Suppression of crossing-over by DNA methylation in Ascobolus

Abstract

Homologous recombination between dispersed DNA repeats creates chromosomal rearrangements that are deleterious to the genome. The methylation associated with DNA repeats in many eukaryotes might serve to inhibit homologous recombination and play a role in preserving genome integrity. We have tested the hypothesis that DNA methylation suppresses meiotic recombination in the fungus Ascobolus immersus. The natural process of methylation-induced premeiotically (MIP) was used to methylate the b2 spore color gene, a 7.5-kb chromosomal recombination hot spot. The frequency of crossing-over between two markers flanking b2 was reduced several hundredfold when b2 was methylated on the two homologs. This demonstrates that DNA methylation strongly inhibits homologous recombination. When b2 was methylated on one homolog only, crossing-over was still reduced 50-fold, indicating that the effect of methylation cannot be limited to the blocking of initiation of recombination on the methylated homolog. On the basis of these and other observations, we propose that DNA methylation perturbs pairing between the two intact homologs before recombination initiation and/or impairs the normal processing of recombination intermediates.[Key Words: Ascobolus immersus; chromosome rearrangements; crossing-over; DNA methylation; meiotic recombination; repeat DNA sequences] Received November 28, 1997; revised version accepted February 20, 1998. Crossing-over between dispersed DNA repeats results in chromosomal rearrangements. In eukaryotes, the destructive potential of dispersed repeats through ectopic homologous recombination is well documented (Rouyer et al. 1987;Montgomery et al. 1991;Small et al. 1997). In yeast, artificial duplications placed in ectopic position can interact and generate chromosomal rearrangements through homologous recombination at high frequency during meiosis (Lichten et al. 1987). In higher eukaryotes, the number of repeats per genome is often so high that no single cell would escape genomic rearrangements if ectopic recombination were to occur at high frequencies. Therefore, factors must exist that limit recombination between dispersed repeats. Thuriaux (1977) pointed out that the frequency of crossing-over per unit of physical DNA length decreases with increasing genome size, and proposed that recombination is confined to genes. According to this hypothesis, satellite DNA sequences and interspersed DNA repeats, which constitute the bulk of the intergenic regions, must be poor substrates for meiotic recombination even when in allelic positions. Nucleotidic divergence (Rayssiguier et al. 1989;Radman and Wagner 1993) and an insufficient length of sequence identity (Shen and Huang 1986;Jinks-Robertson et al. 1993) are two factors known to reduce drastically homologous recombination. Nevertheless, other factors that suppress homologous recombination are required to protect genomes against the threat generated by families of long DNA repeats that have diverged little or not at all (e.g., after recent duplication events)....

DNA methylation, methyltransferases, and cancer

“…Several examples of recombination events between repeats have been identi®ed in the human population and these have had deleterious consequences (Puget et al, 1997;Rouyer et al, 1987;Small et al, 1997). Work with the fungus Ascobolus immersus has demonstrated that induced methylation of a meiotic recombination hotspot reduced the frequency of crossing-over within this region by several hundredfold (Maloisel and Rossignol, 1998). The most direct evidence that DNA methylation suppresses homologous recombination has come from the work in Ascobolus, but several studies support a similar role in mammalian cells.…”

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

“…DNA methylation also represses CO formation (Maloisel and Rossignol 1998) and is sufficient to silence CO hotspots in Arabidopsis (Yelina et al 2015). CO distribution is largely modified in Arabidopsis met1 and ddm1 mutants, which show an increase of proximal recombination events and a simultaneous decrease in pericentromeric and distal regions (Colome-Tatche et al 2012;Melamed-Bessudo and Levy 2012;Mirouze et al 2012;Yelina et al 2012).…”

Repetitive sequence environment distinguishes housekeeping genes

“…Long repeats including LINE-1 elements are normally heavily DNA-methylated (Woodcock et al, 1988;Crowther et al, 1991;Woodcock et al, 1997), a feature of heterochromatin. DNA methylation (and heterochromatin in general) has been reported to suppress homologous recombination (Pàldi et al, 1995;Maloisel and Rossignol, 1998;Schnable et al, 1998;Fu et al, 2002;Yao et al, 2002;Yamada et al, 2004;Myers et al, 2005) as well as transposition (Yoder et al, 1997;Walsh et al, 1998;Hirochika et al, 2000;Robertson, 2001;Bird, 2002;Kato et al, 2003). Accordingly, reports of deletions caused by homologous recombination between LINE-1 elements are rare (Segal et al, 1999) except in cancers (Florl and Schulz, 2003) where LINE-1 elements are frequently hypomethylated (Santourlidis et al, 1999;Takai et al, 2000;Ehrlich, 2002;Carnell and Goodman, 2003;Florl et al, 2004;Roman-Gomez et al, 2005).…”