Introduction

![]() |
Assembly and maintenance of the nucleoprotein filament scaffold on ssDNA

The homology search
Formation of heteroduplex DNA in the D-loop and the ATP-dependent role of Rad54
DNA topology and structure affect hDNA formation and stability

D-loop reversal activities ensure high-fidelity DSB repair and CO avoidance
DNA synthesis at the D-loop
Extended D-loop disruption, second-end annealing, and crossover avoidance
Double Holliday junction processing and the possibility of a crossover
Concluding remarks
Acknowledgments
Supplementary Material
References
- Kowalczykowski S.C. Hunter N. Heyer W.-D. DNA Recombination. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY2016
- The control of DNA repair by the cell cycle.Nat. Cell Biol. 2016; 19 (28008184): 1-9
- Nonhomologous DNA end-joining for repair of DNA double-strand breaks.J. Biol. Chem. 2018; 293 (29247009): 10512-10523
- Repair of DNA double-strand breaks by mammalian alternative end-joining pathways.J. Biol. Chem. 2018; 293 (29530982): 10536-10546
- How cells ensure correct repair of DNA double-strand breaks.J. Biol. Chem. 2018; 293 (29414795): 10502-10511
- End resection at double-strand breaks: mechanism and regulation.Cold Spring Harb. Perspect. Biol. 2014; 6 (25085909)a016436
- Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae.Genetics. 1992; 132 (1427035): 387-402
- Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair.Mol. Cell. Biol. 1994; 14 (8114699): 1613-1625
- Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae.Microbiol. Mol. Biol. Rev. 1999; 63 (10357855): 349-404
- Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis.Nat. Rev. Mol. Cell Biol. 2010; 11 (20177395): 196-207
- Multi-invasions are recombination by-products that induce chromosomal rearrangements.Cell. 2017; 170 (28781165): 760-773
- Regulation of homologous recombination in eukaryotes.Annu. Rev. Genet. 2010; 44 (20690856): 113-139
- Rad51 recombinase and recombination mediators.J. Biol. Chem. 2003; 278 (12912992): 42729-42732
- Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA.Proc. Natl. Acad. Sci. U.S.A. 2001; 98 (11459984): 8419-8424
- Presynaptic filament dynamics in homologous recombination and DNA repair.Crit. Rev. Biochem. Mol. Biol. 2011; 46 (21599536): 240-270
- Mechanics and single-molecule interrogation of DNA recombination.Annu. Rev. Biochem. 2016; 85 (27088880): 193-226
- RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair.Mol. Cell. 2003; 11 (12769856): 1337-1347
- The BRCA2 homologue Brh2 nucleates RAD51 filament formation at a dsDNA-ssDNA junction.Nature. 2005; 433 (15703751): 653-657
- Purified human BRCA2 stimulates RAD51-mediated recombination.Nature. 2010; 467 (20729832): 678-683
- Rad52 protein stimulates DNA strand exchange by Rad51 and replication protein A.Nature. 1998; 391 (9450760): 407-410
- Functional interactions among yeast Rad51 recombinase, Rad52 mediator, and replication protein A in DNA strand exchange.J. Biol. Chem. 2000; 275 (10748203): 15895-15904
- Genetic analysis of gamma-ray mutagenesis in yeast. III. Double-mutant strains.Mutat. Res. 1980; 70 (6988707): 37-48
- Mechanisms and regulation of mitotic recombination in Saccharomyces cerevisiae.Genetics. 2014; 198 (25381364): 795-835
- Human BRCA2 protein promotes RAD51 filament formation on RPA-covered single-stranded DNA.Nat. Struct. Mol. Biol. 2010; 17 (20729859): 1260-1262
- The breast cancer tumor suppressor BRCA2 promotes the specific targeting of RAD51 to single-stranded DNA.Nat. Struct. Mol. Biol. 2010; 17 (20729858): 1263-1265
- Embryonic lethality and radiation hypersensitivity mediated by Rad51 in mice lacking Brca2.Nature. 1997; 386 (9126738): 804-810
- BRCA2 is required for ionizing radiation-induced assembly of rad51 complex in vivo.Cancer Res. 1999; 59 (10446958): 3547-3551
- BRCA2 is required for homology-directed repair of chromosomal breaks.Mol. Cell. 2001; 7 (11239455): 263-272
- BRCA2 is epistatic to the RAD51 paralogs in response to DNA damage.DNA Repair. 2013; 12 (23384538): 306-311
- Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins.Cold Spring Harb. Perspect. Biol. 2015; 7 (25833843)a016600
- Rad52 inactivation is synthetically lethal with BRCA2 deficiency.Proc. Natl. Acad. Sci. U.S.A. 2011; 108 (21148102): 686-691
- Human RAD51 rapidly forms intrinsically dynamic nucleoprotein filaments modulated by nucleotide binding state.Nucleic Acids Res. 2018; 2018 (29481689)
- Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.Nature. 2008; 453 (18497818): 489-494
- DNARECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases.Science. 2015; 349 (26315438): 977-981
- Structural biology: snapshots of DNA repair.Nature. 2008; 453 (18497811): 463-466
- Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA.Proc. Natl. Acad. Sci. U.S.A. 2001; 98 (11459984): 8419-8424
- Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules.Proc. Natl. Acad. Sci. U.S.A. 2009; 106 (19122145): 361-368
- Counting RAD51 proteins disassembling from nucleoprotein filaments under tension.Nature. 2009; 457 (19060884): 745-748
- Structural transitions within human Rad51 nucleoprotein filaments.Proc. Natl. Acad. Sci. U.S.A. 2009; 106 (19622740): 12688-12693
- Elastic behavior of RecA-DNA helical filaments.J. Mol. Biol. 2007; 370 (17559876): 837-845
- DNA dynamics in RecA-DNA filaments: ATP hydrolysis-related flexibility in DNA.Biochemistry. 2003; 42 (14556640): 12085-12094
- On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. I. Bypassing a short heterologous insert in one DNA substrate.J. Biol. Chem. 1992; 267 (1644827): 16438-16443
- Evidence for the coupling of ATP hydrolysis to the final (extension) phase of RecA protein-mediated DNA strand exchange.J. Biol. Chem. 1996; 271 (8621438): 5725-5732
- Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs.Mol. Cell. Biol. 2001; 21 (11283264): 2858-2866
- Rad51 paralogues Rad55-Rad57 balance the antirecombinase Srs2 in Rad51 filament formation.Nature. 2011; 479 (22020281): 245-248
- Rad51 paralogs remodel pre-synaptic Rad51 filaments to stimulate homologous recombination.Cell. 2015; 162 (26186187): 271-286
- The hyper-gene conversion hpr-1 mutation of Saccharomyces cerevisiae is an allele of the SRS2/RADH gene.Genetics. 1991; 127 (1849857): 75-85
- DNA helicase Srs2 disrupts the Rad51 presynaptic filament.Nature. 2003; 423 (12748644): 305-309
- The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments.Nature. 2003; 423 (12748645): 309-312
- The differentiated and conserved roles of Swi5–Sfr1 in homologous recombination.FEBS Lett. 2017; 591 (28423184): 2035-2047
- Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5–Sfr1 complex.Structure. 2012; 20 (22405003): 440-449
- Enhancement of ADP release from the RAD51 presynaptic filament by the SWI5–SFR1 complex.Nucleic Acids Res. 2014; 42 (24078249): 349-358
- Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function.Nucleic Acids Res. 2005; 33 (15944450): 3292-3302
- Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity.Proc. Natl. Acad. Sci. U.S.A. 2004; 101 (15226506): 9988-9993
- Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination.Nucleic Acids Res. 2012; 40 (22362735): 4904-4913
- Two three-strand intermediates are processed during Rad51-driven DNA strand exchange.Nat. Struct. Mol. Biol. 2018; 25 (29323270): 29-36
- Swi5–Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament.Nucleic Acids Res. 2014; 42 (24304898): 2358-2365
- A novel function of Rad54 protein. Stabilization of the Rad51 nucleoprotein filament.J. Biol. Chem. 2003; 278 (12566442): 14029-14036
- Combined optical and topographic imaging reveals different arrangements of human RAD54 with presynaptic and postsynaptic RAD51-DNA filaments.Proc. Natl. Acad. Sci. U.S.A. 2013; 110 (23801766): 11385-11390
- An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing.J. Mol. Biol. 1997; 274 (9398528): 213-221
- Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein.Mol. Cell. 1999; 4 (10619018): 705-714
