Structural characterization and modeling of ncRNA-protein interactions

Recent studies have suggested that noncoding RNA (ncRNA) molecules could play an important role in the regulatory architecture of eukaryotic cells. This new RNA-based regulation might indicate the existence of a hidden layer in the central dogma. In spite of its importance, the large-scale structure as well as the local interaction pattern of the ncRNA regulatory network has not been investigated. In this work, we collected regulatory interactions between ncRNA molecules and their regulated protein targets. We then constructed the ncRNA-protein interaction network corresponding to six model organisms, including Homo sapiens. The large-scale network analysis of ncRNA-protein interactions revealed a high degree of similarity for the degree distribution to that of the transcription regulatory network. Moreover, characterization of the local interaction structure of these networks based on motifs abundance also reveals significant similarities between ncRNA-protein and TFs-gene regulatory networks. Based on the identified motif abundance, we propose an evolutionary model that rebuilds the degree distribution and predicts the observed degree exponent. Taken together, our findings offer insights into the noncoding RNA-mediated regulation and provide knowledge about its structure and evolutionary mechanisms. (C) 2010 Elsevier Ireland Ltd. All rights reserved.