Downloaded from rnajournal.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press BIOINFORMATICS IRBIS: a systematic search for conserved complementarity DMITRI D. PERVOUCHINE1,2 1Centre for Genomic Regulation and UPF, Barcelona 08003, Spain 2Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia ABSTRACT IRBIS is a computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, it follows the “first-fold-then-align” principle in which all possible combinations of complementary k-mers are searched for simultaneous conservation. The novel trimming procedure reduces the size of the search space and improves the performance to the point where large-scale analyses of intra- and intermolecular RNA–RNA interactions become possible. In this article, I provide a rigorous description of the method, benchmarking on simulated and real data, and a set of stringent predictions of intramolecular RNA structure in placental mammals, drosophilids, and nematodes. I discuss two particular cases of long-range RNA structures that are likely to have a causal effect on single- and multiple-exon skipping, one in the mammalian gene Dystonin and the other in the insect gene Ca-α1D.InDystonin, one of the two complementary boxes contains a binding site of Rbfox protein similar to one recently described in Enah gene. I also report that snoRNAs and long noncoding RNAs (lncRNAs) have a high capacity of base-pairing to introns of protein-coding genes, suggesting possible involvement of these transcripts in splicing regulation. I also find that conserved sequences that occur equally likely on both strands of DNA (e.g., transcription factor binding sites) contribute strongly to the false-discovery rate and, therefore, would confound every such analysis. IRBIS is an open-source software that is available at http://genome.crg.es/~dmitri/irbis/. Keywords: RNA–RNA interaction; evolutionary conservation; long-range RNA structure; exon skipping; alternative splicing; Ca-α1D; Dystonin; snoRNA; lncRNA INTRODUCTION ular interactions are driven by the same molecular forces, this distinction is crucial for algorithms because RSS is historically RNA–RNA interactions (RRIs) received increasing attention assumed to be nested (i.e., unknotted; see discussed below), in recent years, especially in the light of growing evidence for while simultaneous prediction of intra- and intermolecular abundant expression of noncoding RNAs (Ponting et al. base-pairings is equivalent to RNA folding with pseudoknots 2009; Derrien et al. 2012). One current hypothesis is that (Pervouchine 2004; Alkan et al. 2006; Huang et al. 2009). Here RRI could specifically guide some of the regulatory programs I discuss the two problems jointly without assuming that RSS in the RNA processing pathway, similar to what small RNAs is nested and, in particular, ascribe long-range intramolecular do in the post-transcriptional gene silencing and translational base-pairings also to RRI. attenuation. RRI plays a fundamental role in the functioning Both RRI and RSS predictions comprise a broad range of of the spliceosome, where small nuclear RNAs (snRNAs) methods that admit single-sequence (de novo) and multi- interact with each other and with the pre-mRNA by form- ple-sequence (comparative) formulations. Most of the de ing hetero-duplexes (Will and Luhrmann 2011). Not only novo methods are based on thermodynamic energy model, snRNAs do this; for instance, the C/D box snoRNA HBII- which assumes additive contributions to the free energy func- 52 contains a sequence that is complementary to HT R 2C tion from elementary structural units (Mathews et al. 1999). mRNA and affects alternative splicing in this disease-associ- However, the optimization method that is used to find the ated gene (Kishore and Stamm 2006). minimum free energy (dynamic programming) is computa- The problem of RRI prediction is technically very similar to tionally efficient only for nested RSS: For arbitrary pseudo- RNA secondary structure (RSS) prediction, with the major knots, it is NP complete (Lyngsø and Pedersen 2000), and difference being that base pairs both within and between even for the most generic type of pseudoknots, the required RNA molecules are allowed. Although intra- and intermolec- time is O(n6) (Rivas and Eddy 1999). Besides this technical Corresponding author: [email protected] Article published online ahead of print. Article and publication date are at © 2014 Pervouchine This article, published in RNA, is available under a http://www.rnajournal.org/cgi/doi/10.1261/rna.045088.114. Freely available Creative Commons License (Attribution 4.0 International), as described at online through the RNA Open Access option. http://creativecommons.org/licenses/by/4.0/. RNA 20:1519–1531; Published by Cold Spring Harbor Laboratory Press for the RNA Society 1519 Downloaded from rnajournal.