Meet Our Researchers

Sara Jones

Postdoctoral Fellow at the Broad Institute of MIT and Harvard
The Question

Recent advances in genome-editing technology have revolutionized experimental biology and hold incredible promise for gene therapy. Current state-of-the-art technologies, including CRISPR-based systems, rely on programmable molecular scissors to cut precise segments of DNA.

However, these technologies are limited because they rely on the cell’s DNA repair machinery to heal the cuts made by the molecular scissors. DNA repair is only activated during cell division, making it difficult to edit the genomes of cells that don’t divide in adults, such as the brain and heart. We need a set of tools that can efficiently create any targeted modification within the genome of any cell type. BroadIgnite funds are allowing us to search for these tools in a promising but as yet poorly understood organism.

The Approach

Current genome editing approaches arose from repurposing existing tools in nature, like the bacterial immune system. Thus, to look for new methods, we decided to search within organisms that naturally possess molecules for precise and efficient DNA restructuring. We found just such a system in the microorganism Oxytricha trifallax, and we are developing an entirely new class of gene-editing tools based on its RNA-guided DNA rearrangement.

During development, O. trifallax undergoes massive genome rearrangement, precisely chopping its genome into hundreds of thousands of pieces that must be accurately unscrambled and reassembled for survival. Several intermediates have been implicated in this process, but the mechanism remains elusive. In order to repurpose this system in mammalian cells, we must first gather a more complete picture of how programmed genome rearrangement occurs in O. trifallax. With BroadIgnite support, we have been developing methods to identify a comprehensive list of the critical players in this intricate process of genome rearrangement. We are using RNA- and DNA-sequencing alongside mass spectrometry to identify critical nucleic acid and protein intermediates throughout the developmental process.

The Results

BroadIgnite funding has been critical in allowing us to pilot small-scale experiments for optimizing our assays. This work will allow us to identify the key components of the DNA rearrangement system—the building blocks of the next genetic editing tool. Once these studies are complete, we aim to use our new understanding of the system to reconstitute the minimally required system in vitro, and ultimately in mammalian cells.

We envision harnessing this RNA-guided DNA rearrangement to develop a new class of genome-engineering tools that will transform the way we study and treat genetic disorders.