A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate. A proxitome-RNA-capture approach captures the transcriptome of the archetypal condensates known as processing bodies and reveals a translational hub based on liquid-liquid phase separation.

Automated summary

This study presents a proximity-biotinylation approach for capturing the RNAs in cellular condensates known as processing bodies (PBs). The researchers found that the RNA composition in PBs is more dynamic compared to the total transcriptome. They identified enriched RNAs involved in cell wall development, plant hormonal signaling, and RNA metabolism within PBs. The study also revealed that RNA-binding proteins and the liquidity of PBs modulate RNA recruitment, and RNAs in PBs can have different fates depending on the size and type of the PB.