Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.

BACKGROUND: Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined. RESULTS: To explore the centromere-proximal meiotic recombination landscape, we map 14,397 crossovers against fully assembled Arabidopsis thaliana (A. thaliana) genomes. A. thaliana centromeres comprise megabase satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome contains a structurally polymorphic region of ~3-4 megabases, which lack crossovers and include the satellite arrays. This polymorphic region is flanked by ~1-2 megabase low-recombination zones. These recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We map crossovers at high-resolution in proximity to CEN3, which resolves punctate centromere-proximal hotspots that overlap gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape is remodelled in DNA methylation mutants. We observe that the centromeric low-recombining zones decrease and increase crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non-recombining zones remain suppressed. CONCLUSION: Our work relates the genetic and epigenetic organization of A. thaliana centromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.

Meiotic recombination within plant centromeres.

Meiosis is a conserved eukaryotic cell division that increases genetic diversity in sexual populations. During meiosis homologous chromosomes pair and undergo recombination that can result in reciprocal genetic exchange, termed crossover. The frequency of crossover is highly variable along chromosomes, with hot spots and cold spots. For example, the centromeres that contain the kinetochore, which attach chromosomes to the microtubular spindle, are crossover cold spots. Plant centromeres typically consist of large tandemly repeated arrays of satellite sequences and retrotransposons, a subset of which assemble CENH3-variant nucleosomes, which bind to kinetochore proteins. Although crossovers are suppressed in centromeres, there is abundant evidence for gene conversion and homologous recombination between repeats, which plays a role in satellite array change. We review the evidence for recombination within plant centromeres and the implications for satellite sequence evolution. We speculate on the genetic and epigenetic features of centromeres that may influence meiotic recombination in these regions. We also highlight unresolved questions relating to centromere function and sequence change and how the advent of new technologies promises to provide insights.

Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis.

During meiosis, homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double-strand breaks (DSBs), which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In Arabidopsis, competing pathways balance the repair of ∼100-200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as noncrossovers. To bias DSB repair toward crossovers, we simultaneously increased dosage of the procrossover E3 ligase gene HEI10 and introduced mutations in the anticrossovers helicase genes RECQ4A and RECQ4B As HEI10 and recq4a recq4b increase interfering and noninterfering crossover pathways, respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased HEI10 dosage increases crossover coincidence, which indicates an effect on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases distally towards the subtelomeres in both HEI10 and recq4a recq4b backgrounds, while the centromeres remain crossover suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.