Homologous recombination repair of DNA double-strand breaks — MRN-CtIP and EXO1/BLM-DNA2 end resection, RPA coating, BRCA1-PALB2-BRCA2 and RAD51-paralog loading of RAD51, strand invasion with RAD54, D-loop extension, and BTR dissolution versus SLX4-MUS81/GEN1 resolution; MRE11/RAD50/NBN/RBBP8/EXO1/BLM/DNA2/RPA/BRCA1/PALB2/BRCA2/RAD51B/RAD51C/RAD51D/XRCC2/XRCC3/RAD51/RAD54L/RAD54B

Homologous recombination (HR) repairs a DNA double-strand break (DSB) by copying the missing information from an intact homologous duplex, normally the sister chromatid, and is therefore restricted to the S and G2 phases of the cell cycle. Once the upstream ATM signalling cascade has marked the break and BRCA1 has displaced 53BP1-RIF1, the DNA ends are resected to expose 3' single-stranded tails. Resection begins with short-range processing by the MRE11-RAD50-NBN (MRN) complex, whose MRE11 endonuclease, stimulated by phosphorylated CtIP (RBBP8), nicks the 5'-terminated strand at a distance from the end and MRE11 3'-5' exonuclease then degrades back toward the break. Long-range resection extends the tail over kilobases through either of two machineries: the 5'-3' exonuclease EXO1, or the RecQ helicase BLM (or WRN) unwinding the duplex while the DNA2 nuclease degrades the 5' strand. The heterotrimeric single-stranded DNA binding protein RPA coats the exposed tails, removing secondary structure and protecting them. BRCA1 binds PALB2, which in turn binds BRCA2; BRCA2 delivers RAD51 to the RPA-coated DNA and stabilises nascent RAD51 filaments, and the RAD51 paralog complexes BCDX2 (RAD51B-RAD51C-RAD51D-XRCC2) and CX3 (RAD51C-XRCC3) assist RAD51 nucleation and filament stability. The RAD51-ssDNA presynaptic filament searches for homology and invades the donor duplex, forming a displacement loop (D-loop); the Swi2/Snf2-family translocases RAD54 (RAD54L) and RAD54B promote homologous pairing and remodel the D-loop. The invading 3' end is extended by DNA polymerase delta, with polymerase eta able to initiate synthesis on D-loops. The D-loop can then be resolved by synthesis-dependent strand annealing, by break-induced replication, or by second-end capture to form a double Holliday junction. Double Holliday junctions are either dissolved into non-crossover products by the BLM-TOP3A-RMI1-RMI2 (BTR) dissolvasome, or cleaved by the structure-specific endonucleases SLX1-SLX4, MUS81-EME1 and GEN1, which can give crossovers.

MODULE:homologous_recombination_dsb_repairDRAFTCONCRETEBiological Processmodules/homologous_recombination_dsb_repair.yaml
double-strand break repair via homologous recombinationGO:0000724
PW:0000202
homologous recombination pathway of double-strand break repair
The module boundary follows the RGD Pathway Ontology term and its diagram. The diagram draws Brca1 associated with the MRN complex and with Rbbp8 (CtIP), the resection components MRN, Rbbp8, Blm, Exo1 and Dna2, the RPA complex coating single-stranded DNA, Rad51 associated with the "Rad51 paralogs/mediators" box, and Rad54b promoting D-loop formation and DNA synthesis; the ATM signalling pathway (PW:0001361) is the upstream diagram link. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0000202.yaml).
GO:0000724
double-strand break repair via homologous recombination
Mapped to PW:0000202 (skos:relatedMatch, from the PW definition cross-reference) in projects/RGD_PATHWAY_ONTOLOGY/data/module_seeds.yaml; used as the module's process concept.
gomodel:65a1f4f800000855
Initiation of double-strand break repair via homologous recombination by the MRN complex (MRE11-RAD50-NBN) (Human).
The project's best-overlap GO-CAM for PW:0000202 (cached under gocams/65a1f4f800000855/). It models RAD50 ATP hydrolysis directly positively regulating MRE11 DNA endonuclease and 3'-5' exonuclease activities, and MRE11 3'-5' exonuclease activity providing input for EXO1 5'-3' DNA exonuclease activity; the resection part of this module is grounded in it. Its ATM and NBN activation nodes belong to modules/atm_dsb_signaling.yaml.
PMID:21325134
BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair.
Long-range resection runs through two reconstituted machineries, which this module treats as a variant set.
Resection occurs via two routes. In one, BLM and DNA2 physically and specifically interact to resect DNA in a process that is ATP-dependent and requires BLM helicase and DNA2 nuclease functions.
PMID:20729832
Purified human BRCA2 stimulates RAD51-mediated recombination.
BRCA2 is the mediator that loads RAD51 onto RPA-coated ssDNA.
BRCA2 acts by targeting RAD51 to ssDNA over double-stranded DNA, enabling RAD51 to displace replication protein-A (RPA) from ssDNA and stabilizing RAD51-ssDNA filaments by blocking ATP hydrolysis.
PMID:14685245
The Bloom's syndrome helicase suppresses crossing over during homologous recombination.
Double Holliday junctions are processed either by BLM-TOP3A dissolution or by classical resolution.
The mechanism, which we term double-junction dissolution, is distinct from classical Holliday junction resolution and prevents exchange of flanking sequences.

