Synthesis-dependent strand annealing

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A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type. Homologous Recombination.jpg
A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.

Synthesis-dependent strand annealing (SDSA) is a major mechanism of homology-directed repair of DNA double-strand breaks (DSBs). Although many of the features of SDSA were first suggested in 1976, [1] the double-Holliday junction model proposed in 1983 [2] was favored by many researchers. In 1994, studies of double-strand gap repair in Drosophila were found to be incompatible with the double-Holliday junction model, leading researchers to propose a model they called synthesis-dependent strand annealing. [3] Subsequent studies of meiotic recombination in S. cerevisiae found that non-crossover products appear earlier than double-Holliday junctions or crossover products, challenging the previous notion that both crossover and non-crossover products are produced by double-Holliday junctions and leading the authors to propose that non-crossover products are generated through SDSA. [4]

In the accompanying Figure, the first step labeled “5’ to 3’ resection” shows the formation of a 3’ ended single DNA strand that in the next step invades a homologous DNA duplex. RNA polymerase III is reported to catalyze formation of a transient RNA-DNA hybrid at double-strand breaks as an essential intermediate step in the repair of the breaks by homologous recombination. [5] Formation of the RNA-DNA hybrid would protect the invading single-stranded DNA from degradation. After the transient RNA-DNA hybrid intermediate is formed the RNA strand is replaced by the Rad51 protein which catalyzes the subsequent stage of strand invasion.

In the SDSA model, repair of double-stranded breaks occurs without the formation of a double Holliday junction, so that the two processes of homologous recombination are identical until just after D-loop formation. [6] In yeast, the D-loop is formed by strand invasion with the help of proteins Rad51 and Rad52, [7] and is then acted on by DNA helicase Srs2 to prevent formation of the double Holliday junction in order for the SDSA pathway to occur. [8] The invading 3' strand is thus extended along the recipient homologous DNA duplex by DNA polymerase in the 5' to 3' direction, so that the D-loop physically translocates – a process referred to as bubble migration DNA synthesis. [9] The resulting single Holliday junction then slides down the DNA duplex in the same direction in a process called branch migration, displacing the extended strand from the template strand. This displaced strand pops up to form a 3' overhang in the original double-stranded break duplex, which can then anneal to the opposite end of the original break through complementary base pairing. Thus DNA synthesis fills in gaps left over from annealing, and extends both ends of the still present single stranded DNA break, ligating all remaining gaps to produce recombinant non-crossover DNA. [10]

SDSA is unique in that D-loop translocation results in conservative rather than semiconservative replication, as the first extended strand is displaced from its template strand, leaving the homologous duplex intact. Therefore, although SDSA produces non-crossover products because flanking markers of heteroduplex DNA are not exchanged, gene conversion may occur, wherein nonreciprocal genetic transfer takes place between two homologous sequences. [11]

Enzymes employed in SDSA during meiosis

Assembly of a nucleoprotein filament comprising single-stranded DNA (ssDNA) and the RecA homolog, Rad51, is a key step necessary for homology search during recombination. In the budding yeast Saccharomyces cerevisiae , Srs2 translocase dismantles Rad51 filaments during meiosis. [12] By directly interacting with Rad51, Srs2 dislodges Rad51 from nucleoprotein filaments thereby inhibiting Rad51-dependent formation of joint molecules and D-loop structures. This dismantling activity is specific for Rad51 since Srs2 does not dismantle DMC1 (a meiosis-specific Rad51 homolog), Rad52 (a Rad 51 mediator) or replication protein A (RPA, a single-stranded DNA binding protein). Srs2 promotes the non-crossover SDSA pathway, apparently by regulating RAD51 binding during strand exchange. [13]

