ZmEMF1a-mediated H2Aub1 and H3K27me3 deposition inhibits endosperm cell proliferation and promotes normal cell differentiation

In mammals and plants, Polycomb Repressive Complexes (PRC1 and PRC2) catalyze histone H2A ubiquitination (H2Aub) and H3K27 trimethylation (H3K27me3), respectively, to repressing gene expression. However, the mechanisms underlying Polycomb Group (PcG)-mediated gene silencing in maize remain unclear.We identified a small kernel mutant, sks1, which exhibits excessive cell proliferation during endosperm development. The mutated gene encodes ZmEMF1a, which interacts with both PRC1 and PRC2 components. We characterized the dynamic landscapes of H3K27me3 and H2Aub1 modifications during maize endosperm development at two critical stages 6 and 10DAP by using ChIP-seq. At 6DAP, ZmEMF1a mainly suppresses downstream gene overexpression through H3K27me3. Notably, at 10 DAP, both histone marks are dramatically reduced in the mutant, demonstrating that ZmEMF1a is essential for the coordinating these two repressive modifications at this stage. Across all stages, ZmEMF1a suppresses specific ZmMADS genes in a stage-specific manner. After 18DAP, the zmemf1a mutant shows over-proliferation of differentiated endosperm cells, such as BETL and AL, along with expanded expression of marker genes (BETL9 and LTP2.2) and increased vitamin B1, B2 and B6 levels. Notably, loss of H3K27me3 and H2Aub on marker genes occurs as early as 10DAP, leading to their upregulation and over-proliferation of differentiated cells. Our findings reveal that ZmEMF1a is essential for H3K27me3 deposition, which restricts endosperm cell proliferation and supports proper cell fate determination in maize. It also supply a valuable genetic resource for improving the vitamin content in maize.