Academic journal article Genetics

The Effect of Sequence Divergence on Recombination between Direct Repeats in Arabidopsis

Academic journal article Genetics

The Effect of Sequence Divergence on Recombination between Direct Repeats in Arabidopsis

Article excerpt

ABSTRACT

It is well established that sequence divergence has an inhibitory effect on homologous recombination. However, a detailed analysis of this relationship is missing for most higher eukaryotes. We have measured the rate of somatic recombination between direct repeats as a function of the number, type, and position of divergent nucleotides in Arabidopsis. We show that a minor divergence level of 0.16% (one mutation in otherwise identical 618 bp) has a profound effect, decreasing the recombination rate approximately threefold. A further increase in the divergence level affects the recombination rate to a smaller extent until a "divergence saturation" effect is reached at relatively low levels of divergence (~0.5%). The type of mismatched nucleotide does not affect recombination rates. The decrease in the rate of recombination caused by a single mismatch was not affected by the position of the mismatch along the repeat. This suggests that most recombination intermediate tracts contain a mismatch and thus are as long as the full length of the 618-bp repeats. Finally, we could deduce an antirecombination efficiency of ~66% for the first mismatch in the repeat. Altogether, this work shows some degree of conservation across kingdoms when compared to previous reports in yeast; it also provides new insight into the effect of sequence divergence on homologous recombination.

HOMOLOGOUS recombination (HR) plays a major role in promoting genetic diversity. Ironically, it is also essential for maintaining genome stability in various ways. It ensures proper chromosome segregation by forming a physical link between homologs during meiosis. It enables the accurate repair of potentially lethal DNA double-strand breaks using a homologous donor sequence as template. It also plays a crucial role in controlling the choice of partners during the recombination process. HR between wrongly chosen partner sequences poses a threat to the organism by ways of genome rearrangements. This is an especially challenging problem in higher eukaryotes, which often have repeat-rich genomes. Plant genomes, for example, contain a high proportion of repetitive elements and are often polyploid, containing two or more divergent (homeologous) genomes. Two important physical factors that affect the rate of HR between DNA fragments are sequence length and divergence. The rate of HR was found to increase with the increase in length of the recombining homologous sequences in several organisms (RUBNITZ and SUBRAMANI 1984; SHEN and HUANG 1986; LISKAY et al. 1987; AHN et al. 1988; PUCHTA and HOHN 1991; DENG and CAPECCHI 1992; JINKS-ROBERTSON et al. 1993; BELL and MCCULLOCH 2003). This increase was often, but not always, linearly dependent on the length.

In general, the rate of HR is lower between divergent sequences than between identical sequences (see review in MODRICH and LAHUE 1996). A single nucleotide heterology was shown to inhibit recombination in bacteria (CLAVERYS and LACKS 1986), in yeast (DATTA et al. 1997), and in mammalian cells (LUKACSOVICH and WALDMAN 1999). In most studies in yeast and bacteria, the relationship between recombination and divergence was log linear (ZAWADZKI et al. 1995; DATTA et al. 1997; VULIC et al. 1997). Interestingly, in yeast the first mismatches were shown to have a much stronger inhibitory effect than the additional mismatches (DATTA et al. 1997), a phenomenon termed as the "rapid drop-off" of recombination. The mechanism responsible for this rapid drop-off effect is the mismatch repair (MMR) machinery. It was shown that in the absence of MMR activities the DNA of distant species could recombine (RAYSSIGUIER et al. 1989). Similarly, in yeast the rapid drop-off was abolished in MMR mutants (DATTA et al. 1997).

In plants, most of our knowledge regarding the effects of sequence divergence on HR rates comes from studies on meiotic recombination between chromosomes or chromosomal segments. For example, homeologous chromosomes in wheat do not normally pair at meiosis except in some pairing mutants (SEARS 1976). …

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