Genome-wide search for coaxial helical stacking motifs

Motif finding in DNA, RNA and proteins plays an important role in life science research. In this paper, we present a computational approach to searching for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking motif occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.

I. INTRODUCTION

Motif finding in DNA, RNA and proteins plays an important role in life science research. Here, we present a method, named CSminer (i.e. Coaxial helical Stacking miner), for finding coaxial helical stackings in genomes. A coaxial helical stacking occurs in an RNA tertiary structure where two separate helical elements form a pseudocontiguous helix [1]. Coaxial helical stacking motifs occur in several large RNA structures, including tRNA [2], pseudoknots [3], group II intron [4] and large ribosomal subunits [5] [6] [7]. Coaxial helical stackings provide thermodynamic stability to the molecule as a whole [8] [9], and reduce the separation between loop regions within junctions [10]. Moreover, coaxial helical stacking interactions form cooperatively with long-range interactions in many RNAs [11] and are thus essential features that distinguish different junction topologies.