Characterization of RNA content in individual phase-separated coacervate microdroplets

Here, the authors demonstrate that single cell RNA sequencing technology can be leveraged to characterize RNA content of individual membrane-free condensates formed by liquid-liquid phase separation processes such as coacervation. Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of biological condensates and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and to which extend single condensates differ in their RNA composition. To address this, we developed an approach to read the RNA content from single synthetic and protein-based condensates using high-throughput sequencing. We find that certain RNAs efficiently accumulate in condensates. These RNAs are strongly enriched in sequence motifs which show high sequence similarity to short interspersed elements (SINEs). We observe similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.

Automated summary

In this study, the authors demonstrate the use of single cell RNA sequencing technology to characterize the RNA content of membrane-free condensates formed by liquid-liquid phase separation processes. They find that certain RNA sequences efficiently accumulate in these condensates and show high sequence similarity to short interspersed elements (SINEs). This study provides a new approach to explore the RNA composition of phase-separated droplets at single condensate resolution.