Mop1 reshapes maize recombination landscape by modulating DNA methylation at MITEs with open chromatin

ABSTRACT: Meiotic recombination ensures genetic diversity and proper chromosome segregation, but its regulation remains not yet completely understood in many species. Here, we investigate the role of Mediator of paramutation1 (Mop1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover (CO) mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with CO numbers significantly reduced in male meiosis but unchanged in females. Sequence analysis of CO-associated motifs reveals increased enrichment of A/T polymer motifs in female mop1 and decreased enrichment of C/G motifs in male mop1 mutants, suggesting a transition to open chromatin states at these regions. Furthermore, we demonstrate that mop1 preferentially introduces new CO sites in females within regions of higher genetic diversity, particularly near miniature inverted-repeat transposable elements (MITEs). Epigenomic profiling reveals that mop1 significantly reduces CHH methylation at MITEs near genes. MITEs that overlap with differentially methylated regions (DMRs) and CO sites exhibit higher levels of histone marks associated with open chromatin, such as H2A.Z and histone acetylation, compared to MITEs outside DMRs or COs. However, the removal of CHH methylation in mop1 at MITEs that introduce COs does not alter the expression of flanking genes. Together, these results highlight the critical role of MOP1 in regulating meiotic recombination by modulating DNA methylation and chromatin states at transposable elements, providing new insights into the epigenetic regulation of meiotic recombination.

ORGANISM(S): Zea mays

PROVIDER: GSE304481 | GEO | 2025/09/15

REPOSITORIES: GEO