ZmEMF1a is required for the maintenance of H2Aub and H3K27me3 modifications in maize kernel development [ChIP-Seq]

Polycomb group (PcG) proteins are known to silence gene expression by modifying histones, such as H2Aub and H3K27me3, which is essential for maintaining cell type and tissue-specific gene expression patterns. However, the impact of PcG proteins on gene regulation through H2Aub and H3K27me3 during maize kernel development remains poorly understood. Here, we characterized a maize miniature seed mutant, mn8, and identified the underlying gene through map-based cloning. We found that Mn8 encodes ZmEMF1a, a plant-specific PcG protein. Mutation in ZmEMF1a leads to significantly reduced kernel size and weight. Molecular analyses showed that ZmEMF1a interacts with PRC1 component ZmRING1 and PRC2 subunit ZmMSI1, which are crucial for the establishment of H2Aub and H3K27me3 modifications. The deficiency of ZmEMF1a resulted in significant reduction in genomic levels of H2Aub and H3K27me3. Combined ChIP-seq and RNA-seq analyses showed that H2Aub is negatively correlated with gene expression in maize, contrasting with the positive correlation observed in Arabidopsis. Compared with wild-type (WT) endosperms, mn8 endosperms exhibited elevated expressions of homology genes of cell proliferation repressors, such as ZmDA1, ZmBB1, ZmES22, ZmMADS8, and ZmMADS14, accompanied with decreased levels of 3K27me3 or H2Aub at these loci. These findings indicate that lack of ZmEMF1a impairs the deposition of H3K27me3 and H2Aub marks at cell division repressor genes. Taken together, our results demonstrate that ZmEMF1a plays a crucial role in regulating maize kernel development by maintaining the levels of H2Aub and H3K27me3 modifications. Two biological replicates of mn8 and B73 endosperm tissues were obtained from two independent F2 ears at 12 DAP. ChIP-seq with Anti-H2Aub and anti-H3K27me3.