Derived from the RGD Pathway Ontology diagram PW:0000202 through the RGD_PATHWAY_ONTOLOGY project's diagram->module route (seed in projects/RGD_PATHWAY_ONTOLOGY/data/module_seeds.yaml, tier related_module_only; related modules atm_dsb_signaling and bacterial_recbcd_end_resection). RGD curates 16 human genes to PW:0000202: BLM BRCA1 BRCA2 DNA2 EXO1 MRE11 NBN RAD50 RAD51 RAD51B RAD51C RAD51D RAD54B RBBP8 XRCC2 XRCC3. All sixteen are modelled as participants. Fifteen gene products not on the RGD list are added because the RGD diagram or description names their role but the gene list omits them: the RPA heterotrimer (RPA1, RPA2, RPA3; drawn as the "Rpa complex"), PALB2 (named in the RGD text as linking BRCA1 and BRCA2, "not shown"), WRN (second RecQ partner of DNA2), RAD54L (the principal RAD54 paralog; RGD lists only RAD54B), the D-loop polymerases (POLD1 and POLD3 of pol delta, and POLH; RGD says only that Rad54b "promotes DNA synthesis"), and the double Holliday junction processing enzymes (TOP3A, RMI1, RMI2, SLX4, SLX1A, MUS81, GEN1; RGD says the HR sub-types are "details not shown"). EME1 and POLD2 are named in prose as partners only. Molecular functions were taken from each protein's experimental GO annotations in QuickGO (November 2026) and, where a gene review exists (BLM, BRCA1, BRCA2, RAD51, RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, PALB2, SLX4, POLD2), checked against its core functions. Boundary decisions. (1) Upstream signalling is not re-modelled. Part 1 is a module_ref to atm_dsb_signaling#brca1_a_arm, the BRCA1-A arm of the pathway-choice node of the ATM module (PW:0001361, which RGD links from the HR diagram and which is mentioned here but not listed as an evidence source). The MRN complex appears in both modules in different roles: as the ATM activator (GO:0043539) in atm_dsb_signaling and as the resection nuclease here. RBBP8 (CtIP) was excluded from the ATM module as "the first step of the HR reaction" and is a participant here, so the two modules are consistent. The ATM module's notes still say that no human HR or NHEJ module exists; that sentence is now out of date. The part is optional because resection and RAD51 loading proceed without the reader competition when 53BP1 is absent. (2) Long-range resection is a ROUTE variant set (EXO1 versus BLM/WRN-DNA2), ONE_OR_MORE, following the reconstitution in PMID:21325134. (3) RPA is a participant, not merely a substrate-binding bystander: it enforces resection polarity, is required for BLM unwinding and is a cofactor of dissolution (PMID:23543748). (4) Mediators. BRCA1 is given an annoton without a molecular function: its experimental MF rows (ubiquitin protein ligase, DNA binding, phosphoprotein binding) belong to other roles, and no GO MF fits its PALB2-recruiting role. BARD1 is not modelled here; it is in the BRCA1-A complex of the referenced ATM node. BRCA2 carries GO:0140619 DNA strand exchange activator activity, the core function of the BRCA2 gene review, although the cached GO-CAMs (gomodel:69a0c46f00002570, gomodel:69a0c46f00002608) type the same activity as protein-macromolecule adaptor activity. (5) RAD51 paralogs are modelled as the two in vivo complexes (PMID:11751635): BCDX2 with GO:0140619 (mediator activity shown for RAD51B-RAD51C, PMID:11751636) and CX3 with four-way junction DNA binding (contributes_to rows in GOA; PMID:20207730, PMID:14716019). The RAD51B review proposes a new "DNA recombinase loader activity" term that would fit BCDX2 better if created. Both are placed in the RAD51-loading part; CX3's later role in junction processing is in its role_description rather than as a separate part. (6) RAD54L and RAD54B are both annotons in the strand-invasion part, with GO:0008094 as in the GO-CAMs (gomodel:680ad14200006156, gomodel:680ad14200007322); RAD54B also has an IDA row for DNA translocase activity. (7) The D-loop polymerase is a REALIZER variant set (pol delta, pol eta). PCNA and RFC, which load pol delta, are context. (8) Double Holliday junction processing is a ROUTE variant set (BTR dissolution versus SLX1-SLX4-MUS81-EME1 and GEN1 resolution). Synthesis-dependent strand annealing (D-loop disruption by helicases such as RTEL1 and BLM, then annealing) and break-induced replication are named in the description but not modelled as separate parts; single-strand annealing (RAD52) is a distinct pathway and is excluded, as are meiotic recombination (SPO11, DMC1) and the replication-fork protection functions of BRCA1/BRCA2/RAD51. (9) No substrate is modelled as a participant; every annoton is an enzyme, a DNA-binding scaffold or a mediator, so the substrate-versus-participant comparator check is not triggered. (10) The seed's best GO-CAM, gomodel:65a1f4f800000855 (MRN initiation of HR), is genuinely on topic and is linked; its ATM and NBN adaptor nodes belong to the ATM module. modules/bacterial_recbcd_end_resection.yaml is the bacterial analogue of the resection steps and is not referenced. GO-CAM and GOA observations for upstream review. In gomodel:65a1f4f800000855 (a DSB repair model) the EXO1 activity is annotated to GO:0110025 DNA strand resection involved in replication fork processing, and the MRE11 and RBBP8 activities of gomodel:65a1f4f800001380 use the same fork term; GO:0000729 DNA double-strand break processing looks like the intended process. In gomodel:613aae0000001005 a RAD51 single-stranded DNA binding activity is located in "presynaptic intermediate filament cytoskeleton", which looks like a mis-picked cellular component. GO:0000730 DNA recombinase assembly is part_of double-strand break repair via synthesis-dependent strand annealing in GO, which is narrower than its use for RAD51 loading in all HR sub-pathways here. No human gene product is annotated to GO:0043150 DNA synthesis involved in double-strand break repair via homologous recombination in QuickGO. RMI1 and RMI2 have no experimental molecular function rows. PANTHER family ids and PTNs are deliberately not asserted.

15Nodes
8Parts
3Variant Sets
6Variants
22Annotons
7Connections

Derived QC

Recommended-field compliance

30.8% recommended fields populated
  • knowledge_gaps[0] · boundary (0/1)
  • knowledge_gaps[0] · status (0/1)
  • knowledge_gaps[0] · provenance (0/1)
  • knowledge_gaps[1] · boundary (0/1)
  • knowledge_gaps[1] · status (0/1)
  • knowledge_gaps[1] · provenance (0/1)
  • knowledge_gaps[2] · boundary (0/1)
  • knowledge_gaps[2] · status (0/1)
  • knowledge_gaps[2] · provenance (0/1)

Module deep research

✗ none found

No MODULE:homologous_recombination_dsb_repair deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • short_range_resection → long_range_resection [NOT_CHECKED]
    DNA end intermediates, not CoA metabolites.
  • rad51_loading → strand_invasion [NOT_CHECKED]
    DNA-protein intermediates, not CoA metabolites.
  • d_loop_extension → junction_processing [NOT_CHECKED]
    DNA joint-molecule intermediates, not CoA metabolites.

