNA-PK. [5] The ring-shaped Ku heterodimer (entry under review) binds the broken ends too. [8][9] Which factors act next helps decide how the break will be repaired.

05 / Pathway choice

How a repair pathway is chosen

The choice between repair pathways depends on two things: the stage of the cell cycle and the structure of the broken ends. [2]

A key decision point is end resection: nucleases trim back the 5′ strand at each end, exposing 3′ single-stranded DNA. Starting resection directs a break towards repair that relies on homologous sequence and away from classical NHEJ. [2] Resection is not the same as choosing homologous recombination, though. Resected ends can also be used by single-strand annealing and alternative end joining. [10][2][4]

Resection is tied to the cell cycle. CDK is proposed to control resection through CtIP: in human cells, mutating its CDK site Thr-847 impairs resection. [11] Homologous recombination is generally restricted to S and G2, when a sister chromatid can serve as the template. [3][2]

Two groups of proteins compete at the break. In G1, 53BP1 (entry under review) and its effector RIF1 (entry under review) limit the accumulation of BRCA1 at breaks. In S and G2, BRCA1 and CtIP oppose RIF1. [12] Downstream of 53BP1 and RIF1, the shieldin complex (entry under review) acts at breaks. Loss of shieldin restores homologous recombination in BRCA1-deficient cells, which shows that this balance can be shifted. [13]

A balance, not a switch

NHEJ does not wait for G1. It repairs most double-strand breaks in mammalian cells and works throughout the cell cycle. [10][9] The phases of the cell cycle shift the balance between pathways; they do not assign each break to one pathway.

06 / At a glance

Homologous recombination and NHEJ compared

The two main pathways differ in what they need and in what they leave behind. The comparison below simplifies both. Each row has exceptions that the mechanism pages explain.

Comparison of homologous recombination and non-homologous end joining
Homologous recombination (HR)Non-homologous end joining (NHEJ)
TemplateCopies an intact homologous molecule, after homology search and strand invasion. [14][15][16]None. The two ends are joined directly. [10]
Cell cycleMainly S and G2, when a sister chromatid is present. [3][2]Throughout the cell cycle. [10][9]
End resectionRequires extensive 5′→3′ resection. [2]Ku binds and shields the ends, inhibiting resection. [9] No extensive resection is needed; the Artemis–DNA-PKcs complex can remove a short stretch, typically fewer than 20 nucleotides. [10]
AccuracyTemplate-directed, but outcomes differ: crossovers can cause loss of heterozygosity and chromosomal translocations, [15] and break-induced replication is associated with genomic instability. [17]Can rejoin compatible ends precisely. Ends that need processing can lose or gain nucleotides; accuracy depends on the end structure. [18]
Core proteinsMRN, CtIP, EXO1, RPA, BRCA1, PALB2, BRCA2, RAD51Ku70/Ku80, DNA-PKcs, XRCC4, XLF, DNA ligase IV

The same break, repaired two ways

The figure follows one break through each pathway, stage by stage. On the left, homologous recombination in the SDSA route; on the right, canonical NHEJ at compatible ends. Each scene is the full mechanism from its own article, shown only at the steps that can be compared.

Same break. Two repair pathways.HR (SDSA) · canonical NHEJ
HR

Homologous recombination

NHEJ

Non-homologous end joining

HR · The break

A double-strand break. An intact sister chromatid lies alongside: it exists only after DNA replication.

NHEJ · The break

The same break. Canonical NHEJ will not need a second DNA molecule.

Schematic: the two scenes share stages, not a biological clock, and each simplifies its pathway. Sartori et al. · 2007 Chang et al. · 2017

Interactive comparisonMade with Molecular Motion
Read the comparison stage by stage 5 stages

  1. The break

    HR: A double-strand break. An intact sister chromatid lies alongside: it exists only after DNA replication.

    NHEJ: The same break. Canonical NHEJ will not need a second DNA molecule.

    Sartori et al. · 2007Chang et al. · 2017

  2. First proteins

    HR: The MRN complex binds the broken ends.

    NHEJ: A ring-shaped Ku heterodimer binds each broken end.

