Studying natural biology
We use synthetic cells to reconstitute and study natural biological processes, and to prototype and validate bioengineering tools that can be later used in live natural cells.
Engineering generalized RNA-protein interactions: a toolbox for regulation and readout of gene expression
We developed and validated protein architecture which binds to single stranded RNA. Using this protein technology, we are developing tools for visualization and quantification of levels of expression of genes of interest. This tool will work by following the reconstitution of a protein probe upon interaction of sequence-specific RNA binding proteins with the mRNA of the gene of interest.
We are also aiming to edit the transcriptome of the gene of interest, selectively decreasing the level of expression of one splice variant (as opposed to cutting the DNA of the gene, which targets all splice variants indiscriminately).
This technology could potentially help in studying non-ER translation events, elucidating mechanisms of synaptic plasticity, as well as studying healthy and diseased translational profiles of genes, e.g., those involved in oncogenesis and other disease processes.
The ability to monitor and perturb RNA in living neurons – which would open up the investigation of many processes that contribute to development, plasticity, and disease progression – would benefit greatly from a method of systematically targeting unmodified RNA sequences for observation and control. The current ssRNA targeting methods are based on the RNA binding protein aptamers, like MS2 or PP7; this require the introduction of aptamer binding sites into the RNA. This work shows that it is possible to develop a ssRNA binding protein that can be engineered to target arbitrary sequences of variable length, thus eliminating the need to engineer the target sites into the RNA of interest.
Popular science description: news release, local copy pdf.
This work was done with Ed Boyden
Thank you for support: NIH and Jeremy Wertheimer Foundation.