Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Abstract

The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes of RNAs that are characterized by structural similarities, and typically consist of multiple RNA families. Recent advances in high-throughput transcriptomics and comparative genomics have produced very large sets of putative noncoding RNAs and regulatory RNA signals. For many of them, evidence for stabilizing selection acting on their secondary structures has been derived, and at least approximate models of their structures have been computed. The overwhelming majority of these hypothetical RNAs cannot be assigned to established families or classes. We present here a structure-based clustering approach that is capable of extracting putative RNA classes from genome-wide surveys for structured RNAs. The LocARNA (local alignment of RNA) tool implements a novel variant of the Sankoff algorithm that is sufficiently fast to deal with several thousand candidate sequences. The method is also robust against false positive predictions, i.e., a contamination of the input data with unstructured or nonconserved sequences. We have successfully tested the LocARNA-based clustering approach on the sequences of the RFAM-seed alignments. Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005) Noncoding RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2): i77–i78). In addition to recovering, e.g., tRNAs as a structure-based class, the method identifies several RNA families, including microRNA and snoRNA candidates, and suggests several novel classes of ncRNAs for which to date no representative has been experimentally characterized.

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

“…S3 and Tables S3 and S4). To determine the degree of secondary structural conservation between culture-derived ncRNA sequences and their counterparts in the metagenome and metatranscriptome, we used RNAfold to compare computationally predicted structures (71)(72)(73)(74). RNAfold predicted very similar core secondary structures between the culture and environmental sequences for most ncRNAs among the top matches (Fig.…”

Computational Prediction of RNA Structural Motifs Involved in Post-Transcriptional Regulatory Processes

“…Several tools exist for finding local structural motifs in a set of long input RNAs. Many existing works use free energy minimization considerations for predicting local motifs, by applying one of three major schemes: use of a sequence-based local alignment to build a motif consensus structure (12, 13); identification of common structures in the RNAs' predicted minimal free energy folds (14-16); or simultaneous alignment of the RNAs and prediction of their secondary structure (17)(18)(19)(20). Recently, some graph theoretical techniques were also proposed for this task (21,22).…”

Iterative estimation of structures of multiple RNA homologs: Turbofold

“…The performance of TurboFold is compared with three other methods that estimate base pairing probabilities 6 : 1) LocARNA [12] (Version 1.5.2a is used, with Vienna RNA Software Package version 1.8.4), 2) RNAalifold [13] (The version included in Vienna RNA Software Package version 1.8.4 is used with command line option '-p' for computation of base pairing probabilities with ClustalW 2.0.11 [14] for computation of input sequence alignment), and 3) Single sequence estimates of base pairing probabilities using a nearest neighbor thermodynamic model [10,15] (as implemented in RNAstructure version 4.5 [15,16]). …”