Function consistency and core coverage

8 gene-function check(s) reflected in core functions · 0 conflict(s) · 18 evidence or coverage gap(s) (32 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
mrn_resection_nuclease PROTEIN_COMPLEX
Gene 		DNA endonuclease activity
GO:0004520 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
mrn_resection_nuclease/resection_mre11 MRE11
UniProtKB:P49959
Complex Unit 		DNA endonuclease activity
GO:0004520 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
mrn_resection_nuclease/resection_rad50 RAD50
UniProtKB:Q92878
Complex Unit 		ATP hydrolysis activity
GO:0016887 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
mrn_resection_nuclease/resection_nbn NBN
UniProtKB:O60934
Complex Unit 		chromatin-protein adaptor activity
GO:0140463 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ctip_resection RBBP8 (CtIP)
UniProtKB:Q99708
Gene 		single-stranded DNA endonuclease activity
GO:0000014 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
exo1_exonuclease EXO1
UniProtKB:Q9UQ84
Gene 		5'-3' DNA exonuclease activity
GO:0035312 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
blm_resection_helicase BLM
UniProtKB:P54132
Gene 		3'-5' DNA helicase activity
GO:0043138 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
wrn_resection_helicase WRN
UniProtKB:Q14191
Gene 		3'-5' DNA helicase activity
GO:0043138 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dna2_resection_nuclease DNA2
UniProtKB:P51530
Gene 		5'-flap endonuclease activity
GO:0017108 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpa_ssdna_binding PROTEIN_COMPLEX
Gene 		single-stranded DNA binding
GO:0003697 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
rpa_ssdna_binding/rpa_rpa1 RPA1
UniProtKB:P27694
Complex Unit 		single-stranded DNA binding
GO:0003697 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpa_ssdna_binding/rpa_rpa2 RPA2
UniProtKB:P15927
Complex Unit 		single-stranded DNA binding
GO:0003697 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rpa_ssdna_binding/rpa_rpa3 RPA3
UniProtKB:P35244
Complex Unit 		single-stranded DNA binding
GO:0003697 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
palb2_adaptor PALB2
UniProtKB:Q86YC2
Gene 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
brca2_mediator BRCA2
UniProtKB:P51587
Gene 		DNA strand exchange activator activity
GO:0140619 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bcdx2_mediator PROTEIN_COMPLEX
Gene 		DNA strand exchange activator activity
GO:0140619 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
bcdx2_mediator/bcdx2_rad51b RAD51B
UniProtKB:O15315
Complex Unit 		single-stranded DNA binding
GO:0003697 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
bcdx2_mediator/bcdx2_rad51d RAD51D
UniProtKB:O75771
Complex Unit 		single-stranded DNA binding
GO:0003697 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cx3_paralog_complex PROTEIN_COMPLEX
Gene 		four-way junction DNA binding
GO:0000400 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
rad51_strand_exchange RAD51
UniProtKB:Q06609
Gene 		DNA strand exchange activity
GO:0000150 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rad54l_translocase RAD54L
UniProtKB:Q92698
Gene 		ATP-dependent activity, acting on DNA
GO:0008094 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rad54b_translocase RAD54B
UniProtKB:Q9Y620
Gene 		ATP-dependent activity, acting on DNA
GO:0008094 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
pol_delta_d_loop PROTEIN_COMPLEX
Gene 		DNA-directed DNA polymerase activity
GO:0003887 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
pol_delta_d_loop/pold_pold1 POLD1
UniProtKB:P28340
Complex Unit 		DNA-directed DNA polymerase activity
GO:0003887 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
pol_eta_d_loop POLH
UniProtKB:Q9Y253
Gene 		DNA-directed DNA polymerase activity
GO:0003887 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
btr_dissolvasome PROTEIN_COMPLEX
Gene 		DNA topoisomerase type I (single strand cut, ATP-independent) activity
GO:0003917 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
btr_dissolvasome/btr_blm BLM
UniProtKB:P54132
Complex Unit 		four-way junction helicase activity
GO:0009378 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
btr_dissolvasome/btr_top3a TOP3A
UniProtKB:Q13472
Complex Unit 		DNA topoisomerase type I (single strand cut, ATP-independent) activity
GO:0003917 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
slx4_scaffold SLX4
UniProtKB:Q8IY92
Gene 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
slx1_resolvase SLX1A
UniProtKB:Q9BQ83
Gene 		crossover junction DNA endonuclease activity
GO:0008821 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
mus81_resolvase MUS81 (with EME1)
UniProtKB:Q96NY9
Gene 		crossover junction DNA endonuclease activity
GO:0008821 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
gen1_resolvase GEN1
UniProtKB:Q17RS7
Gene 		crossover junction DNA endonuclease activity
GO:0008821 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.

Gene-review completeness (13/32 grounded genes reviewed)

7 complete review(s) · 7 with deep research · 19 missing review · 6 reviewed but lacking deep research

Gene Review Complete Deep research
BLM P54132 ✓ 176/188 ✗
BRCA1 P38398 ✓ 249/275 ✓
BRCA2 P51587 ✓ 122/149 ✓
EXO1 Q9UQ84 ✓ ✓ ✗
NBN O60934 ✓ 259/260 ✗
RPA2 P15927 ✗ — —
RPA1 P27694 ✗ — —
POLD1 P28340 ✗ — —
RPA3 P35244 ✗ — —
MRE11 P49959 ✗ — —
DNA2 P51530 ✗ — —
PALB2 Q86YC2 ✓ ✓ ✓
TOP3A Q13472 ✗ — —
WRN Q14191 ✗ — —
POLD3 Q15054 ✗ — —
GEN1 Q17RS7 ✗ — —
RAD54L Q92698 ✗ — —
RAD50 Q92878 ✗ — —
RMI2 Q96E14 ✗ — —
MUS81 Q96NY9 ✗ — —
RBBP8 (CtIP) Q99708 ✗ — —
SLX1 Q9BQ83 ✗ — —
RMI1 Q9H9A7 ✗ — —
POLH Q9Y253 ✗ — —
RAD54B Q9Y620 ✗ — —
RAD51 Q06609 ✓ ✓ ✓
RAD51B O15315 ✓ ✓ ✗
RAD51C O43502 ✓ ✓ ✓
RAD51D O75771 ✓ 144/145 ✗
SLX4 Q8IY92 ✓ 58/59 ✓
XRCC2 O43543 ✓ ✓ ✓
XRCC3 O43542 ✓ ✓ ✗

