Abstract
RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks up to nine vertices; among them, 22 are frequently occurring, 15 of which contain pseudoknots. We then catalog atomic fragments corresponding to the subgraph blocks to define a library of building blocks that can be used for RNA design, which we call RAG-3Dual, as we have done for tree graphs. As an application, we analyze the distribution of these subgraph blocks within ribosomal RNAs of various prokaryotic and eukaryotic species to identify common subgraphs and possible ancestry relationships. Other applications of dual graph partitioning and motif library can be envisioned for RNA structure analysis and design.
Highlights
The range of functions performed by ribonucleic acid (RNA) molecules in cellular processes—from protein synthesis [1] to gene regulation [2,3] and catalysis [4,5]—depends on their secondary (2D) and tertiary (3D) structures
Our analysis reveals subgraphs that are present in all species we analyzed and subgraphs that are common to a subset of species, as well as subgraph blocks that are exclusively present in ribosomal RNAs (rRNAs) structures
These findings suggest that graph partitioning may be useful for evolutionary analysis and that some submotifs may be unique to rRNAs
Summary
The range of functions performed by ribonucleic acid (RNA) molecules in cellular processes—from protein synthesis [1] to gene regulation [2,3] and catalysis [4,5]—depends on their secondary (2D) and tertiary (3D) structures. The single stranded RNA chain folds upon itself to form double-stranded helical and single-stranded loop regions. These 2D structural elements interact with one another to create functional 3D structures. RNA molecules tend to fold in a hierarchical manner [6,7], with complex 3D structures consisting of substructures or submotifs. Such submotifs often correlate with specific function. Common submotifs between two RNAs can suggest functional or evolutionary relationships. Understanding the structure/function relationships of RNA molecules is crucial for manipulating their functions and for designing novel RNA molecules for various industrial and therapeutic applications [8,9]
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