    Symington & Gautier · 2011Tan et al. · 2023

  3. The decision point

    HR: Resection removes the 5′ strand at each end, exposing 3′ single-stranded tails. Starting resection directs the break towards repair that relies on homologous sequence.

    NHEJ: Ku shields the ends and inhibits resection, and the two ends are brought together.

    Symington & Gautier · 2011Tan et al. · 2023Graham et al. · 2016

  4. Template or direct join

    HR: The resected end invades the intact sister chromatid, forming a D-loop: the template that repair will copy.

    NHEJ: XRCC4–DNA ligase IV and XLF gather at the break to join the ends directly.

    Paliwal et al. · 2014Sneeden et al. · 2013Ahnesorg et al. · 2006

  5. Repaired

    HR: DNA synthesis on the template restores the sequence at the break; in this SDSA route no DNA is exchanged.

    NHEJ: The ends are joined without a template. Compatible ends like these can be rejoined precisely.

    Paliwal et al. · 2014Bétermier et al. · 2014
MechanismHomologous recombination

How a broken end is resected, coated with RAD51 and used to copy a template, step by step.

Mechanism · in preparationNon-homologous end joining

How Ku, DNA-PKcs and DNA ligase IV hold two ends together and join them without a template.

07 / Other routes

Other ways to join a break

Two further pathways act on resected ends. Alternative end joining, in which DNA polymerase θ (entry under review) is important, uses short stretches of matching sequence (microhomology), and its microhomology-mediated form is error-prone. [10][19] Single-strand annealing, which depends on RAD52 (entry under review) annealing larger regions of homology, is nonconservative and prone to generating deletions and translocations. [10][1] They become especially important when homologous recombination fails: HR-deficient tumour cells depend on polymerase θ-mediated repair. [19]

08 / Failure

When repair fails

Defects in either main pathway have consequences. Defects in NHEJ proteins increase sensitivity to radiation in cell lines and mouse models, and NHEJ deficiency causes (severe) combined immunodeficiency, because lymphocytes depend on the pathway for V(D)J recombination. [10][9] When homologous recombination is impaired, the result is described as homologous recombination deficiency (HRD), a concept with its own article.

Connections

Where this fits.

Molecular entries

The lesion

Sensing & signalling

Pathway choice & resection control

Other end-joining and annealing routes

Follow the evidence

References & further reading

  1. Mehta & Haber · 2014Sources of DNA double-strand breaks and models of recombinational DNA repair
  2. Symington & Gautier · 2011Double-strand break end resection and repair pathway choice
  3. Sartori et al. · 2007Human CtIP promotes DNA end resection
  4. Ceccaldi et al. · 2016Repair pathway choices and consequences at the double-strand break
  5. Jackson & Bartek · 2009The DNA-damage response in human biology and disease
  6. Scully et al. · 2019DNA double-strand break repair-pathway choice in somatic mammalian cells
  7. Ma et al. · 2002Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination
  8. Walker et al. · 2001Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair
  9. Tan et al. · 2023Double-strand DNA break repair: molecular mechanisms and therapeutic targets
  10. Chang et al. · 2017Non-homologous DNA end joining and alternative pathways to double-strand break repair
  11. Huertas & Jackson · 2009Human CtIP mediates cell cycle control of DNA end resection and double strand break repair
  12. Escribano-Díaz et al. · 2013A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice
  13. Noordermeer et al. · 2018The shieldin complex mediates 53BP1-dependent DNA repair
  14. Wright et al. · 2018Homologous recombination and the repair of DNA double-strand breaks
  15. Paliwal et al. · 2014Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing
  16. Sneeden et al. · 2013Reconstitution of recombination-associated DNA synthesis with human proteins
  17. Kramara et al. · 2018Break-induced replication: the where, the why, and the how
  18. Bétermier et al. · 2014Is non-homologous end-joining really an inherently error-prone process?
  19. Ceccaldi et al. · 2015Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair
  20. Ahnesorg et al. · 2006XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining
  21. Graham et al. · 2016Two-stage synapsis of DNA ends during non-homologous end joining

Every statement on this page is recorded with its supporting references in the page's evidence ledger.