id: MODULE:homologous_recombination_dsb_repair title: 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 description: >- 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. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0000202 title: homologous recombination pathway of double-strand break repair statement: >- 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). - source_id: GO:0000724 title: double-strand break repair via homologous recombination statement: >- 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. - source_id: gomodel:65a1f4f800000855 title: Initiation of double-strand break repair via homologous recombination by the MRN complex (MRE11-RAD50-NBN) (Human). statement: >- 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. - source_id: PMID:21325134 title: BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. statement: Long-range resection runs through two reconstituted machineries, which this module treats as a variant set. supporting_text: "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." - source_id: PMID:20729832 title: Purified human BRCA2 stimulates RAD51-mediated recombination. statement: BRCA2 is the mediator that loads RAD51 onto RPA-coated ssDNA. supporting_text: "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." - source_id: PMID:14685245 title: The Bloom's syndrome helicase suppresses crossing over during homologous recombination. statement: Double Holliday junctions are processed either by BLM-TOP3A dissolution or by classical resolution. supporting_text: "The mechanism, which we term double-junction dissolution, is distinct from classical Holliday junction resolution and prevents exchange of flanking sequences." notes: >- 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. module: id: homologous_recombination_dsb_repair label: Homologous recombination repair of DNA double-strand breaks module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination description: >- The GO process mapped to PW:0000202. The module covers mitotic HR from end resection to junction processing; meiotic recombination is excluded. context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens cellular_components: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break parts: - order: 1 role: upstream DSB signalling and BRCA1-dependent commitment to resection optional: true node: id: hr_upstream_signalling label: ATM signalling and BRCA1 displacement of 53BP1-RIF1 (by reference) description: >- 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. module_ref: atm_dsb_signaling#brca1_a_arm evidence: - source_id: PMID:17965729 statement: CtIP-dependent resection is restricted to S and G2 and is needed for RPA loading and HR. supporting_text: "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." - order: 2 role: short-range end resection by MRN-CtIP node: id: short_range_resection label: MRN-CtIP short-range resection (MRE11 endonuclease and 3'-5' exonuclease) module_type: REACTION description: >- 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. concepts: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing annotons: - id: mrn_resection_nuclease label: MRN complex DNA endonuclease activity at DSB ends participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: MRE11-RAD50-NBN (MRN) complex term: id: GO:0030870 label: Mre11 complex active_units: - id: resection_mre11 label: MRE11 nuclease subunit role: Endonuclease and 3'-5' exonuclease that initiates resection. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MRE11 term: id: UniProtKB:P49959 label: Double-strand break repair protein MRE11 function: preferred_term: DNA endonuclease activity term: id: GO:0004520 label: DNA endonuclease activity - id: resection_rad50 label: RAD50 ATPase subunit role: ATP hydrolysis drives the conformational change that licenses MRE11 nuclease activity. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD50 term: id: UniProtKB:Q92878 label: DNA repair protein RAD50 function: preferred_term: ATP hydrolysis activity term: id: GO:0016887 label: ATP hydrolysis activity - id: resection_nbn label: NBN subunit role: Required for MRN endonucleolytic processing of protein-blocked ends and for CtIP binding. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: NBN term: id: UniProtKB:O60934 label: Nibrin function: preferred_term: chromatin-protein adaptor activity term: id: GO:0140463 label: chromatin-protein adaptor activity function: preferred_term: DNA endonuclease activity term: id: GO:0004520 label: DNA endonuclease activity processes: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:27814491 statement: Human MRN performs sequential endo- and exonucleolytic processing of blocked ends, stimulated by phosphorylated CtIP. supporting_text: "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." gocam_associations: - model: gomodel:65a1f4f800000855 activity: gomodel:65a1f4f800000855/65a1f4f800000979 title: MRE11 DNA endonuclease activity (GO:0004520) - model: gomodel:65a1f4f800000855 activity: gomodel:65a1f4f800000855/65a1f4f800000971 title: MRE11 3'-5'-DNA exonuclease activity (GO:0008296) - model: gomodel:65a1f4f800000855 activity: gomodel:65a1f4f800000855/65a1f4f800000987 title: RAD50 ATP hydrolysis activity (GO:0016887) - id: ctip_resection label: CtIP (RBBP8) stimulation of the MRE11 endonuclease participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RBBP8 (CtIP) term: id: UniProtKB:Q99708 label: DNA endonuclease RBBP8 function: preferred_term: single-stranded DNA endonuclease activity term: id: GO:0000014 label: single-stranded DNA endonuclease activity targets: - preferred_term: MRE11 term: id: UniProtKB:P49959 label: Double-strand break repair protein MRE11 processes: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:17965729 statement: CtIP binds the MRE11 complex and both are required for HR. supporting_text: "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." - source_id: PMID:27814491 statement: Phosphorylated CtIP stimulates hMRN endonucleolytic cleavage. supporting_text: "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." gocam_associations: - model: gomodel:65a1f4f800001380 activity: gomodel:65a1f4f800001380/65a1f4f800001465 title: RBBP8 single-stranded DNA endonuclease activity (GO:0000014) - order: 3 role: long-range end resection node: id: long_range_resection label: Long-range 5'-3' resection by EXO1 or by RecQ helicase-DNA2 module_type: REACTION description: >- From the MRN-CtIP entry site, kilobase-long 3' tails are generated by either of two machineries, both stimulated by MRN and RPA. concepts: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing variant_sets: - id: long_range_resection_machinery label: EXO1 versus BLM/WRN-DNA2 long-range resection axis: resection machinery variant_kind: ROUTE selection: ONE_OR_MORE notes: >- 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. variants: - id: exo1_resection label: EXO1 5'-3' exonuclease route module_type: REACTION annotons: - id: exo1_exonuclease label: EXO1 5'-3' DNA exonuclease activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: EXO1 term: id: UniProtKB:Q9UQ84 label: Exonuclease 1 function: preferred_term: 5'-3' DNA exonuclease activity term: id: GO:0035312 label: 5'-3' DNA exonuclease activity processes: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- Degrades the 5'-terminated strand of double-stranded DNA; its processivity is enhanced by MRN and its end affinity by BLM. evidence: - source_id: PMID:10608837 statement: Human EXO1 has robust 5'-3' exonuclease activity on double-stranded DNA. supporting_text: "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" - source_id: PMID:21325134 statement: EXO1 resection is stimulated by BLM, MRN and RPA. supporting_text: "In the other, EXO1 resects the DNA and is stimulated by BLM, MRN, and RPA." gocam_associations: - model: gomodel:65a1f4f800000855 activity: gomodel:65a1f4f800000855/65a1f4f800000992 title: EXO1 5'-3' DNA exonuclease activity (GO:0035312) - id: recq_dna2_resection label: BLM (or WRN) helicase with DNA2 nuclease route module_type: REACTION annotons: - id: blm_resection_helicase label: BLM 3'-5' DNA helicase unwinding of the break end participant: selector_type: GENE_PRODUCT gene_product: preferred_term: BLM term: id: UniProtKB:P54132 label: RecQ-like DNA helicase BLM function: preferred_term: 3'-5' DNA helicase activity term: id: GO:0043138 label: 3'-5' DNA helicase activity processes: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- Unwinds the duplex end so that DNA2 can degrade the displaced 5' strand; RPA is essential for unwinding and for resection polarity. evidence: - source_id: PMID:21325134 statement: RPA is essential for BLM unwinding and DNA2 5'-3' polarity; MRN recruits BLM. supporting_text: "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." - id: wrn_resection_helicase label: WRN 3'-5' DNA helicase (alternative RecQ partner of DNA2) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: WRN term: id: UniProtKB:Q14191 label: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN function: preferred_term: 3'-5' DNA helicase activity term: id: GO:0043138 label: 3'-5' DNA helicase activity processes: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:25122754 statement: WRN and DNA2 interact and coordinate RPA-dependent 5'-3' resection; WRN and BLM act epistatically with DNA2 in cells. supporting_text: "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." - id: dna2_resection_nuclease label: DNA2 nuclease degradation of the displaced 5' strand participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNA2 term: id: UniProtKB:P51530 label: DNA replication ATP-dependent helicase/nuclease DNA2 function: preferred_term: 5'-flap endonuclease activity term: id: GO:0017108 label: 5'-flap endonuclease activity processes: - preferred_term: DNA double-strand break processing term: id: GO:0000729 label: DNA double-strand break processing locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- Its nuclease, not its weak helicase, is required; RPA bound to the unwound strands restricts DNA2 cleavage to the 5' strand. evidence: - source_id: PMID:21325134 statement: The BLM-DNA2 route requires BLM helicase and DNA2 nuclease functions. supporting_text: "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." - order: 4 role: RPA coating of the single-stranded 3' tails node: id: rpa_coating label: RPA binding to resected single-stranded DNA module_type: REGULATORY_STEP description: >- 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: - id: rpa_ssdna_binding label: RPA complex single-stranded DNA binding participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: replication protein A (RPA) heterotrimer term: id: GO:0005662 label: DNA replication factor A complex active_units: - id: rpa_rpa1 label: RPA1 (RPA70) role: Large subunit carrying the main ssDNA-binding OB folds. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RPA1 term: id: UniProtKB:P27694 label: Replication protein A 70 kDa DNA-binding subunit function: preferred_term: single-stranded DNA binding term: id: GO:0003697 label: single-stranded DNA binding - id: rpa_rpa2 label: RPA2 (RPA32) role: Middle subunit; phosphorylated by PIKKs after damage. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RPA2 term: id: UniProtKB:P15927 label: Replication protein A 32 kDa subunit function: preferred_term: single-stranded DNA binding term: id: GO:0003697 label: single-stranded DNA binding - id: rpa_rpa3 label: RPA3 (RPA14) role: Small structural subunit of the trimerisation core. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RPA3 term: id: UniProtKB:P35244 label: Replication protein A 14 kDa subunit function: preferred_term: single-stranded DNA binding term: id: GO:0003697 label: single-stranded DNA binding function: preferred_term: single-stranded DNA binding term: id: GO:0003697 label: single-stranded DNA binding locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:17965729 statement: CtIP-dependent resection is what recruits RPA to DSBs. supporting_text: "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." gocam_associations: - model: gomodel:65039e8700000196 activity: gomodel:65039e8700000196/65039e8700000242 title: DNA replication factor A complex damaged DNA binding (GO:0003684) - order: 5 role: mediator-dependent RAD51 loading (presynaptic filament assembly) node: id: rad51_loading label: BRCA1-PALB2-BRCA2 and RAD51 paralog loading of RAD51 onto RPA-ssDNA module_type: REGULATORY_STEP description: >- 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. concepts: - preferred_term: DNA recombinase assembly term: id: GO:0000730 label: DNA recombinase assembly annotons: - id: brca1_palb2_recruitment label: BRCA1 recruitment of PALB2-BRCA2 to resected DSBs participant: selector_type: GENE_PRODUCT gene_product: preferred_term: BRCA1 term: id: UniProtKB:P38398 label: Breast cancer type 1 susceptibility protein processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:19369211 statement: PALB2 binds BRCA1 directly and scaffolds the BRCA1-PALB2-BRCA2 complex; disrupting it impairs HR. supporting_text: "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." - id: palb2_adaptor label: PALB2 adaptor linking BRCA1 to BRCA2 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PALB2 term: id: UniProtKB:Q86YC2 label: Partner and localizer of BRCA2 function: preferred_term: protein-macromolecule adaptor activity term: id: GO:0030674 label: protein-macromolecule adaptor activity targets: - preferred_term: BRCA1 term: id: UniProtKB:P38398 label: Breast cancer type 1 susceptibility protein - preferred_term: BRCA2 term: id: UniProtKB:P51587 label: Breast cancer type 2 susceptibility protein processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:19369211 statement: PALB2 is the molecular adaptor between BRCA1 and BRCA2 for loading of BRCA2-RAD51. supporting_text: "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." - id: brca2_mediator label: BRCA2 RAD51 mediator (DNA strand exchange activator) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: BRCA2 term: id: UniProtKB:P51587 label: Breast cancer type 2 susceptibility protein function: preferred_term: DNA strand exchange activator activity term: id: GO:0140619 label: DNA strand exchange activator activity targets: - preferred_term: RAD51 term: id: UniProtKB:Q06609 label: DNA repair protein RAD51 homolog 1 processes: - preferred_term: DNA recombinase assembly term: id: GO:0000730 label: DNA recombinase assembly locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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). evidence: - source_id: PMID:20729832 statement: Purified BRCA2 promotes RAD51 assembly on ssDNA and RPA displacement. supporting_text: "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)." - source_id: PMID:20729859 statement: BRCA2 promotes RAD51 binding to RPA-coated ssDNA. supporting_text: "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." gocam_associations: - model: gomodel:69a0c46f00002570 activity: gomodel:69a0c46f00002570/69a0c46f00002580 title: BRCA2 protein-macromolecule adaptor activity (GO:0030674) - id: bcdx2_mediator label: BCDX2 RAD51 paralog complex mediator activity participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: BCDX2 complex term: id: GO:0033063 label: Rad51B-Rad51C-Rad51D-XRCC2 complex active_units: - id: bcdx2_rad51b label: RAD51B role: ssDNA-binding paralog subunit; with RAD51C relieves RPA inhibition of RAD51. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD51B term: id: UniProtKB:O15315 label: DNA repair protein RAD51 homolog 2 function: preferred_term: single-stranded DNA binding term: id: GO:0003697 label: single-stranded DNA binding - id: bcdx2_rad51c label: RAD51C role: Shared subunit of BCDX2 and CX3. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD51C term: id: UniProtKB:O43502 label: DNA repair protein RAD51 homolog 3 - id: bcdx2_rad51d label: RAD51D role: ssDNA-binding ATPase subunit. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD51D term: id: UniProtKB:O75771 label: DNA repair protein RAD51 homolog 4 function: preferred_term: single-stranded DNA binding term: id: GO:0003697 label: single-stranded DNA binding - id: bcdx2_xrcc2 label: XRCC2 role: Subunit bound to RAD51D. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: XRCC2 term: id: UniProtKB:O43543 label: DNA repair protein XRCC2 function: preferred_term: DNA strand exchange activator activity term: id: GO:0140619 label: DNA strand exchange activator activity targets: - preferred_term: RAD51 term: id: UniProtKB:Q06609 label: DNA repair protein RAD51 homolog 1 processes: - preferred_term: DNA recombinase assembly term: id: GO:0000730 label: DNA recombinase assembly locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:11751635 statement: The five paralogs form two complexes, BCDX2 and CX3; BCDX2 binds ssDNA and gapped DNA. supporting_text: "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." - source_id: PMID:11751636 statement: RAD51B-RAD51C relieves RPA competition and acts as a recombination mediator. supporting_text: "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." - id: cx3_paralog_complex label: CX3 RAD51 paralog complex (RAD51C-XRCC3) participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: CX3 complex term: id: GO:0033065 label: Rad51C-XRCC3 complex active_units: - id: cx3_rad51c label: RAD51C role: Shared subunit of BCDX2 and CX3. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD51C term: id: UniProtKB:O43502 label: DNA repair protein RAD51 homolog 3 - id: cx3_xrcc3 label: XRCC3 role: Partner of RAD51C in CX3. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: XRCC3 term: id: UniProtKB:O43542 label: DNA repair protein XRCC3 function: preferred_term: four-way junction DNA binding term: id: GO:0000400 label: four-way junction DNA binding processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:20207730 statement: Purified BCDX2 and CX3 bind Holliday junctions and forks with high specificity. supporting_text: "We show that both complexes bind with exceptionally high specificity to the DNA junctions with little binding observed elsewhere on the DNAs." - source_id: PMID:14716019 statement: RAD51C and XRCC3 are needed for HJ branch migration and resolution activity in extracts. supporting_text: "Here, we show that extracts from cells carrying mutations in the recombination/repair genes RAD51C or XRCC3 have reduced levels of HJ resolvase activity." - order: 6 role: homology search, strand invasion and D-loop formation node: id: strand_invasion label: RAD51 strand exchange and RAD54-assisted D-loop formation module_type: REACTION description: >- 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. concepts: - preferred_term: DNA strand invasion term: id: GO:0042148 label: DNA strand invasion annotons: - id: rad51_strand_exchange label: RAD51 DNA strand exchange activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD51 term: id: UniProtKB:Q06609 label: DNA repair protein RAD51 homolog 1 function: preferred_term: DNA strand exchange activity term: id: GO:0000150 label: DNA strand exchange activity processes: - preferred_term: DNA strand invasion term: id: GO:0042148 label: DNA strand invasion locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: The recombinase; RecA homolog whose ATP-bound filament performs homology search and strand exchange. evidence: - source_id: PMID:8929543 statement: Human RAD51 promotes ATP-dependent homologous pairing and strand exchange, stimulated by RPA. supporting_text: "Joint molecule formation was dependent upon ATP hydrolysis and DNA homology and was stimulated by the single-strand DNA-binding protein RP-A." gocam_associations: - model: gomodel:680ad14200006156 activity: gomodel:680ad14200006156/680ad14200006159 title: RAD51 DNA strand exchange activity (GO:0000150) - model: gomodel:680ad14200007322 activity: gomodel:680ad14200007322/680ad14200007323 title: RAD51 DNA strand exchange activity (GO:0000150) - model: gomodel:69a0c46f00002570 activity: gomodel:69a0c46f00002570/69a0c46f00002571 title: RAD51 DNA strand exchange activity (GO:0000150) - model: gomodel:65039e8700000196 activity: gomodel:65039e8700000196/65039e8700000250 title: RAD51 DNA strand exchange activity (GO:0000150) - id: rad54l_translocase label: RAD54 (RAD54L) ATP-dependent DNA translocation in D-loop formation participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD54L term: id: UniProtKB:Q92698 label: DNA repair and recombination protein RAD54-like function: preferred_term: ATP-dependent activity, acting on DNA term: id: GO:0008094 label: ATP-dependent activity, acting on DNA targets: - preferred_term: RAD51 term: id: UniProtKB:Q06609 label: DNA repair protein RAD51 homolog 1 processes: - preferred_term: DNA strand invasion term: id: GO:0042148 label: DNA strand invasion locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:12205100 statement: RAD54 opens duplex DNA and cooperates with RAD51 in homologous DNA pairing. supporting_text: "Importantly, we demonstrate that hRad51 and hRad54 functionally cooperate in the homologous DNA pairing reaction that forms recombination DNA intermediates." gocam_associations: - model: gomodel:680ad14200007322 activity: gomodel:680ad14200007322/680ad14200007331 title: RAD54L ATP-dependent activity, acting on DNA (GO:0008094) - id: rad54b_translocase label: RAD54B ATP-dependent DNA translocation in D-loop formation participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAD54B term: id: UniProtKB:Q9Y620 label: DNA repair and recombination protein RAD54B function: preferred_term: ATP-dependent activity, acting on DNA term: id: GO:0008094 label: ATP-dependent activity, acting on DNA targets: - preferred_term: RAD51 term: id: UniProtKB:Q06609 label: DNA repair protein RAD51 homolog 1 processes: - preferred_term: DNA strand invasion term: id: GO:0042148 label: DNA strand invasion locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: The RAD54 paralog drawn on the RGD diagram (enhances D-loop formation). evidence: - source_id: PMID:16428451 statement: RAD54B interacts physically and functionally with RAD51 like RAD54, and the two paralogs are partly redundant for HR. supporting_text: "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." gocam_associations: - model: gomodel:680ad14200006156 activity: gomodel:680ad14200006156/680ad14200006162 title: RAD54B ATP-dependent activity, acting on DNA (GO:0008094) - order: 7 role: recombination-associated DNA synthesis from the invading 3' end node: id: d_loop_extension label: DNA synthesis extending the invading strand in the D-loop module_type: REACTION description: >- 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. concepts: - preferred_term: DNA synthesis involved in double-strand break repair via homologous recombination term: id: GO:0043150 label: DNA synthesis involved in double-strand break repair via homologous recombination variant_sets: - id: d_loop_polymerase label: Polymerase delta versus polymerase eta on the D-loop axis: DNA polymerase carrying out D-loop extension variant_kind: REALIZER selection: ONE_OR_MORE notes: >- 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). variants: - id: pol_delta_extension label: DNA polymerase delta module_type: REACTION annotons: - id: pol_delta_d_loop label: Pol delta DNA-directed DNA polymerase activity on the D-loop participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: DNA polymerase delta holoenzyme term: id: GO:0043625 label: delta DNA polymerase complex active_units: - id: pold_pold1 label: POLD1 catalytic subunit role: Polymerase and 3'-5' proofreading exonuclease. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: POLD1 term: id: UniProtKB:P28340 label: DNA polymerase delta catalytic subunit function: preferred_term: DNA-directed DNA polymerase activity term: id: GO:0003887 label: DNA-directed DNA polymerase activity - id: pold_pold3 label: POLD3 accessory subunit role: PCNA-binding subunit required for BIR-type synthesis. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: POLD3 term: id: UniProtKB:Q15054 label: DNA polymerase delta subunit 3 function: preferred_term: DNA-directed DNA polymerase activity term: id: GO:0003887 label: DNA-directed DNA polymerase activity processes: - preferred_term: DNA synthesis involved in double-strand break repair via homologous recombination term: id: GO:0043150 label: DNA synthesis involved in double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:39596481 statement: Pol delta synthesises DNA from the invading 3' end in a RAD51-generated D-loop. supporting_text: "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" - id: pol_eta_extension label: DNA polymerase eta module_type: REACTION annotons: - id: pol_eta_d_loop label: Pol eta DNA-directed DNA polymerase activity on the D-loop participant: selector_type: GENE_PRODUCT gene_product: preferred_term: POLH term: id: UniProtKB:Q9Y253 label: DNA polymerase eta function: preferred_term: DNA-directed DNA polymerase activity term: id: GO:0003887 label: DNA-directed DNA polymerase activity processes: - preferred_term: DNA synthesis involved in double-strand break repair via homologous recombination term: id: GO:0043150 label: DNA synthesis involved in double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: Initiates recombination-associated synthesis on D-loops, stimulated by PALB2 and BRCA2. evidence: - source_id: PMID:24485656 statement: PALB2 and BRCA2 stimulate pol eta-dependent DNA synthesis on D-loop substrates. supporting_text: "PALB2 and BRCA2 stimulate Polη-dependent DNA synthesis on D loop substrates." - order: 8 role: processing of joint molecules node: id: junction_processing label: Dissolution or nucleolytic resolution of double Holliday junctions module_type: REACTION description: >- 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_sets: - id: dhj_processing_route label: BTR dissolution versus SLX4-MUS81/GEN1 resolution axis: double Holliday junction processing route variant_kind: ROUTE selection: ONE_OR_MORE notes: >- 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. variants: - id: btr_dissolution label: BLM-TOP3A-RMI1-RMI2 (BTR) dissolution module_type: REACTION annotons: - id: btr_dissolvasome label: BTR complex double Holliday junction dissolution participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: BTR dissolvasome term: id: GO:0031422 label: RecQ family helicase-topoisomerase III complex active_units: - id: btr_blm label: BLM helicase role: Branch-migrates the two junctions toward each other (convergent branch migration). participant: selector_type: GENE_PRODUCT gene_product: preferred_term: BLM term: id: UniProtKB:P54132 label: RecQ-like DNA helicase BLM function: preferred_term: four-way junction helicase activity term: id: GO:0009378 label: four-way junction helicase activity - id: btr_top3a label: TOP3A topoisomerase role: Type IA topoisomerase that decatenates the resulting hemicatenane. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TOP3A term: id: UniProtKB:Q13472 label: DNA topoisomerase 3-alpha function: preferred_term: DNA topoisomerase type I (single strand cut, ATP-independent) activity term: id: GO:0003917 label: DNA topoisomerase type I (single strand cut, ATP-independent) activity - id: btr_rmi1 label: RMI1 role: OB-fold accessory subunit stimulating TOP3A; binds RPA. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RMI1 term: id: UniProtKB:Q9H9A7 label: RecQ-mediated genome instability protein 1 - id: btr_rmi2 label: RMI2 role: OB-fold partner of RMI1. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RMI2 term: id: UniProtKB:Q96E14 label: RecQ-mediated genome instability protein 2 function: preferred_term: DNA topoisomerase type I (single strand cut, ATP-independent) activity term: id: GO:0003917 label: DNA topoisomerase type I (single strand cut, ATP-independent) activity processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- Non-crossover dissolution; its loss in Bloom syndrome raises sister chromatid exchange. RMI1 and RMI2 are not on the RGD list. evidence: - source_id: PMID:14685245 statement: BLM and TOP3A together dissolve a double Holliday junction. supporting_text: "Here, we show that BLM and hTOPO IIIalpha together effect the resolution of a recombination intermediate containing a double Holliday junction." - source_id: PMID:23543748 statement: The BTR complex of BLM, TOP3A, RMI1 and RMI2 dissolves dHJs to non-crossovers; RPA is a cofactor. supporting_text: "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)." - id: nucleolytic_resolution label: Holliday junction resolution by SLX1-SLX4-MUS81-EME1 and GEN1 module_type: REACTION annotons: - id: slx4_scaffold label: SLX4 nuclease scaffold participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SLX4 term: id: UniProtKB:Q8IY92 label: Structure-specific endonuclease subunit SLX4 function: preferred_term: protein-macromolecule adaptor activity term: id: GO:0030674 label: protein-macromolecule adaptor activity targets: - preferred_term: SLX1 term: id: UniProtKB:Q9BQ83 label: Structure-specific endonuclease subunit SLX1 - preferred_term: MUS81 term: id: UniProtKB:Q96NY9 label: Structure-specific endonuclease subunit MUS81 processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- Docking platform that assembles SLX1 and MUS81-EME1 (and XPF-ERCC1) and enhances their nuclease activities. evidence: - source_id: PMID:19595721 statement: SLX4 scaffolds SLX1 and MUS81-EME1 and enhances their activities; its loss reduces DSB-induced HR. supporting_text: "Furthermore, SLX4 enhances the nuclease activity of SLX1, MUS81, and XPF." - id: slx1_resolvase label: SLX1 crossover junction endonuclease participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SLX1A term: id: UniProtKB:Q9BQ83 label: Structure-specific endonuclease subunit SLX1 function: preferred_term: crossover junction DNA endonuclease activity term: id: GO:0008821 label: crossover junction DNA endonuclease activity processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: Catalytic subunit of the SLX1-SLX4 Holliday junction resolvase. evidence: - source_id: PMID:19596235 