The centrality of RNA for engineering gene expression

Abstract

Synthetic biology holds promise as both a framework for rationally engineering biological systems and a way to revolutionize how we fundamentally understand them. Essential to realizing this promise is the development of strategies and tools to reliably and predictably control and characterize sophisticated patterns of gene expression. Here we review the role that RNA can play towards this goal and make a case for why this versatile, designable, and increasingly characterizable molecule is one of the most powerful substrates for engineering gene expression at our disposal. We discuss current natural and synthetic RNA regulators of gene expression acting at key points of control – transcription, mRNA degradation, and translation. We also consider RNA structural probing and computational RNA structure predication tools as a way to study RNA structure and ultimately function. Finally, we discuss how next-generation sequencing methods are being applied to the study of RNA and to the characterization of RNA's many properties throughout the cell.

A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future

“…Recently however, there has been a resurgence of interest in engineering and applying synthetic RNA regulators to control gene expression [4,5]. This has been motivated by our increasing appreciation of the widespread use of RNA regulation in natural systems [4] and our deepening knowledge of RNA folding and function.…”

Design criteria for synthetic riboswitches acting on transcription

“…6 Regulation of transcription is of special interest, as it allows for a tight regulation in an early step of gene expression. 7 Furthermore, transcriptional control can be employed to regulate both protein expression as well as noncoding RNAs. In bacteria, riboswitches regulating transcription usually contain an intrinsic rho-independent terminator in the expression platform.…”

Transposons Tn 10 and Tn 5

“…Accordingly, custom-designed riboregulators have become an integral part of the discipline (70). Towards this end researchers have turned to modifying natural antisense systems rather than the de novo development of riboregulators to create novel orthogonal (high specificity with low off-target pairing) yet homogenous (similar kinetics and mechanism of pairing) RNA-based regulators of gene expression (71). These antisense RNAs can be designed to sense external metabolites as well as protein concentrations, and provide specific regulation of gene expression based on RNA: RNA interactions.…”