Modeling Recursive RNA Interference

Wallace F Marshall,John S Mattick

doi:10.1371/journal.pcbi.1000183

Wallace F Marshall, John S Mattick

Open Access

https://doi.org/10.1371/journal.pcbi.1000183

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Abstract

An important application of the RNA interference (RNAi) pathway is its use as a small RNA-based regulatory system commonly exploited to suppress expression of target genes to test their function in vivo. In several published experiments, RNAi has been used to inactivate components of the RNAi pathway itself, a procedure termed recursive RNAi in this report. The theoretical basis of recursive RNAi is unclear since the procedure could potentially be self-defeating, and in practice the effectiveness of recursive RNAi in published experiments is highly variable. A mathematical model for recursive RNAi was developed and used to investigate the range of conditions under which the procedure should be effective. The model predicts that the effectiveness of recursive RNAi is strongly dependent on the efficacy of RNAi at knocking down target gene expression. This efficacy is known to vary highly between different cell types, and comparison of the model predictions to published experimental data suggests that variation in RNAi efficacy may be the main cause of discrepancies between published recursive RNAi experiments in different organisms. The model suggests potential ways to optimize the effectiveness of recursive RNAi both for screening of RNAi components as well as for improved temporal control of gene expression in switch off–switch on experiments.

Highlights

RNA interference (RNAi) is an RNA-mediated pathway of gene silencing mediated by small RNA molecules [1,2]
RNAi technology has emerged as a powerful tool for artificially controlling gene expression, but it only works because cells have evolved small RNA based regulatory pathways in the first place
RNA interference is a gene regulatory system in which small RNA molecules turn off genes that have similar sequences to the small RNAs

Summary

Introduction

RNA interference (RNAi) is an RNA-mediated pathway of gene silencing mediated by small RNA molecules [1,2]. RNAi technology has emerged as a powerful tool for artificially controlling gene expression, but it only works because cells have evolved small RNA based regulatory pathways in the first place. Natural regulatory pathways taking advantage of small RNAs include classical RNAi, which probably acts in host defense against viruses and transposons, and microRNA-based (miRNA) regulatory pathways that regulate endogenous genes [3]. Compared to more classical regulatory networks based on transcription factors or kinases, the signal-processing properties of small RNA-based regulatory systems have not been extensively investigated at a theoretical level. One advantage of having a theoretical understanding of such pathways is that one could potentially predict the performance and response of systems that have been altered in defined ways, facilitating a ‘‘synthetic biology’’ of small RNA-mediated regulatory circuits [4,5]. In this report the RNAi system is explored theoretically by considering its behavior following addition of an artificial negative feedback loop

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