Divergence between SDSA and double-Holliday junction occurs when the D-loop is disassembled allow the nascent strand to anneal to other resected end of the DSB (in the double-Holliday junction model the strand displaced by D-loop extension anneals to the other end of the DSB in "2nd end capture"). Research in Drosophila melanogaster identified the Bloom syndrome helicase (Blm) as the enzyme promoting dissassembly of the D-loop. [14] [15] [16] Similarly, S. cerevisiae Sgs1, an ortholog of BLM, appears to be a central regulator of most of the recombination events that occur during S. cerevisiae meiosis. [17] Sgs1(BLM) may disassemble D-loop structures analogous to early strand invasion intermediates and thus promote NCO formation by SDSA. [17] The Sgs1 helicase forms a conserved complex with the topoisomerase III (Top3)-RMI1 heterodimer (that catalyzes DNA single strand passage). This complex, called STR (for its three components), promotes early formation of NCO recombinants by SDSA during meiosis. [18]

As reviewed by Uringa et al. [19] the RTEL1 helicase is proposed to regulate recombination during meiosis in the worm Caenorhabditis elegans . RTEL1 is a key protein in repair of DSBs. It disrupts D-loops and is thought to promote NCO outcomes through SDSA.

The number of DSBs created during meiosis can substantially exceed the number of final CO events. In the plant Arabidopsis thaliana , only about 4% of DSBs are repaired by CO recombination, [20] suggesting that most DSBs are repaired by NCO recombination. Data based on tetrad analysis from several species of fungi show that only a minority (on average about 34%) of recombination events during meiosis are COs (see Whitehouse, [21] Tables 19 and 38 for summaries of data from S. cerevisiae , Podospora anserina , Sordaria fimicola and Sordaria brevicollis). In the fruit fly D. melanogaster during meiosis in females there is at least a 3:1 ratio of NCOs to COs. [22] These observations indicate that the majority of recombination events during meiosis are NCOs, and suggest that SDSA is the principal pathway for recombination during meiosis.

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<span class="mw-page-title-main">Chromosomal crossover</span> Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

<span class="mw-page-title-main">Genetic recombination</span> Production of offspring with combinations of traits that differ from those found in either parent

Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes ; & (2) intrachromosomal recombination, occurring through crossing over.

RecQ helicase is a family of helicase enzymes initially found in Escherichia coli that has been shown to be important in genome maintenance. They function through catalyzing the reaction ATP + H2O → ADP + P and thus driving the unwinding of paired DNA and translocating in the 3' to 5' direction. These enzymes can also drive the reaction NTP + H2O → NDP + P to drive the unwinding of either DNA or RNA.

Gene conversion is the process by which one DNA sequence replaces a homologous sequence such that the sequences become identical after the conversion event. Gene conversion can be either allelic, meaning that one allele of the same gene replaces another allele, or ectopic, meaning that one paralogous DNA sequence converts another.

<span class="mw-page-title-main">Heteroduplex</span>

A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms.

<span class="mw-page-title-main">Homologous recombination</span> Genetic recombination between identical or highly similar strands of genetic material

Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids.

<span class="mw-page-title-main">Synapsis</span> Biological phenomenon in meiosis

Synapsis or Syzygy is the pairing of two chromosomes that occurs during meiosis. It allows matching-up of homologous pairs prior to their segregation, and possible chromosomal crossover between them. Synapsis takes place during prophase I of meiosis. When homologous chromosomes synapse, their ends are first attached to the nuclear envelope. These end-membrane complexes then migrate, assisted by the extranuclear cytoskeleton, until matching ends have been paired. Then the intervening regions of the chromosome are brought together, and may be connected by a protein-DNA complex called the synaptonemal complex. During synapsis, autosomes are held together by the synaptonemal complex along their whole length, whereas for sex chromosomes, this only takes place at one end of each chromosome.

<span class="mw-page-title-main">Holliday junction</span> Branched nucleic acid structure

A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after Robin Holliday, the molecular biologist who proposed its existence in 1964.

Mitotic recombination is a type of genetic recombination that may occur in somatic cells during their preparation for mitosis in both sexual and asexual organisms. In asexual organisms, the study of mitotic recombination is one way to understand genetic linkage because it is the only source of recombination within an individual. Additionally, mitotic recombination can result in the expression of recessive alleles in an otherwise heterozygous individual. This expression has important implications for the study of tumorigenesis and lethal recessive alleles. Mitotic homologous recombination occurs mainly between sister chromatids subsequent to replication. Inter-sister homologous recombination is ordinarily genetically silent. During mitosis the incidence of recombination between non-sister homologous chromatids is only about 1% of that between sister chromatids.

