Homologous recombination
Homologous recombination repairs a broken DNA molecule by copying the missing information from an intact one. Follow the break from end resection to a restored chromosome.
01 / The pathway
What homologous recombination does
Homologous recombination (HR) repairs a DNA double-strand break using an intact DNA molecule with the same sequence as a template. The broken end searches for that sequence, invades it and uses it to copy what was lost, and the chromosome is restored. [1][2][3] The pathway passes through several intermediates that can be reversed, which helps it repair breaks accurately. [1]
HR protects the genome, and mutations in HR proteins such as BRCA1, BRCA2 and PALB2 are associated with cancer. [4] Related recombination processes also restart broken replication forks and maintain eroded telomeres. [5]
02 / Context
When cells use homologous recombination
HR needs a template, and after DNA replication the identical sister chromatid provides one. HR is generally restricted to the S and G2 phases. [6][7] CDK is proposed to control resection through CtIP: in human cells, mutating its CDK site Thr-847 impairs resection. [8] How cells choose between HR and other pathways is covered in the overview of double-strand break repair.
03 / The mechanism
The mechanism, step by step
The interactive figure follows one route through HR, synthesis-dependent strand annealing (SDSA), in four chapters. It is a model of one outcome, not the only one: other ways of completing HR are described below. [2]
One route through homologous recombination: synthesis-dependent strand annealing. Shapes, distances and timing are schematic.
Read the complete repair sequence 13 steps
Begin with a break across both DNA strands. A second DNA molecule represents the sister chromatid that will provide the repair template.
The MRN complex is placed at the broken ends. The scene introduces the damage-sensing machinery before the DNA is processed.
Processing the 5′ ends exposes short 3′ single-stranded tails. The example places BRCA1 alongside MRN to introduce this early phase of repair.
CtIP is important for resection but is omitted from this simplified scene. BRCA1 is not the nuclease doing the cutting.
The example uses EXO1 to extend resection. Follow the exposed tails: their polarity matters for the later DNA synthesis step.
One route is illustrated; alternative resection machinery is not shown.
RPA occupies the exposed single-stranded DNA. In this model, the early resection actors leave the scene so the change in DNA occupancy is easier to follow.
The number and spacing of protein copies are schematic.
BRCA2 helps RAD51 assemble on single-stranded DNA that is occupied by RPA. Watch the right-hand tail: the first RAD51 units take the place of RPA.
More RAD51 units assemble on the tail. This protein–DNA filament prepares the strand for engagement with a homologous DNA template.
The scene aligns the RAD51-coated tail with the sister chromatid. It separates template engagement from strand pairing so each event can be inspected.
Alignment is illustrative; the model does not simulate a physical homology search.
The exposed strand pairs with the complementary strand of the sister chromatid. The other sister strand is displaced locally, creating a D-loop intermediate.
A DNA polymerase can extend the invading 3′ end using the sister chromatid as a template. Newly drawn DNA represents synthesis, rather than movement of an existing strand.
Accessory factors such as PCNA and RFC are omitted from the scene.
In the SDSA route shown here, the extended strand leaves the sister chromatid. The template duplex closes again.
The extended strand pairs with the complementary tail at the other end of the original break. The two sides can now be reconnected.
Gap filling and sealing finish the schematic repair. The ending belongs to the SDSA route; other homologous recombination outcomes are outside this example.
1. Recognising and preparing the break
The MRN complex (MRE11, RAD50 and NBS1) binds the broken ends. [7] Together with CtIP (entry under review), it starts end resection: the 5′ strand at each end is removed, exposing a 3′ single-stranded tail. [6] The tails created by MRN and CtIP are then extended by EXO1, or by the BLM helicase and the nuclease DNA2 acting in a complex (DNA2–BLM (entry under review)). [9] This scheme was worked out mainly in budding yeast, and initiation and extension are not necessarily separate phases. [7]
BRCA1 does not cut DNA itself. With CtIP, it opposes 53BP1 and RIF1 at breaks. [10] In Brca1-deficient mouse cells, deleting 53BP1 largely restored HR, which the authors attribute to 53BP1 partially blocking resection. [11]
2. Protecting the single-stranded DNA
The exposed single-stranded DNA is quickly coated by RPA. RPA protects the DNA, but it must be replaced by the recombinase RAD51 before repair can continue. [12]
3. Building the RAD51 filament: BRCA1, PALB2 and BRCA2
PALB2 (entry under review) physically links BRCA1 to BRCA2. BRCA1 helps bring PALB2 and BRCA2 to sites of damage, and the BRCA1–PALB2 interaction is needed for HR. [13] BRCA2 then helps RAD51 assemble on the RPA-coated DNA, forming a protein–DNA filament. [12]
4. Homology search and strand invasion
The RAD51 filament searches for a matching sequence, usually on the sister chromatid. When it finds one, the single-stranded end pairs with the complementary strand of the template and displaces the other strand, forming a D-loop. [2][3] The interactive figure aligns the two molecules for clarity; it does not simulate the physical search.