Details

Context
Homo sapiensNCBITaxon:9606
site of double-strand breakGO:0035861
Homologous recombination repair of DNA double-strand breaksBiological Processhomologous_recombination_dsb_repair
double-strand break repair via homologous recombinationGO:0000724
Context
Homo sapiensNCBITaxon:9606
site of double-strand breakGO:0035861

Connections

BRCA1-CtIP displacement of 53BP1-RIF1 licenses resection; ATM and CDK phosphorylation of CtIP activates the MRN-CtIP nuclease.
MRN-CtIP clipping creates the entry point for EXO1 and BLM-DNA2 (MRE11 exonuclease directly provides input for EXO1 in gomodel:65a1f4f800000855).
long_range_resection -> rpa_coating Provides Input For
Resection exposes the 3' single-stranded tails that RPA binds.
rpa_coating -> rad51_loading Provides Input For
Mediators load RAD51 onto RPA-coated ssDNA and displace RPA.
The RAD51-ssDNA presynaptic filament performs homology search and invasion.
strand_invasion -> d_loop_extension Provides Input For
The invading 3' end in the D-loop is the primer for repair synthesis.
Extension and second-end capture generate the double Holliday junction processed in the last step.
Part 1: upstream DSB signalling and BRCA1-dependent commitment to resection (optional)
ATM signalling and BRCA1 displacement of 53BP1-RIF1 (by reference)hr_upstream_signalling

Included by reference to the HR-favouring BRCA1-A arm of the ATM DSB signalling module, whose upstream parts model MRN sensing, ATM activation, gammaH2AX-MDC1 amplification and the RNF8/RNF168 ubiquitin cascade. Marked optional because the reaction steps below can proceed without the reader competition when 53BP1 is absent, and because ATR and DNA-PK partly substitute for ATM.

Realized by module atm_dsb_signaling#brca1_a_arm

PMID:17965729
CtIP-dependent resection is restricted to S and G2 and is needed for RPA loading and HR.
Moreover, we reveal that CtIP is required for DSB resection, and thereby for recruitment of replication protein A (RPA) and the protein kinase ATR to DSBs, and for the ensuing ATR activation.
Part 2: short-range end resection by MRN-CtIP
MRN-CtIP short-range resection (MRE11 endonuclease and 3'-5' exonuclease)Reactionshort_range_resection

Phosphorylated CtIP stimulates the MRE11 endonuclease within MRN to nick the 5'-terminated strand internally; MRE11 3'-5' exonuclease then degrades back toward the end, removing protein-blocked ends and creating the entry site for long-range resection.

DNA double-strand break processingGO:0000729

Annotons

MRN complex DNA endonuclease activity at DSB ends
mrn_resection_nuclease
Participant: Protein Complex: MRE11-RAD50-NBN (MRN) complex
Protein Complex:
MRE11-RAD50-NBN (MRN) complexGO:0030870
Active units:
MRE11 nuclease subunit
Participant: Gene Product: MRE11
Gene Product:
MRE11UniProtKB:P49959
Role: Endonuclease and 3'-5' exonuclease that initiates resection.
Function:
DNA endonuclease activityGO:0004520
RAD50 ATPase subunit
Participant: Gene Product: RAD50
Gene Product:
RAD50UniProtKB:Q92878
Role: ATP hydrolysis drives the conformational change that licenses MRE11 nuclease activity.
Function:
ATP hydrolysis activityGO:0016887
NBN subunit
Participant: Gene Product: NBN
Gene Product:
NBNUniProtKB:O60934
Role: Required for MRN endonucleolytic processing of protein-blocked ends and for CtIP binding.
Function:
chromatin-protein adaptor activityGO:0140463

Function

DNA endonuclease activityGO:0004520

Processes

DNA double-strand break processingGO:0000729

Locations

site of double-strand breakGO:0035861

The same MRN complex that activates ATM (modelled in atm_dsb_signaling); here its nuclease role. MRE11 3'-5' exonuclease (GO:0008296 in the GO-CAMs) completes the short-range step.

PMID:27814491
Human MRN performs sequential endo- and exonucleolytic processing of blocked ends, stimulated by phosphorylated CtIP.
Here we show that hMRN catalyzes sequential endonucleolytic and exonucleolytic activities on both 5' and 3' strands of DNA ends containing protein adducts, and that Nbs1, ATP, and adducts are essential for this function.
CtIP (RBBP8) stimulation of the MRE11 endonuclease
ctip_resection
Participant: Gene Product: RBBP8 (CtIP)
Gene Product:
RBBP8 (CtIP)UniProtKB:Q99708

Function

single-stranded DNA endonuclease activityGO:0000014
Targets: MRE11UniProtKB:P49959

Processes

DNA double-strand break processingGO:0000729

Locations

site of double-strand breakGO:0035861

CDK- and ATM/ATR-phosphorylated CtIP binds NBN and BRCA1 and acts as the co-factor that switches on MRE11 endonuclease cleavage. Its own nuclease activity (the function asserted, following the GO-CAM and GOA IMP rows) is less certain than its co-factor role.

