Meixia Zhao,  Jia-Chi Ku,  Beibei Liu, Diya Yang,  Liangwei Yin,  Tyshawn J. Ferrell,  Claire E. Stoll,  Wei Guo, Xinyan Zhang,  Dafang Wang,  Chung-Ju Rachel Wang, and Damon Lisch

PNAS February 16, 2021 118 (7) e2009475118

Significance

Meiotic recombination is regulated by both genetic and epigenetic factors such as DNA methylation. In maize, we found that the mop1 mutation removes CHH (where H = A, T, or C) methylation that is immediately adjacent to sites of frequent recombination in both chromosomal arms and pericentromeric regions. We further found that the mop1 mutation increased meiotic recombination frequencies in chromosomal arms but decreased them in pericentromeric regions. Our data demonstrate that although CHH methylation is present at a much lower level than CG and CHG methylation, it has a substantial effect on recombination frequencies, suggesting an important role for RNA-directed DNA methylation in meiotic recombination in maize.

Abstract

Meiotic recombination is a fundamental process that generates genetic diversity and ensures the accurate segregation of homologous chromosomes. While a great deal is known about genetic factors that regulate recombination, relatively little is known about epigenetic factors, such as DNA methylation. In maize, we examined the effects on meiotic recombination of a mutation in a component of the RNA-directed DNA methylation pathway, Mop1 (Mediator of paramutation1), as well as a mutation in a component of the trans-acting small interference RNA biogenesis pathway, Lbl1 (Leafbladeless1). MOP1 is of particular interest with respect to recombination because it is responsible for methylation of transposable elements that are immediately adjacent to transcriptionally active genes. In the mop1 mutant, we found that meiotic recombination is uniformly decreased in pericentromeric regions but is generally increased in gene rich chromosomal arms. This observation was further confirmed by cytogenetic analysis showing that although overall crossover numbers are unchanged, they occur more frequently in chromosomal arms in mop1 mutants. Using whole genome bisulfite sequencing, our data show that crossover redistribution is driven by loss of CHH (where H = A, T, or C) methylation within regions near genes. In contrast to what we observed in mop1 mutants, no significant changes were observed in the frequency of meiotic recombination in lbl1 mutants. Our data demonstrate that CHH methylation has a significant impact on the overall recombination landscape in maize despite its low frequency relative to CG and CHG methylation.

See: https://www.pnas.org/content/118/7/e2009475118

Figure 1: Strategy to construct the backcross (BC1) populations and measure recombination frequency. (A) Genetic pipeline to construct backcross populations from different F1 genotypes. B73 and Mo17 are two maize inbred lines. (B) Schematic diagram to measure recombination frequency. A (a) and B (b) represent polymorphic markers between the B73 and Mo17 genomes.