New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants

Abstract

MicroRNAs (miRNAs) are a family of short non-coding RNAs that play significant roles as post-transcriptional regulators. Consequently, various methods have been proposed to identify precursor miRNAs (pre-miRNAs), among which the comparative studies of miRNA structures are the most important. To measure and classify the structural similarity of miRNAs, we propose a new three-dimensional (3D) graphical representation of the secondary structure of miRNAs, in which an miRNA secondary structure is initially transformed into a characteristic sequence based on physicochemical properties and frequency of base. A numerical characterization of the 3D graph is used to represent the miRNA secondary structure. We then utilize a novel Euclidean distance method based on this expression to compute the distance of different miRNA sequences for the sequence similarity analysis. Finally, we use this sequence similarity analysis method to identify plant pre-miRNAs among three commonly used datasets. Results show that the method is reasonable and effective.

Fig. 1. Overall framework of the proposed method.

Fig. 2. The secondary structure of the RNA sequence of the TSV-3 and AIMV-3.

Fig. 3. The 3D graphical representation of the RNA secondary structure of viruses TSV-3 and AIMV-3.

Fig. 4. Example of the base coordinate calculation.

Fig. 5. Illustration of the steps of our method for calculating the distance between sequences. (A) shows the calculation steps for Pattern 1; (B) shows the calculation steps for Pattern 2.