PMID:17965729
CtIP binds the MRE11 complex and both are required for HR.
Furthermore, we establish that CtIP physically and functionally interacts with the MRE11 complex, and that both CtIP and MRE11 are required for efficient homologous recombination.
PMID:27814491
Phosphorylated CtIP stimulates hMRN endonucleolytic cleavage.
The hMRN endonucleolytic cleavage events are further stimulated by the phosphorylated form of the human C-terminal binding protein-interacting protein (CtIP) DNA repair enzyme, establishing a role for CtIP in regulating hMRN activity.
Part 3: long-range end resection
Long-range 5'-3' resection by EXO1 or by RecQ helicase-DNA2Reactionlong_range_resection

From the MRN-CtIP entry site, kilobase-long 3' tails are generated by either of two machineries, both stimulated by MRN and RPA.

DNA double-strand break processingGO:0000729
Variant set: EXO1 versus BLM/WRN-DNA2 long-range resection by resection machinery [Route] (One Or More)

The two routes act in parallel and are partly redundant in cells; loss of both is needed to abolish long-range resection. ONE_OR_MORE because both can operate on the same break.

EXO1 5'-3' exonuclease routeReactionexo1_resection

Annotons

EXO1 5'-3' DNA exonuclease activity
exo1_exonuclease
Participant: Gene Product: EXO1
Gene Product:
EXO1UniProtKB:Q9UQ84

Function

5'-3' DNA exonuclease activityGO:0035312

Processes

DNA double-strand break processingGO:0000729

Locations

site of double-strand breakGO:0035861

Degrades the 5'-terminated strand of double-stranded DNA; its processivity is enhanced by MRN and its end affinity by BLM.

PMID:10608837
Human EXO1 has robust 5'-3' exonuclease activity on double-stranded DNA.
the RAD2 domain of human exonuclease 1 (HEX1-N2) exhibits both a robust 5' to 3' exonuclease activity on single- and double-stranded DNA substrates as well as a flap structure-specific endonuclease activity
PMID:21325134
EXO1 resection is stimulated by BLM, MRN and RPA.
In the other, EXO1 resects the DNA and is stimulated by BLM, MRN, and RPA.
BLM (or WRN) helicase with DNA2 nuclease routeReactionrecq_dna2_resection

Annotons

BLM 3'-5' DNA helicase unwinding of the break end
blm_resection_helicase
Participant: Gene Product: BLM
Gene Product:
BLMUniProtKB:P54132

Function

3'-5' DNA helicase activityGO:0043138

Processes

DNA double-strand break processingGO:0000729

Locations

site of double-strand breakGO:0035861

Unwinds the duplex end so that DNA2 can degrade the displaced 5' strand; RPA is essential for unwinding and for resection polarity.

PMID:21325134
RPA is essential for BLM unwinding and DNA2 5'-3' polarity; MRN recruits BLM.
RPA is essential for both DNA unwinding by BLM and enforcing 5' → 3' resection polarity by DNA2. MRN accelerates processing by recruiting BLM to the end.
WRN 3'-5' DNA helicase (alternative RecQ partner of DNA2)
wrn_resection_helicase
Participant: Gene Product: WRN
Gene Product:
WRNUniProtKB:Q14191

Function

3'-5' DNA helicase activityGO:0043138

Processes

DNA double-strand break processingGO:0000729

Locations

site of double-strand breakGO:0035861

Can substitute for BLM as the helicase partner of DNA2. Not on the RGD gene list; added because it is the second human RecQ helicase shown to resect with DNA2, epistatically in cells and with purified proteins.

PMID:25122754
WRN and DNA2 interact and coordinate RPA-dependent 5'-3' resection; WRN and BLM act epistatically with DNA2 in cells.
Our biochemical experiments show that WRN and DNA2 interact physically and coordinate their enzymatic activities to mediate 5'-3' DNA end resection in a reaction dependent on RPA.
DNA2 nuclease degradation of the displaced 5' strand
dna2_resection_nuclease
Participant: Gene Product: DNA2
Gene Product:
DNA2UniProtKB:P51530

Function

5'-flap endonuclease activityGO:0017108

Processes

DNA double-strand break processingGO:0000729

Locations

site of double-strand breakGO:0035861

Its nuclease, not its weak helicase, is required; RPA bound to the unwound strands restricts DNA2 cleavage to the 5' strand.

PMID:21325134
The BLM-DNA2 route requires BLM helicase and DNA2 nuclease functions.
In one, BLM and DNA2 physically and specifically interact to resect DNA in a process that is ATP-dependent and requires BLM helicase and DNA2 nuclease functions.
Part 4: RPA coating of the single-stranded 3' tails
RPA binding to resected single-stranded DNARegulatory Steprpa_coating

The RPA1-RPA2-RPA3 heterotrimer binds the exposed ssDNA, removes secondary structure, enforces 5'-3' resection polarity and signals to ATR; it must then be displaced by RAD51 with the help of mediators.

Annotons

RPA complex single-stranded DNA binding
rpa_ssdna_binding
Participant: Protein Complex: replication protein A (RPA) heterotrimer
Protein Complex:
replication protein A (RPA) heterotrimerGO:0005662
Active units:
RPA1 (RPA70)
Participant: Gene Product: RPA1
Gene Product:
RPA1UniProtKB:P27694
Role: Large subunit carrying the main ssDNA-binding OB folds.
Function:
single-stranded DNA bindingGO:0003697
RPA2 (RPA32)
Participant: Gene Product: RPA2
Gene Product:
RPA2UniProtKB:P15927
Role: Middle subunit; phosphorylated by PIKKs after damage.
Function:
single-stranded DNA bindingGO:0003697
RPA3 (RPA14)
Participant: Gene Product: RPA3
Gene Product:
RPA3UniProtKB:P35244
Role: Small structural subunit of the trimerisation core.
Function:
single-stranded DNA bindingGO:0003697

Function

single-stranded DNA bindingGO:0003697

Locations

site of double-strand breakGO:0035861

Not on the RGD gene list, but drawn on the RGD diagram as the "Rpa complex"; included because every downstream step acts on RPA-ssDNA.