- Exchange of DNA base pairs that coincides with recognition of homology promoted by E. coli RecA protein.Mol. Cell. 2004; 15 (15383285): 965-975
- Enhancement of RAD51 recombinase activity by the tumor suppressor PALB2.Nat. Struct. Mol. Biol. 2010; 17 (20871616): 1255-1259
- Promotion of homologous recombination and genomic stability by RAD51AP1 via RAD51 recombinase enhancement.Mol. Cell. 2007; 28 (17996711): 482-490
- Bipartite stimulatory action of the Hop2-Mnd1 complex on the Rad51 recombinase.Genes Dev. 2007; 21 (17639080): 1747-1757
- RAD51AP1 is a structure-specific DNA binding protein that stimulates joint molecule formation during RAD51-mediated homologous recombination.Mol. Cell. 2007; 28 (17996710): 468-481
- Monitoring homology search during DNA double-strand break repair in vivo.Mol. Cell. 2013; 50 (23523370): 261-272
- BRCA1–BARD1 promotes RAD51-mediated homologous DNA pairing.Nature. 2017; 550 (28976962): 360-365
- DNA sequence alignment by microhomology sampling during homologous recombination.Cell. 2015; 160 (25684365): 856-869
- DNA sequence alignment during homologous recombination.J. Biol. Chem. 2016; 291 (27129270): 11572-11580
- ATP hydrolysis promotes duplex DNA release by the RecA presynaptic complex.J. Biol. Chem. 2016; 291 (27587394): 22218-22230
- The role of negative superhelicity and length of homology in the formation of paranemic joints promoted by RecA protein.J. Biol. Chem. 1998; 273 (9575157): 12120-12127
- Synapsis and the formation of paranemic joints by E. coli RecA protein.Cell. 1983; 34 (6313216): 931-939
- Visualization of the paranemic joining of homologous DNA molecules catalyzed by the RecA protein of Escherichia coli.Proc. Natl. Acad. Sci. U.S.A. 1986; 83 (3515345): 2066-2070
- Visualizing RAD51-mediated joint molecules: implications for recombination mechanism and the effect of sequence heterology.Nucleic Acids Res. 2011; 39 (20817928): 155-167
- Nek1 regulates Rad54 to orchestrate homologous recombination and replication fork stability.Mol. Cell. 2016; 62 (27264870): 903-917
- Yeast Rad54 promotes Rad51-dependent homologous DNA pairing via ATP hydrolysis-driven change in DNA double helix conformation.J. Biol. Chem. 1999; 274 (10506208): 29453-29462
- Human Rad54 protein stimulates DNA strand exchange activity of hRad51 protein in the presence of Ca2+.J. Biol. Chem. 2004; 279 (15466868): 52042-52051
- Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA filaments.Mol. Cell. 2002; 10 (12453424): 1175-1188
- Superhelicity-driven homologous DNA pairing by yeast recombination factors Rad51 and Rad54.Mol. Cell. 2000; 6 (11030336): 563-572
- Rad54 functions as a heteroduplex DNA pump modulated by its DNA substrates and Rad51 during D loop formation.Mol. Cell. 2014; 53 (24486020): 420-432
- Transcription-dependent dynamic supercoiling is a short-range genomic force.Nat. Struct. Mol. Biol. 2013; 20 (23416947): 396-403
- Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin.J. Biol. Chem. 2003; 278 (12514177): 9212-9218
- A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing.J. Biol. Chem. 2004; 279 (15105430): 27824-27829
- The importance of being supercoiled: how DNA mechanics regulate dynamic processes.Biochim. Biophys. Acta. 2012; 1819 (22233557): 632-638
- Top3–Rmi1 dissolve Rad51-mediated D loops by a topoisomerase-based mechanism.Mol. Cell. 2015; 57 (25699708): 595-606
- Mutations in homologous recombination genes rescue top3 slow growth in Saccharomyces cerevisiae.Genetics. 2002; 162 (12399378): 647-662
- Srs2 promotes synthesis-dependent strand annealing by disrupting DNA polymerase delta-extending D-loops.eLife. 2017; 6 (28535142)e22195
- Interchromosomal crossover in human cells is associated with long gene conversion tracts.Mol. Cell. Biol. 2007; 27 (17515608): 5261-5274
- Yeast intrachromosomal recombination: long gene conversion tracts are preferentially associated with reciprocal exchange and require the RAD1 and RAD3 gene products.Genetics. 1989; 123 (2558957): 683-694