statement: SLX1-SLX4 symmetrically cleaves Holliday junctions. supporting_text: "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." - id: mus81_resolvase label: MUS81-EME1 crossover junction endonuclease participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MUS81 (with EME1) term: id: UniProtKB:Q96NY9 label: Structure-specific endonuclease subunit MUS81 function: preferred_term: crossover junction DNA endonuclease activity term: id: GO:0008821 label: crossover junction DNA endonuclease activity processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- 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. evidence: - source_id: PMID:19596236 statement: SLX4 binds MUS81 and docks multiple structure-specific endonucleases. supporting_text: "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." - id: gen1_resolvase label: GEN1 Holliday junction resolvase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: GEN1 term: id: UniProtKB:Q17RS7 label: Flap endonuclease GEN homolog 1 function: preferred_term: crossover junction DNA endonuclease activity term: id: GO:0008821 label: crossover junction DNA endonuclease activity processes: - preferred_term: double-strand break repair via homologous recombination term: id: GO:0000724 label: double-strand break repair via homologous recombination locations: - preferred_term: site of double-strand break term: id: GO:0035861 label: site of double-strand break role_description: >- Rad2/XPG-family resolvase that cuts junctions symmetrically into ligatable nicked duplexes; active mainly once the nuclear envelope breaks down in mitosis. evidence: - source_id: PMID:19020614 statement: GEN1 resolves Holliday junctions by symmetrical cleavage. supporting_text: "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." connections: - source: hr_upstream_signalling target: short_range_resection connection_type: POSITIVELY_REGULATES description: >- BRCA1-CtIP displacement of 53BP1-RIF1 licenses resection; ATM and CDK phosphorylation of CtIP activates the MRN-CtIP nuclease. - source: short_range_resection target: long_range_resection connection_type: PRECEDES chaining_status: NOT_APPLICABLE chaining_note: DNA end intermediates, not CoA metabolites. description: >- MRN-CtIP clipping creates the entry point for EXO1 and BLM-DNA2 (MRE11 exonuclease directly provides input for EXO1 in gomodel:65a1f4f800000855). - source: long_range_resection target: rpa_coating connection_type: PROVIDES_INPUT_FOR description: Resection exposes the 3' single-stranded tails that RPA binds. - source: rpa_coating target: rad51_loading connection_type: PROVIDES_INPUT_FOR description: Mediators load RAD51 onto RPA-coated ssDNA and displace RPA. - source: rad51_loading target: strand_invasion connection_type: PRECEDES chaining_status: NOT_APPLICABLE chaining_note: DNA-protein intermediates, not CoA metabolites. description: The RAD51-ssDNA presynaptic filament performs homology search and invasion. - source: strand_invasion target: d_loop_extension connection_type: PROVIDES_INPUT_FOR description: The invading 3' end in the D-loop is the primer for repair synthesis. - source: d_loop_extension target: junction_processing connection_type: PRECEDES chaining_status: NOT_APPLICABLE chaining_note: DNA joint-molecule intermediates, not CoA metabolites. description: Extension and second-end capture generate the double Holliday junction processed in the last step. knowledge_gaps: - gap_statement: >- Which polymerase extends the invading strand in human DSB repair is not settled: pol delta is required in yeast HR and BIR, pol eta initiates D-loop synthesis with PALB2 and BRCA2 in vitro and at blocked forks, and the relative contribution of each (and of other polymerases) at two-ended DSBs in human cells is not known. gap_kind: - BIOLOGY - gap_statement: >- The molecular mechanism of the RAD51 paralog complexes is unclear: how BCDX2 promotes RAD51 nucleation (filament capping, remodelling or RPA displacement), and whether CX3 acts on RAD51 filaments, on Holliday junctions, or both, in human cells. gap_kind: - BIOLOGY - gap_statement: >- Whether CtIP has intrinsic nuclease activity that contributes to resection in human cells, or acts only as the phosphorylation-dependent co-factor of the MRE11 endonuclease, remains debated. gap_kind: - BIOLOGY