We discussed a paper by Yelina et al. (2015) titled “DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis” (PMID: 26494791; doi: 10.1101/gad.270876.115) in our journal club today. It’s a pretty interesting paper with intriguing topic and smart experimental designs.
The authors previously identified two meiotic crossover hot spots, 3a and 3b on subtelomeric regions of Chromasome 3 in Arabidopsis (Yelina et al., 2012). These crossover hot spots have low CG methylation compared to average genome methylation level or regions in between 3a and 3b. They then tested if increasing DNA methylation in 3a and 3b could suppress meiotic crossover rate by expressing inverted-repeat (IR) transgene, which would trigger RdDM in targeted regions. Interestingly, meiotic crossover rate significantly decreased in several IR expressed lines (Figure 1 and 2, Table 1). Other RdDM markers, such as increased H3K9me2 and denser nucleosome occupancy were also detected in IR targeted regions (Figure 3). There results indicate that crossover rate is negatively correlated with DNA methylation in euchromatic regions.
It is thus obvious to ask that if crossover rate would significantly elevate if genome-wide demethylation occurred. The authors used met1/+ plants to test this hypothesis. However, overall crossover rates were similar in Col/Ler vs met1 Col/Ler. Regional remodeling of crossover around subtelomeric and pericentromeric regions was observed (Figure 4C). They showed that the remodeling of crossover in met1 was dependent on crossover interference pathway (Figure 4G). The analysis of crossover in met1 mutant suggests that genome-wide demethylation has different effect on crossover in euchromatic and centromeric regions. Very interestingly, the met1 mutation causes increased crossover in euchromatic regions, but vise versa in pericentromeric regions (Figure 5D). They further showed that double strand DNA breakage (DSB) was similar in met1 and WT in Arabidopsis (Figure 6), which ruled out the possibility that crossover remodeling in met1 was due to altered DSB.
A few brilliant technique/experiments were used in this research. I think it’s very smart to study meiotic crossover by studying pollen DNA. More information about pollen typing could be found in Drouaud and Mézard (2011). The crossover detecting system by using GFP/RFP that inserts into different positions on same chromosome is also very neat. More information about the GFP/RFP lines can be found in Yelina et al. (2012) paper.
Drouaud, J., & Mézard, C. (2011). Characterization of meiotic crossovers in pollen from Arabidopsis thaliana. DNA Recombination: Methods and Protocols, 223-249.
Yelina, N. E., Choi, K., Chelysheva, L., Macaulay, M., De Snoo, B., Wijnker, E., … & Mezard, C. (2012). Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants. PLoS Genet, 8(8), e1002844.
Yelina, N. E., Lambing, C., Hardcastle, T. J., Zhao, X., Santos, B., & Henderson, I. R. (2015). DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis. Genes Dev, 29, 2183-2202.