RNA interference and Register Machines (extended abstract)

TL;DR

This paper models RNA interference as a Minsky register machine to explore its computational properties, analyzing its complexity and proposing a recursive, probabilistic extension to improve accuracy.

Contribution

It introduces a novel computational model of RNAi as a register machine and develops a recursive, probabilistic version to address initial inaccuracies.

Findings

RNAi can be represented as a Minsky register machine.

Recursive RNAi improves the computational accuracy of the model.

Probabilistic termination analysis reveals system behavior.

Abstract

RNA interference (RNAi) is a mechanism whereby small RNAs (siRNAs) directly control gene expression without assistance from proteins. This mechanism consists of interactions between RNAs and small RNAs both of which may be single or double stranded. The target of the mechanism is mRNA to be degraded or aberrated, while the initiator is double stranded RNA (dsRNA) to be cleaved into siRNAs. Observing the digital nature of RNAi, we represent RNAi as a Minsky register machine such that (i) The two registers hold single and double stranded RNAs respectively, and (ii) Machine's instructions are interpreted by interactions of enzyme (Dicer), siRNA (with RISC com- plex) and polymerization (RdRp) to the appropriate registers. Interpreting RNAi as a computational structure, we can investigate the computational meaning of RNAi, especially its complexity. Initially, the machine is configured as a Chemical Ground Form (CGF), which generates incorrect jumps. To remedy this problem, the system is remodeled as recursive RNAi, in which siRNA targets not only mRNA but also the machine instructional analogues of Dicer and RISC. Finally, probabilistic termination is investigated in the recursive RNAi system.