PMID:17965729
CtIP-dependent resection is what recruits RPA to DSBs.
Moreover, we reveal that CtIP is required for DSB resection, and thereby for recruitment of replication protein A (RPA) and the protein kinase ATR to DSBs, and for the ensuing ATR activation.
Part 5: mediator-dependent RAD51 loading (presynaptic filament assembly)
BRCA1-PALB2-BRCA2 and RAD51 paralog loading of RAD51 onto RPA-ssDNARegulatory Steprad51_loading

BRCA1 recruits PALB2 through a coiled-coil interaction; PALB2 binds BRCA2, which binds RAD51 through its BRC repeats and C-terminal domain, targets it to RPA-coated ssDNA and stabilises the nascent filament. The RAD51 paralog complexes act as additional mediators of RAD51 nucleation and filament stability.

DNA recombinase assemblyGO:0000730

Annotons

BRCA1 recruitment of PALB2-BRCA2 to resected DSBs
brca1_palb2_recruitment
Participant: Gene Product: BRCA1
Gene Product:
BRCA1UniProtKB:P38398

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

BRCA1 (with BARD1) binds PALB2 through its coiled-coil domain. No molecular function is asserted for this role: BRCA1's experimental MF rows (ubiquitin ligase, DNA binding, phosphoprotein binding) belong to other roles, and GO has no recombination-mediator term that fits the BRCA1-PALB2 interaction. Its BRCA1-A role is in the referenced atm_dsb_signaling node.

PMID:19369211
PALB2 binds BRCA1 directly and scaffolds the BRCA1-PALB2-BRCA2 complex; disrupting it impairs HR.
Here, we report that PALB2, the partner and localizer of BRCA2, binds directly to BRCA1, and serves as the molecular scaffold in the formation of the BRCA1-PALB2-BRCA2 complex.
PALB2 adaptor linking BRCA1 to BRCA2
palb2_adaptor
Participant: Gene Product: PALB2
Gene Product:
PALB2UniProtKB:Q86YC2

Function

protein-macromolecule adaptor activityGO:0030674
Targets: BRCA1UniProtKB:P38398 BRCA2UniProtKB:P51587

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Not on the RGD gene list (the RGD description names it as "not shown"); added because it is the physical link between BRCA1 and BRCA2. PALB2 also binds DNA and RAD51 directly.

PMID:19369211
PALB2 is the molecular adaptor between BRCA1 and BRCA2 for loading of BRCA2-RAD51.
We propose that, via its direct interaction with PALB2, BRCA1 fine-tunes recombinational repair partly through its modulatory role in the PALB2-dependent loading of BRCA2-RAD51 repair machinery at DNA breaks.
BRCA2 RAD51 mediator (DNA strand exchange activator)
brca2_mediator
Participant: Gene Product: BRCA2
Gene Product:
BRCA2UniProtKB:P51587

Function

DNA strand exchange activator activityGO:0140619
Targets: RAD51UniProtKB:Q06609

Processes

DNA recombinase assemblyGO:0000730

Locations

site of double-strand breakGO:0035861

The canonical recombination mediator. The BRCA2 gene review's core function is GO:0140619; the cached GO-CAMs type the same activity as protein-macromolecule adaptor activity (GO:0030674).

PMID:20729832
Purified BRCA2 promotes RAD51 assembly on ssDNA and RPA displacement.
Here we report the purification of full-length BRCA2 and show that it both binds RAD51 and potentiates recombinational DNA repair by promoting assembly of RAD51 onto single-stranded DNA (ssDNA).
PMID:20729859
BRCA2 promotes RAD51 binding to RPA-coated ssDNA.
We report the purification of full-length human BRCA2 and show that it binds to ~6 RAD51 molecules and promotes RAD51 binding to ssDNA coated by replication protein A (RPA), in a manner that is stimulated by DSS1.
BCDX2 RAD51 paralog complex mediator activity
bcdx2_mediator
Participant: Protein Complex: BCDX2 complex
Protein Complex:
BCDX2 complexGO:0033063
Active units:
RAD51B
Participant: Gene Product: RAD51B
Gene Product:
RAD51BUniProtKB:O15315
Role: ssDNA-binding paralog subunit; with RAD51C relieves RPA inhibition of RAD51.
Function:
single-stranded DNA bindingGO:0003697
RAD51C
Participant: Gene Product: RAD51C
Gene Product:
RAD51CUniProtKB:O43502
Role: Shared subunit of BCDX2 and CX3.
RAD51D
Participant: Gene Product: RAD51D
Gene Product:
RAD51DUniProtKB:O75771
Role: ssDNA-binding ATPase subunit.
Function:
single-stranded DNA bindingGO:0003697
XRCC2
Participant: Gene Product: XRCC2
Gene Product:
XRCC2UniProtKB:O43543
Role: Subunit bound to RAD51D.

Function

DNA strand exchange activator activityGO:0140619
Targets: RAD51UniProtKB:Q06609

Processes

DNA recombinase assemblyGO:0000730

Locations

site of double-strand breakGO:0035861

Acts early, before or during RAD51 filament assembly. The mediator activity is demonstrated for the RAD51B-RAD51C subcomplex; it is asserted for BCDX2 as the in vivo complex containing it.

PMID:11751635
The five paralogs form two complexes, BCDX2 and CX3; BCDX2 binds ssDNA and gapped DNA.
Here, we show that the five paralogs exist in two distinct complexes in human cells: one contains RAD51B, RAD51C, RAD51D, and XRCC2 (defined as BCDX2), whereas the other consists of RAD51C with XRCC3.
PMID:11751636
RAD51B-RAD51C relieves RPA competition and acts as a recombination mediator.
The competition by RPA for substrate binding can be partially alleviated by Rad51B-Rad51C. This recombination mediator function of Rad51B-Rad51C is likely required for the assembly of the Rad51-ssDNA nucleoprotein filament in vivo.
CX3 RAD51 paralog complex (RAD51C-XRCC3)
cx3_paralog_complex
Participant: Protein Complex: CX3 complex
Protein Complex:
CX3 complexGO:0033065
Active units:
RAD51C
Participant: Gene Product: RAD51C
Gene Product:
RAD51CUniProtKB:O43502
Role: Shared subunit of BCDX2 and CX3.
XRCC3
Participant: Gene Product: XRCC3
Gene Product:
XRCC3UniProtKB:O43542
Role: Partner of RAD51C in CX3.

