Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis

Cereal endosperm represents 60% of the calories consumed by human beings worldwide. In addition, cereals also serve as the primary feedstock for livestock. However, the regulatory mechanism of cereal endosperm and seed development is largely unknown. Polycomb complex has been shown to play a key role in the regulation of endosperm development in Arabidopsis, but its role in cereal endosperm development remains obscure. Additionally, the enzyme activities of the polycomb complexes have not been demonstrated in plants. Here we purified the rice OsFIE2-polycomb complex using tandem affinity purification and demonstrated its specific H3 methyltransferase activity. We found that the OsFIE2 gene product was responsible for H3K27me3 production specifically in vivo. Genetic studies showed that a reduction of OsFIE2 expression led to smaller seeds, partially filled seeds, and partial loss of seed dormancy. Gene expression and proteomics analyses found that the starch synthesis rate limiting step enzyme and multiple storage proteins are down-regulated in OsFIE2 reduction lines. Genome wide ChIP–Seq data analysis shows that H3K27me3 is associated with many genes in the young seeds. The H3K27me3 modification and gene expression in a key helix-loop-helix transcription factor is shown to be regulated by OsFIE2. Our results suggest that OsFIE2-polycomb complex positively regulates rice endosperm development and grain filling via a mechanism highly different from that in Arabidopsis.
Author Summary Rice is the staple food for over half of the world's population and an important feedstock for livestock. The rice grain is mainly endosperm tissue. The regulatory mechanism of rice endosperm development is still largely unknown thus far. Understanding the underlying mechanism will lead to crop yield and quality improvement in the long term, besides gaining new knowledge. Polycomb complex is a protein complex with a potential role in endosperm development according to prior publications. In this manuscript, we purified the rice OsFIE2-polycomb protein complex and demonstrated the enzyme activity of the complex. Genetic studies showed that a reduction of polycomb group gene OsFIE2 expression led to smaller seeds, partially filled seeds, and seed germination before seed maturation. Gene expression and proteomics analyses found that the starch synthesis rate limiting step enzyme and multiple storage proteins are down-regulated while a key transcription factor is up-regulated in OsFIE2 reduction lines. In addition, we identified many loci in the rice genome whose histone proteins are modified by the polycomb complex enzyme via a method called ChIP–Seq. Our results demonstrate that OsFIE2-polycomb complex positively regulates rice grain development via a mechanism distinct from that in Arabidopsis and provide new insight into the regulation of rice grain development.