Decoys and Tough Decoys (TuDs)

Decoy and Tough Decoy overview

We designed a proof-of-concept circuit to test the in vivo functionality of decoy and tough decoy (TuD) RNA, a mechanism of conditional output actuation that could interface with our upstream RNA strand displacement cascade.

Double Repression System Design

To develop a mechanism of actuation for our circuitry, we considered using a tight RNA interference-based double repression system that could be characterized by a distinct switch between the on and off states. We investigated the use of decoy and tough decoy (TuD) RNA, which were novel RNA interference technologies inspired by Haraguchi et al. (Nucleic Acids Res. 2009). This mechanism would allow for conditional expression of our desired output, a yellow fluorescent protein, based on the informational processing assessment characterized by the upstream RNA strand displacement cascades.

Decoy RNA and TuD RNA serve as novel RNA interference technologies that can relieve miRNA repression of a particular gene. In accordance with the central dogma of biology, transcribed mRNA strands are translated by cellular machinery into proteins. Mammalian cells incorporate RNA interference technologies to regulate gene expression through the presence of miRNA strands, which can complementarily bind to regions of mRNA and suppress the translation into a protein. Decoy and TuD RNA work to relieve this repression, by complementarily binding to regions of miRNA to inhibit their repressive functions. While decoy RNAs are merely single strands of RNA with miRNA-binding domains, TuD RNAs incorporate a stabilizing stem-loop structure, with two antisense miRNA-binding domains that can allow for additional miRNA coordination. We observed from the Haraguchi et al. study that the particular TuD RNA structure yielded increased levels of activity compared to decoy RNA, so we attempted to assess the functionalities of both designs.

Furthermore, the studies showed that a small 4-nucleotide bulge sequence in the miRNA-binding domains of decoy and TuD RNA increased their abilities to relieve repression of protein expression. The bulge in the miRNA-binding sequence likely assisted the decoy and TuD RNA in disrupting RISC complex activity in mammalian cells. This characteristic informed our decision to test two different decoy and TuD RNA species – one that lacked a 4-nucleotide bulge in the miRNA-binding domain, and one that had the bulge sequence.

Source: Kitamura 1998.

Circuit Design

In order to assess the in vivo functionality of decoy and TuD RNA, we designed a proof-of-concept double repression circuit that would be implemented and tested in mammalian cells. We tested different parameters to characterize the functionality of the different components. Our circuit begins with a constitutively (always) expressed yellow fluorescent protein, with the mRNA transcript containing several binding domains for a particular miRNA. We then introduce the miRNA into the system, resulting in repression of the protein expression. Finally, upon introducing decoy and TuD RNA into the system, the repression is subsequently relieved, allowing for expression of the yellow fluorescent protein.

We tested two different ratios of eYFP, eYFP intronic mKate, and decoy. The first had a ratio of 1:1:1 and the second had 1:1:2. In the instance with more decoy, the FIT-C yellow population was more relieved, resulting in higher intensity.

Ultimately in increasing the relative concentration of decoy that was transfected, we observed a slight relief of repression of the system. We are currently working on better optimizing our transfection ratios so that our system can be tightly regulated and have a defined switching behavior between on and off states for protein expression. We also plan to use decoys or tough decoys as conditional outputs of upstream strand displacement that could be used to trigger protein expression in specific cases.

Conclusion

Through our testing of decoys and TuDs, we demonstrated induction of downstream protein effects through the RNA strand displacement motif. We can change levels of protein expression by interacting with the RNA pathways by which they are produced; either through repression or double repression systems at the protein translation level.