[PhD Thesis Presentation_Zoom] - Ms. Kamila Mustafina - "Engineering Synthetic Riboswitches for Mammalian Cells"
Presenter: Ms. Kamila Mustafina
Supervisor: Prof. Yohei Yokobayashi
Unit: Nucleic Acid Chemistry and Engineering Unit
Title: Engineering Synthetic Riboswitches for Mammalian Cells
Riboswitches are natural and artificial noncoding RNA elements capable of controlling gene expression in response to chemical signals without direct involvement of protein factors. One strategy for engineering synthetic riboswitches is to combine an aptamer –a short RNA sequence that specifically binds to a ligand– and a self-cleaving ribozyme to create an aptazyme whose self-cleavage activity is regulated by the aptamer ligand. These aptazymes can be embedded in the 3’UTR of mRNAs to chemically control gene expression in mammalian cells. This property of riboswitches opens a wide area of applications in biology and medicine. However, engineering riboswitches that function efficiently in mammalian cells remains challenging, partly due to the difficulties associated with generating and screening aptamers and aptazymes that function in the cellular environment rather than in test tubes.
In this thesis, I introduce two new ribozyme scaffolds for aptazyme engineering in mammalian cells. First, I identified highly active variants in mammalian cells from the twister and pistol ribozyme families. Then I used them as scaffolds for a new aptazyme architecture, where the aptamer is placed immediately upstream of the ribozyme in a tandem configuration. I optimized this design in mammalian cells, and then generated randomized libraries of 4096 aptazyme variants for high-throughput in vitro screening to identify switches with high ON/OFF ratios. Although the method allowed characterization of a large number of variants, their activities were not always reproducible when tested in cells.
Therefore, in addition to in vitro screening, I explored rational design approaches for the same tandem architecture. I fine-tuned the activity of the aptazyme by systematically varying the length of the inserted competing stem and introducing single-nucleotide mismatches and spacers. Using this method, I developed mammalian riboswitches with ON/OFF ratios greater than 6.0 for the twister scaffold, and greater than 5.0 for the circularly permuted pistol scaffold.
Lastly, learning from the experience of high-throughput in vitro screening and rational design in cells, I used high-throughput sequencing to directly screen for functional aptazymes in mammalian cells by quantifying the uncleaved fractions of aptazyme-embedded mRNAs. I verified this method with a small twister ribozyme library containing 256 variants and then applied it for a larger circularly permuted pistol ribozyme library consisting of 1024 variants.
This work expands both the tools and the methods available in the field of RNA engineering. Riboswitches based on the new ribozyme scaffolds provide compact and tunable tools for controlling gene expression. Rational and high-throughput design strategies developed in this thesis can be applied to generate other RNA devices for biomedical and synthetic biology applications.