Modifying meiotic recombination by targeting chromatin modifiers to crossover hotspots in Arabidopsis

The impact of specific chromatin modifications on meiotic crossover frequency is usually inferred from correlative studies, leaving open the question of causality. To address this, we used a dCas9-based system to target histone H3 methylation modifiers to defined genomic loci. Targeting methyltransferases responsible for H3K9me3 and H3K27me3 had little effect on recombination at selected hotspots, whereas targeting H3K4me3- and H3K36me3-associated enzymes often silenced the endogenous genes. The strongest effect was observed with the demethylase JMJ14, which reduced local H3K4me3 levels and decreased crossover frequency within the targeted interval. This was accompanied by reduced transcription of a long non-coding RNA (lncRNA) located at the hotspot and altered crossover topology. Suppressed recombination was also seen at neighbouring, untargeted hotspots. Conversely, directing the transcriptional activator VP64 to the same region elevated lncRNA expression, increased crossover frequency, and raised H3K4me3 levels. Our results reveal a causal relationship between H3K4me3, transcription, and local crossover activity, demonstrating that H3K4me3 levels are tightly associated with both transcriptional output and recombination frequency at specific genomic sites.