3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice

Trimethylation of histone H3 lysine 27 (H3K27me3) confers a repressive chromatin state and is dynamically deposited and removed to regulate gene expression throughout plant growth and development. Nevertheless, the three-dimensional epigenome architecture linked to H3K27me3 and its regulatory role in controlling rice development remain unclear.

Here, we employ long-read ChIA-PET to map the genome topology associated with H3K27me3 in rice, identifying hundreds of repressive chromatin spatial clusters within chromosomes. The T-DNA insertional mutagenesis of EMBRYONIC FLOWER 2b (OsEMF2b) leads to disruption of H3K27me3-associated chromatin interaction networks. Notably, we discover that the three key flowering time loci, Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/Rice Flowering Locus T1 (RFT1) form an inter-chromosomal repressive chromatin spatial cluster as a cis-interaction hub. Further investigation reveals that Ghd7, Ghd8, and Hd1 undergo liquid-liquid phase separation and bind to Ehd1-Hd3a/RFT1 repressive chromatin spatial cluster as trans flowering regulators.

Our findings elucidate a multi-dimensional topological framework of H3K27me3-associated loci in rice and identify a spatial flowering gene cluster regulated by the phase-separated repressor complex of Ghd7, Ghd8, and Hd1. These results expand our knowledge of the structural basis of the three-dimensional genome governing the transcriptional coordination of florigens in rice.