UC Santa Barbara
Towards artificial chromatin: In vitro transcription with DNA liquids
DNA organization within a cell is multifaceted & dynamic, and has received intense study in recent decades. As a more complete understanding of chromatin organization emerges, there are increasing efforts to examine how such organization, and dynamic re-organization, relates to gene expression. While disruptions in chromatin organization have been shown to induce changes in transcriptional output, transcriptional activity has also been observed to trigger nuclear repositioning. It thus remains unclear which biological process drives the other or, more likely, if the interplay is much more intricate.
To begin probing this incredibly complex relationship, we use a simple in vitro platform – comprised of self-assembling DNA nanostars (NSs) – to examine transcription from genes integrated into higher order nucleic acid complexes. These NSs can be tuned to adopt distinct phases, either a solid-like percolated network or a phase-separated liquid, depending on the strength of inter-NS interactions. With increasing reports describing the liquid-like behavior of chromatin, including the liquid-liquid phase separation exhibited by the nucleolus and heterochromatin domains, we implement the DNA-liquid phase into a cell-free gene expression system to examine how the integration of genes into a biomolecular liquid affects transcriptional output and, inversely, how transcribed RNA may alter that environment.