Data and codes for "ricePSP: a comprehensive database of rice phase separation-associated proteins"

Multivalent interactions between proteins with intrinsically disordered regions (IDRs) or prion-like domains (PrDs) can lead to liquid-liquid phase separation (LLPS) and formation of membraneless condensates, which play vital roles in diverse biological process such as ribosome biogenesis and RNA metabolism, RNA processing and alternative splicing, transcriptional regulation, DNA damage response, and three-dimensional (3D) chromatin compartmentalization. To globally identify phase separation-associated proteins in the model crop plant rice, we predict the phase separation scores of all the annotated proteins, and constructed a comprehensive database of rice phase separation-associated proteins (ricePSP). We find > 11,000 proteins with high PS scores and > 1300 proteins containing PrDs. These PSPs are further validated with uncertain three-dimensional structures predicted by AlphaFold. With the database, we demonstrat the usability of ricePSP in identifying flowering-related phase-separation proteins and understanding the mechanism of flowering regulation from the aspects of phase separation. ricePSP provides a useful resource for studying of crop phase-separation-associated proteins and might improve our understanding of their mechanisms in regulating complicated genetic traits in crops.