Condensation and activator/repressor control of a transcription-regulated biomolecular liquid

TL;DR

This paper presents a model system coupling DNA nanostars and transcription to study phase separation dynamics, revealing how transcription can regulate biomolecular condensate formation and function.

Contribution

It introduces a programmable in vitro platform linking transcription activity to phase separation, enabling detailed study of non-equilibrium biomolecular condensate dynamics.

Findings

DNA nanostars form droplets in response to RNA synthesis

Droplet formation exhibits delay and non-linear kinetics

Droplets can regulate transcription by sequestering components

Abstract

Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA) to compartmentalize biomolecules via liquid-liquid phase separation (LLPS). Here, we develop a model biomolecular system that permits quantitative investigation of such dynamics, particularly by coupling a phase-separating system of DNA nanostars to an in vitro transcription reaction. The DNA nanostars' sequence is designed such that they self-assemble into liquid droplets only in the presence of a transcribed single-stranded RNA linker. We find that nanostar droplets form with a substantial delay and non-linear response to the kinetics of RNA synthesis. In addition, we utilize the compartments generated by the phase-separation process to engineer an activator/repressor network, where the transcription reaction activates the formation of droplets, and then droplets suppress the transcription reaction by segregating transcription components inside them. Our work on transcription-driven liquid-liquid phase separation constitutes a robust and programmable platform to explore non-equilibrium reaction-phase transition dynamics and could also provide a foundation to understand the dynamics of transcriptional condensate assembly in cells.