Fig. 2: Structural motif extraction for the RNA structure library.
From: RNA structure-wide discovery of functional interactions with multiplexed RNA motif library
Motif extraction obtains RNA structures from datasets to design the RNA structure library in FOREST. Extraction 1: A method to extract a validated stem–loop structure. In this study, pre-miRNA, a region surrounded by mature miRNAs, was recognized as a validated stem-loop motif, and the loop region with a part of the stem was extracted from human pre-miRNAs registered in miRBase. The Dicer cleavage site determined the boundary of the extracted pre-miRNA loop motif. We also extracted experimentally validated RNA stems from the data set of the high-throughput mapping method for RNA–RNA interactions. Extraction 2: A method for extracting terminal loop motifs from long and continuous RNAs. The extraction method comprehensively extracts single-terminal loop motifs defined as a single hairpin loop and its associated stem motifs (including internal loops and bulge loops). Subsequently, recognition of the combination of multiple single terminal loops can reconfigure and extract multi-terminal loops. The examples are representative motifs selected from the libraries conducted in this study (maximum length of the structure region: 116 nt). See also Supplementary Figs. 2–4.
