Controlling Cells through RNA Folding

Cells have an amazing ability to process information, make decisions, and change their state in response to changing environments. This ability is encoded within the cellular DNA genome, which is converted into RNA and protein molecules through the basic processes of gene expression. Among the many functions these RNAs and proteins perform is regulating their own expression. In fact RNAs are now known to regulate almost all aspects of gene expression, and play central roles in controlling some of life’s most basic processes.

As with many biomolecules, RNA function is intimately related to its structure. Being a single-stranded polymer of nucleotides, RNA can fold back on itself to form structures that enable certain RNAs to block or allow gene expression processes. Central questions in biology and bioengineering are then: How do RNAs fold inside cells?, and How can we engineer these folds to control gene expression? In this talk I will present our recent work including two new accomplishments that address both of these questions.

I will start by describing SHAPE-Seq, our technology that couples chemical probing with next-generation sequencing to characterize RNA structures on an ‘omics’ scale. I will also describe our recent innovations in using SHAPE-Seq to simultaneously characterize the structures and functions of RNA regulatory molecules as they exist inside cells. Using examples from two RNA translational repressors used in synthetic biology, I will show how this in-cell SHAPE-Seq technique is producing quantitative measures of cellular RNA structure at single-nucleotide resolution that we can now directly link to RNA regulatory function. 

I will then present our work on engineering RNA molecules that control the basic process of RNA transcription, and on how our knowledge of the RNA structure/function relationship has allowed us to engineer an RNA regulatory mechanism not found in nature. This new mechanism, called Small Transcription Activating RNAs, or STARs, allows new types of RNA-based genetic circuits and logics to be built with intriguing properties. I will conclude with thoughts about how our work is leading us to ask deep scientific questions about the fundamental processes of RNA folding and function, and the role of RNAs in nature.