Function

four-way junction DNA bindingGO:0000400

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Acts on RAD51 filament stability and later in Holliday junction processing; the junction-binding activity (contributes_to rows on RAD51C and XRCC3 in GOA) is the best-supported molecular activity, which is why it is placed with the mediators but carries a junction-binding function.

PMID:20207730
Purified BCDX2 and CX3 bind Holliday junctions and forks with high specificity.
We show that both complexes bind with exceptionally high specificity to the DNA junctions with little binding observed elsewhere on the DNAs.
PMID:14716019
RAD51C and XRCC3 are needed for HJ branch migration and resolution activity in extracts.
Here, we show that extracts from cells carrying mutations in the recombination/repair genes RAD51C or XRCC3 have reduced levels of HJ resolvase activity.
Part 6: homology search, strand invasion and D-loop formation
RAD51 strand exchange and RAD54-assisted D-loop formationReactionstrand_invasion

The RAD51-ssDNA filament searches for homology and invades the donor duplex to form a D-loop. RAD54 (RAD54L) and RAD54B, Swi2/Snf2-family dsDNA translocases stimulated by RAD51, open the donor duplex, promote homologous pairing and later remove RAD51 from the heteroduplex so that synthesis can begin.

DNA strand invasionGO:0042148

Annotons

RAD51 DNA strand exchange activity
rad51_strand_exchange
Participant: Gene Product: RAD51
Gene Product:
RAD51UniProtKB:Q06609

Function

DNA strand exchange activityGO:0000150

Processes

DNA strand invasionGO:0042148

Locations

site of double-strand breakGO:0035861

The recombinase; RecA homolog whose ATP-bound filament performs homology search and strand exchange.

PMID:8929543
Human RAD51 promotes ATP-dependent homologous pairing and strand exchange, stimulated by RPA.
Joint molecule formation was dependent upon ATP hydrolysis and DNA homology and was stimulated by the single-strand DNA-binding protein RP-A.
RAD54 (RAD54L) ATP-dependent DNA translocation in D-loop formation
rad54l_translocase
Participant: Gene Product: RAD54L
Gene Product:
RAD54LUniProtKB:Q92698

Function

ATP-dependent activity, acting on DNAGO:0008094
Targets: RAD51UniProtKB:Q06609

Processes

DNA strand invasionGO:0042148

Locations

site of double-strand breakGO:0035861

Not on the RGD gene list (RGD lists only RAD54B), but RAD54 is the principal RAD54 paralog in mitotic HR; in mouse cells the two paralogs are partly redundant.

PMID:12205100
RAD54 opens duplex DNA and cooperates with RAD51 in homologous DNA pairing.
Importantly, we demonstrate that hRad51 and hRad54 functionally cooperate in the homologous DNA pairing reaction that forms recombination DNA intermediates.
RAD54B ATP-dependent DNA translocation in D-loop formation
rad54b_translocase
Participant: Gene Product: RAD54B
Gene Product:
RAD54BUniProtKB:Q9Y620

Function

ATP-dependent activity, acting on DNAGO:0008094
Targets: RAD51UniProtKB:Q06609

Processes

DNA strand invasionGO:0042148

Locations

site of double-strand breakGO:0035861

The RAD54 paralog drawn on the RGD diagram (enhances D-loop formation).

PMID:16428451
RAD54B interacts physically and functionally with RAD51 like RAD54, and the two paralogs are partly redundant for HR.
Here we show that a mammalian Rad54 paralog, Rad54B, displays physical and functional interactions with Rad51 and DNA that are similar to those of Rad54.
Part 7: recombination-associated DNA synthesis from the invading 3' end
DNA synthesis extending the invading strand in the D-loopReactiond_loop_extension

The invading 3' end primes DNA synthesis on the donor template, extending the D-loop. The polymerase is not on the RGD list or diagram (RGD writes that Rad54b "promotes DNA synthesis"), and two polymerases are supported.

DNA synthesis involved in double-strand break repair via homologous recombinationGO:0043150
Variant set: Polymerase delta versus polymerase eta on the D-loop by DNA polymerase carrying out D-loop extension [Realizer] (One Or More)

Pol delta is the genetically established HR and BIR polymerase in yeast and is presumed to be the main one in human cells; pol eta initiates D-loop synthesis stimulated by PALB2 and BRCA2, particularly at blocked replication forks. Their relative contributions in human DSB repair are not settled (see knowledge_gaps).

DNA polymerase deltaReactionpol_delta_extension

Annotons

Pol delta DNA-directed DNA polymerase activity on the D-loop
pol_delta_d_loop
Participant: Protein Complex: DNA polymerase delta holoenzyme
Protein Complex:
DNA polymerase delta holoenzymeGO:0043625
Active units:
POLD1 catalytic subunit
Participant: Gene Product: POLD1
Gene Product:
POLD1UniProtKB:P28340
Role: Polymerase and 3'-5' proofreading exonuclease.
Function:
DNA-directed DNA polymerase activityGO:0003887
POLD3 accessory subunit
Participant: Gene Product: POLD3
Gene Product:
POLD3UniProtKB:Q15054
Role: PCNA-binding subunit required for BIR-type synthesis.

Function

DNA-directed DNA polymerase activityGO:0003887

Processes

DNA synthesis involved in double-strand break repair via homologous recombinationGO:0043150

Locations

site of double-strand breakGO:0035861

Extends the invading strand; in break-induced replication it synthesises both strands in a migrating D-loop. POLD2 (reviewed separately) is the second core subunit.

PMID:39596481
Pol delta synthesises DNA from the invading 3' end in a RAD51-generated D-loop.
BIR requires DNA Polδ [92,93,94], which synthesizes nascent DNA from a primer with a 3′OH end in a D-loop during recombination by ‘synapsis’ catalyzed by RAD51
DNA polymerase etaReactionpol_eta_extension

Annotons

Pol eta DNA-directed DNA polymerase activity on the D-loop
pol_eta_d_loop
Participant: Gene Product: POLH
Gene Product:
POLHUniProtKB:Q9Y253

Function

DNA-directed DNA polymerase activityGO:0003887

Processes

DNA synthesis involved in double-strand break repair via homologous recombinationGO:0043150

Locations

site of double-strand breakGO:0035861

Initiates recombination-associated synthesis on D-loops, stimulated by PALB2 and BRCA2.