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Pervouchine limitation, there is a fundamental problem that the additive for long, continuous helices occurring in long-range eukary- model is insufficient to describe entropy contribution of loops otic RSS. in molecules with pseudoknots and that important steric and This line of reasoning was elaborated in our recent reports topological limitations also need to be taken into account on conserved long-range RSS in introns of mammalian (Pervouchine 2004). Consequently, RRI prediction methods and insect genes (Raker et al. 2009; Pervouchine et al. avoid intramolecular interactions to be computationally effi- 2012). The strategy, which shares some technical ideas with cient (Mückstein et al. 2006; Wenzel et al. 2012). The best GUUGle (Gerlach and Giegerich 2006), was to convert se- current trade-off approach uses precomputed accessibility quences into hash tables that store the location of each k- profiles in addition to free energy scoring of exposed binding mer and to apply set-theoretic intersection (1) with the re- sites (Mückstein et al. 2006; Tafer et al. 2011). Some methods verse complement and (2) across orthologs to detect instances gain additional speed by simplifications to the free energy of simultaneous complementarity and conservation. One im- model, which makes them practicable on a genome-wide scale portant advantage of this method is that poorly conserved re- as, for instance, microRNA target finders, although elimina- gions do not need to be aligned and, on the contrary, the lack tion of the internal RNA structure results in a dramatic in- of conservation becomes useful when assigning statistical sig- crease of false-positive predictions (Rehmsmeier et al. 2004; nificance to conserved “islands” immersed in a nonconserved John et al. 2006; Ragan et al. 2009). intronic background (Raker et al. 2009). By construction, In contrast, comparative methods take advantage of the there are neither constraints on the distance between base evolutionary information to reduce the false-positive rate pairs nor limitations on pseudoknots. This technique, in (Gardner and Giegerich 2004). Simultaneous alignment and fact, applies to a broader range of settings than RSSs near folding, known as the Sankoff algorithm, is computationally splice sites. Figure 1 illustrates a general formulation in which overexpensive (Sankoff 1985). Instead, most existing methods the input is organized as a collection of unaligned orthologous take a so-called “first-align-then-fold” route in which a mul- sequence segments. In particular, such collection could con- tiple sequence alignment (MSA) is analyzed, for instance, as a sist of intronic windows adjacent to orthologous donor and profile by a single-sequence algorithm (Seemann et al. 2010, acceptor splice sites or of orthologous miRNA precursors 2011; Li et al. 2011) or by a probabilistic model (Knudsen and 3′-UTRs in a miRNA target search, etc. The aim is to iden- and Hein 2003; Pedersen et al. 2006; Rivas et al. 2012). This tify all pairs of complementary k-mers that occur in sufficient- approach strongly depends on the accuracy of MSA, and al- ly many orthologous segments—no matter where, since the though some improvement can be achieved by considering positions in unaligned sequences are not matched. suboptimal sequence alignments (Will et al. 2013), the major This setup is implemented here as a computational pipe- limitation remains that MSA does not always exist. The oppo- line called IRBIS (intermolecular RNA interaction search, site, “first-fold-then-align” route has not been systematical- where “B” acknowledges a BLAT-like algorithm) (Kent ly investigated because optimal single-sequence predictions 2002), which is designed to search for conserved, long-range are not accurate enough to build a consistent alignment RRI. The pipeline is fully automated and contains all necessary (Shapiro and Zhang 1990; Hochsmann et al. 2003; Gardner preprocessing steps, including genomic sequence download, and Giegerich 2004). identification of orthologous segments, selection of unique Recent studies on RSSs in eukaryotic genes revealed wide- orthologs, etc. (Supplemental Material). Compared to the spread occurrence of long-range RRI with diverse functions previous analyses (Raker et al. 2009; Pervouchine et al. such as riboswitches (Li and Breaker 2013) and mediators 2012), which were restricted to short segments and to a rela- of exon skipping (Lovci et al. 2013), mutually exclusive tively small number of their combinations, IRBIS