Homologous recombination (HR) is the high-fidelity repair pathway for DNA double-strand breaks (DSBs), operating exclusively in S/G2 phase when a sister chromatid template is available. HR uses the intact homologous sequence to restore the original base sequence without error — in contrast to non-homologous end joining (NHEJ), which can introduce deletions and mutations at repair junctions. The HR pathway is orchestrated by BRCA1, BRCA2, and RAD51, and its loss defines a class of tumours ('BRCAness') with characteristic genomic scars and exquisite sensitivity to PARP inhibitors through synthetic lethality.
HR begins with DSB detection by MRN, which recruits ATM and promotes 5′→3′ DNA end resection to generate 3′ single-stranded DNA (ssDNA) overhangs. RPA covers ssDNA to prevent secondary structure formation. BRCA1 (recruited via ubiquitin/RAP80 cascade) bridges to PALB2, which recruits BRCA2. BRCA2 displaces RPA and loads RAD51 monomers onto ssDNA, forming a nucleoprotein filament. The RAD51-ssDNA filament performs strand invasion of the homologous duplex sister chromatid, using it as a template for accurate DNA synthesis before resolution and ligation.
HR begins with DSB detection by MRN, which recruits ATM and promotes 5′→3′ DNA end resection to generate 3′ single-stranded DNA (ssDNA) overhangs. RPA covers ssDNA to prevent secondary structure formation. BRCA1 (recruited via ubiquitin/RAP80 cascade) bridges to PALB2, which recruits BRCA2. BRCA2 displaces RPA and loads RAD51 monomers onto ssDNA, forming a nucleoprotein filament. The RAD51-ssDNA filament performs strand invasion of the homologous duplex sister chromatid, using it as a template for accurate DNA synthesis before resolution and ligation.
Homologous Recombination Repair
Replication protein A (RPA) coats 3′ ssDNA overhangs, preventing secondary structure and activating ATR kinase. HR is restricted to S/G2 phase by CDK1/2-mediated phosphorylation of CtIP, ensuring the sister chromatid template is present before HR is initiated.
BRCA1 (recruited via RNF168 ubiquitin cascade and RAP80) directly binds PALB2 via its coiled-coil domain. PALB2 acts as a molecular bridge to BRCA2, co-localising BRCA2 with the ssDNA substrate. This three-component assembly (BRCA1–PALB2–BRCA2) is the central scaffold of the HR repair complex.
BRCA2 (with DSS1) displaces RPA from ssDNA and loads RAD51 monomers in an ATP-dependent reaction, forming a right-handed helical RAD51-ssDNA nucleoprotein filament. This filament has the capacity to search homologous duplex DNA sequences over megabase distances.
The RAD51-ssDNA filament performs strand invasion of the intact sister chromatid at the homologous sequence, forming a displacement loop (D-loop). The 3′ ssDNA end within the D-loop serves as primer for DNA synthesis using the sister chromatid as error-free template.
DNA Pol δ/ε extends the invaded strand using the sister chromatid template. After second end capture (double-strand break repair pathway) or dissolution (synthesis-dependent strand annealing, SDSA), Holiday junctions are resolved by GEN1/MUS81-EME1 or dissolved by BLM-TOP3α-RMI1/2, restoring the original sequence with high fidelity.
BRCA1/2 germline mutations confer 50–70% lifetime breast cancer risk and 40–45% ovarian cancer risk. HR deficiency (HRD) — from BRCA1/2 mutation, BRCA1 promoter methylation, or other HR gene mutations (PALB2, RAD51C, RAD51D, ATM) — defines the 'BRCAness' phenotype, characterised by a specific genomic scar signature (SBS3, large-scale state transitions, telomeric allelic imbalance). HRD-positive tumours accumulate structural variants (deletions, tandem duplications) rather than point mutations as their primary mutation class.
PARP inhibitors (olaparib, niraparib, rucaparib, talazoparib) exploit synthetic lethality with HR deficiency. In BRCA1/2-deficient cells, PARP inhibition traps PARP1 on SSB repair intermediates as covalent PARP-DNA complexes. Replication forks collide with these complexes, generating DSBs that HR-deficient cells cannot accurately repair, leading to mitotic catastrophe and cell death. PARP inhibitors are approved for germline BRCA1/2-mutant breast, ovarian, pancreatic, and prostate cancers.
What is the difference between HR and NHEJ for DSB repair?
Homologous recombination (HR) uses the sister chromatid as a template to restore the exact original sequence, operating in S/G2 phase. Non-homologous end joining (NHEJ) directly ligates broken DNA ends without a template, operating throughout the cell cycle (dominant in G1) but introducing small deletions or insertions at repair junctions. HR is error-free; NHEJ is error-prone but rapid. BRCA1 loss shifts DSB repair from HR to NHEJ/MMEJ, causing characteristic structural variants.
What is PARP trapping and why does it differ from catalytic PARP inhibition?
Catalytic PARP inhibition simply reduces PARP enzymatic activity (NAD+ consumption). PARP trapping — the more cytotoxic mechanism of current PARP inhibitors — involves the inhibitor stabilising the PARP1-DNA complex after nick detection, preventing PARP release and creating a physical 'roadblock' on DNA that is lethal when encountered by a replication fork. Talazoparib is the most potent PARP trapper; niraparib and olaparib have intermediate trapping; veliparib has poor trapping despite catalytic inhibition.
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Content is based on peer-reviewed scientific literature including data from NCBI, UniProt, PubMed, and TCGA. Gene links reference curated molecular biology databases. For educational purposes only; does not constitute clinical advice.