5. Copying the template
A DNA polymerase, polymerase δ in reconstitution experiments with human proteins, extends the invading 3′ end using the template, restoring the sequence lost at the break. [3]
04 / Outcomes
Different ways to finish repair
After DNA synthesis, HR can finish in more than one way. The intermediates differ, and so can the outcomes. [1]
- Synthesis-dependent strand annealing (SDSA)
- The extended strand leaves the template and anneals to the other side of the break, and the gaps are filled. This is the route the interactive figure follows. In the standard model it gives non-crossover products, and in human cells it is promoted by the RECQ5 helicase. [2][14]
- Double Holliday junctions
- If the second end of the break is also captured, the two molecules can become joined by a double Holliday junction. BLM and topoisomerase IIIα can dissolve it without exchanging the DNA on either side. [15][2] Alternatively, nucleases can resolve the junction by cutting it, which can produce a crossover. [2][14]
- Break-induced replication (BIR)
- When only one end of a break shares homology with a template, as at a collapsed replication fork or in the lengthening of telomeres, cells rely on break-induced replication, in which the invading strand copies the template. In budding yeast, BIR is remarkably mutagenic compared with normal replication. [14] BIR also acts at eroded telomeres; its synthesis is unusual and is associated with genomic instability. [5]
05 / Accuracy
How accurate is homologous recombination?
HR copies a template, and when that template is the identical sister chromatid, repair is usually accurate. [1] It is not error-free in every case. Crossovers are one source of risk: in mitotic cells, crossover outcomes are suppressed, which prevents loss of heterozygosity and chromosomal translocations. [2] Dissolution of double Holliday junctions avoids exchanging the DNA flanking the break. [15] Break-induced replication is associated with genomic instability. [5]
06 / Failure
What happens when homologous recombination fails?
If any of these steps cannot be carried out, for example because BRCA1 or BRCA2 has lost its function, breaks must be handled in other ways. Impaired HR function is called homologous recombination deficiency.
Connections
Where this fits.
Molecular entries
End resection
- MRE11Meiotic recombination 11 homolog
- RAD50RAD50 double-strand break repair proteinEntry under review
- NBS1Nibrin (NBN)Entry under review
- CtIPCtBP-interacting protein (RBBP8)Entry under review
- EXO1Exonuclease 1
- DNA2–BLMDNA2 nuclease–helicase with BLM helicaseEntry under review
- BRCA1Breast cancer type 1 susceptibility protein
Single-stranded DNA and the RAD51 filament
Completing repair
- Strand invasionHomology search and strand invasionEntry under review
- SynthesisRepair DNA synthesisEntry under review
- ResolutionResolution of recombination intermediatesEntry under review
Follow the evidence
References & further reading
- Wright et al. · 2018Homologous recombination and the repair of DNA double-strand breaks
- Paliwal et al. · 2014Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing
- Sneeden et al. · 2013Reconstitution of recombination-associated DNA synthesis with human proteins
- Moynahan & Jasin · 2010Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis
- Kramara et al. · 2018Break-induced replication: the where, the why, and the how
- Sartori et al. · 2007Human CtIP promotes DNA end resection
- Symington & Gautier · 2011Double-strand break end resection and repair pathway choice
- Huertas & Jackson · 2009Human CtIP mediates cell cycle control of DNA end resection and double strand break repair
- Chang et al. · 2017Non-homologous DNA end joining and alternative pathways to double-strand break repair
- Escribano-Díaz et al. · 2013A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice
- Bunting et al. · 201053BP1 inhibits homologous recombination in Brca1-deficient cells by blocking resection of DNA breaks
- Jensen et al. · 2010Purified human BRCA2 stimulates RAD51-mediated recombination
- Zhang et al. · 2009PALB2 links BRCA1 and BRCA2 in the DNA-damage response
- Mehta & Haber · 2014Sources of DNA double-strand breaks and models of recombinational DNA repair
- Wu & Hickson · 2003The Bloom’s syndrome helicase suppresses crossing over during homologous recombination
Every statement on this page is recorded with its supporting references in the page's evidence ledger.