Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs

Abstract

Recent genome-wide computational screens that search for conservation of RNA secondary structure in whole-genome alignments (WGAs) have predicted thousands of structural noncoding RNAs (ncRNAs). The sensitivity of such approaches, however, is limited, due to their reliance on sequence-based whole-genome aligners, which regularly misalign structural ncRNAs. This suggests that many more structural ncRNAs may remain undetected. Structure-based alignment, which could increase the sensitivity, has been prohibitive for genome-wide screens due to its extreme computational costs. Breaking this barrier, we present the pipeline REAPR (RE-Alignment for Prediction of structural ncRNA), which efficiently realigns whole genomes based on RNA sequence and structure, thus allowing us to boost the performance of de novo ncRNA predictors, such as RNAz. Key to the pipeline's efficiency is the development of a novel banding technique for multiple RNA alignment. REAPR significantly outperforms the widely used predictors RNAz and EvoFold in genomewide screens; in direct comparison to the most recent RNAz screen on D. melanogaster, REAPR predicts twice as many highconfidence ncRNA candidates. Moreover, modENCODE RNA-seq experiments confirm a substantial number of its predictions as transcripts. REAPR's advancement of de novo structural characterization of ncRNAs complements the identification of transcripts from rapidly accumulating RNA-seq data.[Supplemental material is available for this article.]

glu-RNA

“…Recently, Will et al [10] reported many novel ncRNAs using structured-based whole genome realignment. In their method, existing whole genome sequence alignment was used as the base alignment.…”

“…The idea of banded alignment has been used in both sequence alignment and structural alignment programs [9,10,11,12,13]. By applying dynamic programming in banded search space, the running time complexity of alignment programs can be reduced.…”

“…This space reduction significantly reduces the running time complexity of structural alignment. This heuristics is adopted by other structural alignment programs [6,10,12]. For example, a constant deviation (Δ) is used in Will et al's work to define a banded region for structural alignment.…”

“…Thus, a node with index (x, y) has three directed edges to nodes (x+1, y +1), (x+1, y), and (x, y +1). Any legal alignment between x and y can be visualized as a path in G. The similarity between two alignments can thus be represented by the distance of their corresponding paths, as suggested by Will et al [10].…”

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs

“…Because recent studies have suggested that re-alignment of genome sequence alignments reveals new non-coding RNAs [19], this function will be useful.…”