- The double-strand-break repair model for recombination.Cell. 1983; 33 (6380756): 25-35
- Generating crossovers by resolution of nicked Holliday junctions: a role for Mus81-Eme1 in meiosis.Mol. Cell. 2003; 12 (14527420): 761-774
- Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination.Genes Dev. 2009; 23 (19136626): 67-79
- Eukaryotic DNA polymerases in homologous recombination.Annu. Rev. Genet. 2016; 50 (27893960): 393-421
- PCNA is required for initiation of recombination-associated DNA synthesis by DNA polymerase δ.Mol. Cell. 2009; 36 (19941829): 704-713
- Reconstitution of recombination-associated DNA synthesis with human proteins.Nucleic Acids Res. 2013; 41 (23535143): 4913-4925
- Reconstitution of DNA repair synthesis in vitro and the role of polymerase and helicase activities.DNA Repair. 2011; 10 (21565563): 567-576
- Role of DNA replication proteins in double-strand break-induced recombination in Saccharomyces cerevisiae.Mol. Cell. Biol. 2004; 24 (15282291): 6891-6899
- Strand displacement synthesis by yeast DNA polymerase ϵ.Nucleic Acids Res. 2016; 44 (27325747): 8229-8240
- DNA synthesis dependent on genetic recombination: characterization of a reaction catalyzed by purified bacteriophage T4 proteins.Cell. 1986; 47 (3022939): 793-806
- Pif1 helicase and Pol δ promote recombination-coupled DNA synthesis via bubble migration.Nature. 2013; 502 (24025768): 393-396
- Drosophila BLM in double-strand break repair by synthesis-dependent strand annealing.Science. 2003; 299 (12522255): 265-267
- Acute inactivation of the replicative helicase in human cells triggers MCM8–9-dependent DNA synthesis.Genes Dev. 2017; 31 (28487407): 816-829
- Evidence for multiple cycles of strand invasion during repair of double-strand gaps in Drosophila.Genetics. 2004; 167 (15238522): 699-705
- Template switching during break-induced replication.Nature. 2007; 447 (17410126): 102-105
- The dissolution of double Holliday junctions.Cold Spring Harb. Perspect. Biol. 2014; 6 (24984776)a016477
- Multifunctional roles of Saccharomyces cerevisiae Srs2 protein in replication, recombination and repair.FEMS Yeast Res. 2017; 17 (28011904)
- Rad52 promotes postinvasion steps of meiotic double-strand-break repair.Mol. Cell. 2008; 29 (18313389): 517-524
- DNA annealing by RAD52 protein is stimulated by specific interaction with the complex of replication protein A and single-stranded DNA.Proc. Natl. Acad. Sci. U.S.A. 1998; 95 (9600915): 6049-6054
- Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes.Proc. Natl. Acad. Sci. U.S.A. 2008; 105 (19074292): 20274-20279
- Targeted inactivation of mouse RAD52 reduces homologous recombination but not resistance to ionizing radiation.Mol. Cell. Biol. 1998; 18 (9774658): 6423-6429
- Human cell assays for synthesis-dependent strand annealing and crossing over during double-strand break repair.G3. 2017; 7 (28179392): 1191-1199
- Double Holliday junctions are intermediates of DNA break repair.Nature. 2010; 464 (20348905): 937-941
- Holliday junction resolvases.Cold Spring Harb. Perspect. Biol. 2014; 6 (25183833)a023192
- Processing of joint molecule intermediates by structure-selective endonucleases during homologous recombination in eukaryotes.Chromosoma. 2011; 120 (21369956): 109-127
- The SMX DNA repair tri-nuclease.Mol. Cell. 2017; 65 (28257701): 848-860
Article info
Publication history
Footnotes
This work was supported by National Institutes of Health Grants GM58015 and CA92276 (to the W. D. H. laboratory). This is the third article in the Thematic Minireview series “DNA double-strand break repair and pathway choice.” The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
This article contains Figs. S1–S3.
Identification
Copyright
User license
Creative Commons Attribution (CC BY 4.0) |
Permitted
- Read, print & download
- Redistribute or republish the final article
- Text & data mine
- Translate the article
- Reuse portions or extracts from the article in other works
- Sell or re-use for commercial purposes
Elsevier's open access license policy