8. Gene conversion accounts for interallelic recombination

14.8 Gene conversion accounts for interallelic recombination

Key terms defined in this section

Gene conversion is the alteration of one strand of a heteroduplex DNA to make it complementary with the other strand at any position(s) where there were mispaired bases.
Postmeiotic segregation describes the segregation of two strands of a duplex DNA that bear different information (created by heteroduplex formation during meiosis) when a subsequent replication allows the strands to separate.

The involvement of heteroduplex DNA explains the characteristics of recombination between alleles; indeed, allelic recombination provided the impetus for the development of the heteroduplex model. When recombination between alleles was discovered, the natural assumption was that it takes place by the same mechanism of reciprocal recombination that applies to more distant loci. That is to say that an individual breakage and reunion event occurs within the locus to generate a reciprocal pair of recombinant chromosomes. However, in the close quarters of a single gene, the formation of heteroduplex DNA itself is usually responsible for the recombination event.

Figure 14.14 Spore formation in the Ascomycetes allows determination of the genetic constitution of each of the DNA strands involved in meiosis.

Individual recombination events can be studied in the Ascomycetes fungi, because the products of a single meiosis are held together in a large cell, the ascus. Even better, the four haploid nuclei produced by meiosis are arranged in a linear order. Actually, a mitosis occurs after the production of these four nuclei, giving a linear series of eight haploid nuclei. Figure 14.14 shows that each of these nuclei effectively represents the genetic character of one of the eight strands of the four chromosomes produced by the meiosis.

Meiosis in a heterozygote should generate four copies of each allele. This is seen in the majority of spores. But there are some spores with abnormal ratios. They are explained by the formation and correction of heteroduplex DNA in the region in which the alleles differ. The figure illustrates a recombination event in which a length of hybrid DNA occurs on one of the four meiotic chromosomes, a possible outcome of recombination initiated by a double-strand break.

Suppose that two alleles differ by a single point mutation. When a strand exchange occurs to generate heteroduplex DNA, the two strands of the heteroduplex will be mispaired at the site of mutation. So each strand of DNA carries different genetic information. If no change is made in the sequence, the strands separate at the ensuing replication, each giving rise to a duplex that perpetuates its information. This event is called postmeiotic segregation, because it reflects the separation of DNA strands after meiosis. Its importance is that it demonstrates directly the existence of heteroduplex DNA in recombining alleles.

Another effect is seen when examining recombination between alleles: the proportions of the alleles differ from the initial 4:4 ratio. This effect is called gene conversion. It describes a nonreciprocal transfer of information from one chromatid to another.

Gene conversion results from exchange of strands between DNA molecules, and the change in sequence may have either of two causes at the molecular level:

Figure 14.5 Recombination is initiated by a double-strand break, followed by formation of single-stranded 3 F ends, one of which migrates to a homologous duplex.

• As indicated by the double-strand break model in Figure 14.5, one DNA duplex may act as a donor of genetic information that directly replaces the corresponding sequences in the recipient duplex by a process of strand exchange and gap filling.
  
• As part of the exchange process, heteroduplex DNA is generated when a single strand from one duplex pairs with its complement in the other duplex. Repair systems recognize mispaired bases in heteroduplex DNA, and may then excise and replace one of the strands to restore complementarity. Such an event changes the strand of DNA representing one allele into the sequence of the other allele.

Figure 14.2 Recombination between two paired duplex DNAs could involve reciprocal single-strand exchange, branch migration, and nicking.

Figure 14.4 Resolution of a Holliday junction can generate parental or recombinant duplexes, depending on which strands are nicked. Both types of product have a region of heteroduplex DNA.

Gene conversion does not depend on crossing Vover, but is correlated with it. A large proportion of the aberrant asci show genetic recombination between two markers on either side of a site of interallelic gene conversion. This is exactly what would be predicted if the aberrant ratios result from initiation of the recombination process as shown in Figure 14.2 or 14.5, but with an approximately equal probability of resolving the structure with or without recombination (as indicated in Figure 14.4). The implication is that fungal chromosomes initiate crossing-over about twice as often as would be expected from the frequency of recombination between distant genes.

Various biases are seen when recombination is examined at the molecular level. Either direction of gene conversion may be equally likely, or allele-specific effects may create a preference for one direction. Gradients of recombination may fall away from hotspots. We now know that hotspots represent sites at which double Vstrand breaks are initiated, and the gradient is correlated with the extent to which the gap at the hotspot is enlarged and converted to long single-stranded ends (as discussed previously).

Some information about the extent of gene conversion is provided by the sequences of members of gene clusters. Usually, the products of a recombination event will separate and become unavailable for analysis at the level of DNA sequence. However, when a chromosome carries two (non Vallelic) genes that are related, they may recombine by an "unequal crossing-over" event, as discussed in 4 Clusters and repeats. All we need to note for now is that a heteroduplex may be formed between the two nonallelic genes. Gene conversion effectively converts one of the nonallelic genes to the sequence of the other.

The presence of more than one gene copy on the same chromosome provides a footprint to trace these events. For example, if heteroduplex formation and gene conversion occurred over part of one gene, this part may have a sequence identical with or very closely related to the other gene, while the remaining part shows more divergence. Available sequences suggest that gene conversion events may extend for considerable distances, up to a few thousand bases.