RNAMotif, an RNA secondary structure definition and search algorithm

Abstract

RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.

Figure 1

Examples of RNA structure motifs and descriptor constraints with important conserved nucleotides and scoring values. (A) A helical stem closed by a tetraloop. (B) An E-loop motif. (C) The core of the E-loop depicted with the observed non-canonical base pairing interactions. The most significant structural elements within the motif are shown within the dotted box. The structural components (stems or single-stranded regions) that flank this internal loop can vary in length and composition. (D) E-loop descriptor derived from the constraints shown in (B). Additional constraints for the stems flanking the core motif not shown were used in the overall score calculations reported in Table 2.

Figure 1

Examples of RNA structure motifs and descriptor constraints with important conserved nucleotides and scoring values. (A) A helical stem closed by a tetraloop. (B) An E-loop motif. (C) The core of the E-loop depicted with the observed non-canonical base pairing interactions. The most significant structural elements within the motif are shown within the dotted box. The structural components (stems or single-stranded regions) that flank this internal loop can vary in length and composition. (D) E-loop descriptor derived from the constraints shown in (B). Additional constraints for the stems flanking the core motif not shown were used in the overall score calculations reported in Table 2.

Figure 1

Examples of RNA structure motifs and descriptor constraints with important conserved nucleotides and scoring values. (A) A helical stem closed by a tetraloop. (B) An E-loop motif. (C) The core of the E-loop depicted with the observed non-canonical base pairing interactions. The most significant structural elements within the motif are shown within the dotted box. The structural components (stems or single-stranded regions) that flank this internal loop can vary in length and composition. (D) E-loop descriptor derived from the constraints shown in (B). Additional constraints for the stems flanking the core motif not shown were used in the overall score calculations reported in Table 2.

Figure 2

Models for the IRE structure and generic descriptor. (A) IRE bulge model. (B) IRE internal loop model. (C) Descriptor that captures both types of IRE.

Figure 3

SRP-RNA alignment and structure. (A) Structure-based alignment of the domain IV stem–loop region of SRP-RNA based on the full-length alignment from the SRP-RNA website (http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html). Sequences of a few representative organisms from the three major phylogenetic kingdoms (Bacteria, Archaea and Eukarya) are shown here. The top two lines of the alignment show the base pairing schema. ( and ) are used to denote the 5′ and 3′ sides of a helix, respectively, and the numbers indicate the paired segments. (B) A consensus diagram of the SRP-RNA structure derived from analyzing the alignment of over 100 organisms. The biases in nucleotides and range of size variations in loops and helices are shown. An RNAMotif descriptor (not shown) was derived based on the constraints shown here.

Figure 4

Summary of results of a RNAMotif search for SRP-RNA. (A) Score distribution of true and false hits based on RNAMotif scores in a search of the GenBank nucleotide database with an SRP-RNA descriptor. (B) Summary of scores for true and false hits.