Phase separation of Arabidopsis EMB1579 controls transcription, mRNA splicing, and development

Tight regulation of gene transcription and mRNA splicing is essential for plant growth and development. Here we demonstrate that a plant-specific protein, EMBRYO DEFECTIVE 1579 (EMB1579), controls multiple growth and developmental processes inArabidopsis. We demonstrate that EMB1579 forms liquid-like condensates both in vitro and in vivo, and the formation of normal-sized EMB1579 condensates is crucial for its cellular functions. We found that some chromosomal and RNA-related proteins interact with EMB1579 compartments, and loss of function ofEMB1579affects global gene transcription and mRNA splicing. Using floral transition as a physiological process, we demonstrate that EMB1579 is involved inFLOWERING LOCUS C(FLC)-mediated repression of flowering. Interestingly, we found that EMB1579 physically interacts with a homologue ofDrosophilanucleosome remodeling factor 55-kDa (p55) called MULTIPLE SUPPRESSOR OF IRA 4 (MSI4), which has been implicated in repressing the expression ofFLCby forming a complex with DNA Damage Binding Protein 1 (DDB1) and Cullin 4 (CUL4). This complex, named CUL4-DDB1(MSI4), physically associates with a CURLY LEAF (CLF)-containing Polycomb Repressive Complex 2 (CLF-PRC2). We further demonstrate that EMB1579 interacts with CUL4 and DDB1, and EMB1579 condensates can recruit and condense MSI4 and DDB1. Furthermore,emb1579phenocopiesmsi4in terms of the level of H3K27 trimethylation onFLC. This allows us to propose that EMB1579 condensates recruit and condense CUL4-DDB1(MSI4)complex, which facilitates the interaction of CUL4-DDB1(MSI4)with CLF-PRC2 and promotes the role of CLF-PRC2 in establishing and/or maintaining the level of H3K27 trimethylation onFLC. Thus, we report a new mechanism for regulating plant gene transcription, mRNA splicing, and growth and development.