Beyond Editing: Exploring and Engineering a Living Genome Using a Dead Molecule

Synthetic manipulation of the genome is key to understanding the genetic makeup of living organisms, and holds great promise for curing diseases. Despite significant advances of CRISPR technology development to editing the genome sequence or regulating gene expression, genome engineering, broadly defined, is still in its infancy for studying and engineering diverse features inherent to the genome. Beyond editing, our lab has previously developed a nuclease-dead Cas9 (dCas9) platform for synthetic transcriptional or epigenetic control on the genome. Here I present recent data that expands the dCas9 platform for exploring 3D chromosome interaction with nuclear compartments. We applied CRISPR tools to synthetic biology, and developed a class of input-output (I/O) molecular devices that combine dCas9 regulators with cellular sensors including GPCRs (G-Protein Coupled Receptors). We apply dCas9 tools to gain a quantitative understanding of the relationship between genotype and phenotype, and report how this quantitative relationship determines cell fate. Via this work, we aim to lay out a generic bioengineering platform that allow multi-purpose interrogation of the genome, including studying the genome function ranging from nanoscales to microscales, devising synthetic biology approaches to design mammalian cells for therapy, and probing the genome for its casual and quantitative relationship to phenotypes.