<span class="mw-page-title-main">Sister chromatid exchange</span>

Sister chromatid exchange (SCE) is the exchange of genetic material between two identical sister chromatids.

Chromosome segregation is the process in eukaryotes by which two sister chromatids formed as a consequence of DNA replication, or paired homologous chromosomes, separate from each other and migrate to opposite poles of the nucleus. This segregation process occurs during both mitosis and meiosis. Chromosome segregation also occurs in prokaryotes. However, in contrast to eukaryotic chromosome segregation, replication and segregation are not temporally separated. Instead segregation occurs progressively following replication.

<span class="mw-page-title-main">Bloom syndrome protein</span> Mammalian protein found in humans

Bloom syndrome protein is a protein that in humans is encoded by the BLM gene and is not expressed in Bloom syndrome.

<span class="mw-page-title-main">Exonuclease 1</span> Protein-coding gene in the species Homo sapiens

Exonuclease 1 is an enzyme that in humans is encoded by the EXO1 gene.

<span class="mw-page-title-main">TOP3A</span> Protein-coding gene in the species Homo sapiens

DNA topoisomerase 3-alpha is an enzyme that in humans is encoded by the TOP3A gene.

<span class="mw-page-title-main">DMC1 (gene)</span> Protein-coding gene in the species Homo sapiens

Meiotic recombination protein DMC1/LIM15 homolog is a protein that in humans is encoded by the DMC1 gene.

<span class="mw-page-title-main">MUS81</span> Protein-coding gene in the species Homo sapiens

Crossover junction endonuclease MUS81 is an enzyme that in humans is encoded by the MUS81 gene.

<span class="mw-page-title-main">FANCM</span> Mammalian protein found in Homo sapiens

Fanconi anemia, complementation group M, also known as FANCM is a human gene. It is an emerging target in cancer therapy, in particular cancers with specific genetic deficiencies.

Sgs1, also known as slow growth suppressor 1, is a DNA helicase protein found in Saccharomyces cerevisiae. It is a homolog of the bacterial RecQ helicase. Like the other members of the RecQ helicase family, Sgs1 is important for DNA repair. In particular, Sgs1 collaborates with other proteins to repair double-strand breaks during homologous recombination in eukaryotes.

<span class="mw-page-title-main">Crossover interference</span> Phenomenon in genetics

Crossover interference is the term used to refer to the non-random placement of crossovers with respect to each other during meiosis. The term is attributed to Hermann Joseph Muller, who observed that one crossover "interferes with the coincident occurrence of another crossing over in the same pair of chromosomes, and I have accordingly termed this phenomenon ‘interference’."

<span class="mw-page-title-main">Double-strand break repair model</span>

A double-strand break repair model refers to the various models of pathways that cells undertake to repair double strand-breaks (DSB). DSB repair is an important cellular process, as the accumulation of unrepaired DSB could lead to chromosomal rearrangements, tumorigenesis or even cell death. In human cells, there are two main DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR relies on undamaged template DNA as reference to repair the DSB, resulting in the restoration of the original sequence. NHEJ modifies and ligates the damaged ends regardless of homology. In terms of DSB repair pathway choice, most mammalian cells appear to favor NHEJ rather than HR. This is because the employment of HR may lead to gene deletion or amplification in cells which contains repetitive sequences. In terms of repair models in the cell cycle, HR is only possible during the S and G2 phases, while NHEJ can occur throughout whole process. These repair pathways are all regulated by the overarching DNA damage response mechanism. Besides HR and NHEJ, there are also other repair models which exists in cells. Some are categorized under HR, such as synthesis-dependent strain annealing, break-induced replication, and single-strand annealing; while others are an entirely alternate repair model, namely, the pathway microhomology-mediated end joining (MMEJ).

References

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