Premeiotic chromatin states orchestrate gene expression during male gametogenesis in rice

Male meiocyte specification from somatic tissue and male germ line development require extensive epigenetic reconfiguration. However, how the extent and the timing of the reconfiguration required for gene expression during the male lineage development remains unclear in rice.

Here, we integrate cell type-specific transcriptomic and epigenomic profiling across the rice male germline, from meiocytes to sperm cells. We show that gene expression programs in male gametic cells are largely prefigured by chromatin states established in meiocytes. In particular, H3K4me3 deposition initiated during meiosis is broadly maintained throughout development, whereas H3K27me3 is progressively reduced, contributing to stage-specific gene activation. DNA methylation patterns are largely stable, except for a transient reduction of CHH methylation in early microspores, accompanied by increased chromatin accessibility and enhanced H3K4me3. Notably, genes activated during microspore development are depleted of gene body DNA methylation (gbM), while gbM-enriched genes are preferentially repressed in sperm cells. Functional analysis of H3K4 methyltransferases demonstrates that pre-establishment of H3K4me3 is required for proper microspore gene expression and development.

Our findings reveal that a premeiotic chromatin blueprint is maintained to instruct transcriptional programs during male gametogenesis. This epigenetic configuration preferentially activates non-constitutive genes lacking gbM, suggesting a mechanism that may enhance regulatory flexibility and facilitate haploid selection. These results provide a conceptual framework for how chromatin state inheritance shapes gene expression and evolutionary dynamics in the plant male germline.