PMID:24485656
PALB2 and BRCA2 stimulate pol eta-dependent DNA synthesis on D-loop substrates.
PALB2 and BRCA2 stimulate Polη-dependent DNA synthesis on D loop substrates.
Part 8: processing of joint molecules
Dissolution or nucleolytic resolution of double Holliday junctionsReactionjunction_processing

After second-end capture, the double Holliday junction is either dissolved by the BTR complex, giving only non-crossovers, or cut by structure-specific endonucleases, giving crossovers or non-crossovers. SDSA and BIR avoid double Holliday junctions and are not modelled as separate parts (see notes).

Variant set: BTR dissolution versus SLX4-MUS81/GEN1 resolution by double Holliday junction processing route [Route] (One Or More)

Dissolution is the primary route in S/G2; junctions that escape it are resolved in late G2/M by SLX1-SLX4-MUS81-EME1 and in mitosis by GEN1, so all may act in one cell cycle.

BLM-TOP3A-RMI1-RMI2 (BTR) dissolutionReactionbtr_dissolution

Annotons

BTR complex double Holliday junction dissolution
btr_dissolvasome
Participant: Protein Complex: BTR dissolvasome
Protein Complex:
BTR dissolvasomeGO:0031422
Active units:
BLM helicase
Participant: Gene Product: BLM
Gene Product:
BLMUniProtKB:P54132
Role: Branch-migrates the two junctions toward each other (convergent branch migration).
Function:
four-way junction helicase activityGO:0009378
TOP3A topoisomerase
Participant: Gene Product: TOP3A
Gene Product:
TOP3AUniProtKB:Q13472
Role: Type IA topoisomerase that decatenates the resulting hemicatenane.
Function:
DNA topoisomerase type I (single strand cut, ATP-independent) activityGO:0003917
RMI1
Participant: Gene Product: RMI1
Gene Product:
RMI1UniProtKB:Q9H9A7
Role: OB-fold accessory subunit stimulating TOP3A; binds RPA.
RMI2
Participant: Gene Product: RMI2
Gene Product:
RMI2UniProtKB:Q96E14
Role: OB-fold partner of RMI1.

Function

DNA topoisomerase type I (single strand cut, ATP-independent) activityGO:0003917

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Non-crossover dissolution; its loss in Bloom syndrome raises sister chromatid exchange. RMI1 and RMI2 are not on the RGD list.

PMID:14685245
BLM and TOP3A together dissolve a double Holliday junction.
Here, we show that BLM and hTOPO IIIalpha together effect the resolution of a recombination intermediate containing a double Holliday junction.
PMID:23543748
The BTR complex of BLM, TOP3A, RMI1 and RMI2 dissolves dHJs to non-crossovers; RPA is a cofactor.
The conserved BTR complex, composed of the Bloom's syndrome helicase (BLM), topoisomerase IIIα, RMI1, and RMI2, regulates homologous recombination in favor of non-crossover formation via the dissolution of the double Holliday Junction (dHJ).
Holliday junction resolution by SLX1-SLX4-MUS81-EME1 and GEN1Reactionnucleolytic_resolution

Annotons

SLX4 nuclease scaffold
slx4_scaffold
Participant: Gene Product: SLX4
Gene Product:
SLX4UniProtKB:Q8IY92

Function

protein-macromolecule adaptor activityGO:0030674
Targets: SLX1UniProtKB:Q9BQ83 MUS81UniProtKB:Q96NY9

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Docking platform that assembles SLX1 and MUS81-EME1 (and XPF-ERCC1) and enhances their nuclease activities.

PMID:19595721
SLX4 scaffolds SLX1 and MUS81-EME1 and enhances their activities; its loss reduces DSB-induced HR.
Furthermore, SLX4 enhances the nuclease activity of SLX1, MUS81, and XPF.
SLX1 crossover junction endonuclease
slx1_resolvase
Participant: Gene Product: SLX1A
Gene Product:
SLX1AUniProtKB:Q9BQ83

Function

crossover junction DNA endonuclease activityGO:0008821

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Catalytic subunit of the SLX1-SLX4 Holliday junction resolvase.

PMID:19596235
SLX1-SLX4 symmetrically cleaves Holliday junctions.
SLX4 complexes cleave 3' flap, 5' flap, and replication fork structures; yet unlike other endonucleases associated with SLX4, the SLX1-SLX4 module promotes symmetrical cleavage of static and migrating Holliday junctions (HJs), identifying SLX1-SLX4 as a HJ resolvase.
MUS81-EME1 crossover junction endonuclease
mus81_resolvase
Participant: Gene Product: MUS81 (with EME1)
Gene Product:
MUS81 (with EME1)UniProtKB:Q96NY9

Function

crossover junction DNA endonuclease activityGO:0008821

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Catalytic subunit of MUS81-EME1 (EME1 is the non-catalytic partner); recruited to SLX4 in G2/M to form the SLX-MUS81 resolvase that nicks and counter-nicks the junction.

PMID:19596236
SLX4 binds MUS81 and docks multiple structure-specific endonucleases.
Furthermore, we show that SLX4 binds the XPF(ERCC4) and MUS81 subunits of the XPF-ERCC1 and MUS81-EME1 endonucleases and is required for DNA interstrand crosslink repair.
GEN1 Holliday junction resolvase
gen1_resolvase
Participant: Gene Product: GEN1
Gene Product:
GEN1UniProtKB:Q17RS7

Function

crossover junction DNA endonuclease activityGO:0008821

Processes

double-strand break repair via homologous recombinationGO:0000724

Locations

site of double-strand breakGO:0035861

Rad2/XPG-family resolvase that cuts junctions symmetrically into ligatable nicked duplexes; active mainly once the nuclear envelope breaks down in mitosis.

PMID:19020614
GEN1 resolves Holliday junctions by symmetrical cleavage.
Recombinant GEN1 and Yen1 resolve Holliday junctions by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated.