Detangling DNA: Single-Cell Approaches to Understanding Plasticity in Cellular Reprogramming

Cellular reprogramming continues to generate new cell types, increasingly expanding our perspective of cellular plasticity. Despite improved genetic tools and epigenetic modulations, reprogramming remains a rare cellular event. Recent studies in reprogramming indicate that changes in DNA topology precede changes in gene expression, suggesting that transcriptional and epigenetic realignment require particular 3D genome conformations. In this talk, I will describe how I identified molecular roadblocks in reprogramming that arise from tradeoffs between transcription and proliferation rates. Utilizing single cells RNAseq (scRNAseq), I recently identified topoisomerases, enzymes that curate DNA topology, as regulators of cellular reprogramming. Supported by topoisomerase activity, elite cells maintain high rates of transcription and replication to reprogram at near-deterministic rates. My discovery highlights how topological stress impacts the function of gene networks (e.g. native or synthetic circuits) and constrains cellular transitions. I will discuss how this finding opens completely new questions about how the structure of the genome stabilizes cellular identity and suggests strategies to improve the design of synthetic gene circuits.