ZmEMF1a is required for the maintenance of H2Aub and H3K27me3 modifications in maize kernel development

Polycomb group (PcG) proteins silence gene expression by depositing histone modifications such as H2Aub and H3K27me3, and this process is essential for maintaining cell type and tissue-specific gene expression patterns. However, the role of PcG proteins in regulating gene expression through H2Aub and H3K27me3 during maize kernel development remains poorly understood.

Here, we characterize a maize miniature seed mutant, mn8, and identify the causal gene as ZmEMF1a, a plant-specific PcG protein. A mutation in ZmEMF1a significantly reduces kernel size and weight. Molecular analyses demonstrate that ZmEMF1a interacts with ZmRING1 (a PRC1 component) and ZmMSI1 (a PRC2 component), which are essential for the establishment of H2Aub and H3K27me3 modifications. Loss of ZmEMF1a leads to a significant reduction in genomic levels of both H2Aub and H3K27me3. Integrated ChIP-seq and RNA-seq analyses revealed that H2Aub is negatively correlated with gene expression in maize, contrasting with the positive correlation reported in Arabidopsis. Compared with wild-type endosperms, mn8 endosperms exhibit up-regulated expression of cell proliferation repressor homologs, such as ZmDA1, ZmBB1, ZmES22, ZmMADS8, and ZmMADS14. Concurrently, these loci show reduced levels of H3K27me3 or H2Aub modifications. These findings suggest that ZmEMF1a deficiency disrupts the deposition of H3K27me3 and H2Aub marks at cell division regulators.

Our results indicate that ZmEMF1a plays a crucial role in regulating maize kernel development by maintaining H2Aub and H3K27me3 modification levels.