RNAnet – A RNA Based Toy Model to Study Biological Networks

Non-coding RNAs (ncRNAs) regulate a variety of cellular processes by binding to either other ncRNAs, mRNAs or even DNA. Recent research in this field led to the discovery of several novel classes of ncRNAs and modes of function, such as transcriptional and post-transcriptional regulation of gene expression. As a new approach in the study of RNA molecules and their interactions, we construct a network of interacting RNAs as a toy model of regulatory gene network. We use the Vienna RNA package for calculating RNA-RNA cofold structures and we employ these features for defining three classes of interacting agents or “genes”: sensors, transmitters and responders, depending on their folding and cofolding characteristics. We further study the variation of network structure under different environmental conditions by increasing the folding temperature. As a preliminary study of this regulatory network toy-model, we present several possible extensions of the network approach to RNA modeling