Abstract
BackgroundWith the advances in next-generation sequencing technologies, it is possible to determine RNA-RNA interaction and RNA structure predictions on a genome-wide level. The reads from these experiments usually are chimeric, with each arm generated from one of the interaction partners. Owing to short read lengths, often these sequenced arms ambiguously map to multiple locations. Thus, inferring the origin of these can be quite complicated. Here we present ChiRA, a generic framework for sensitive annotation of these chimeric reads, which in turn can be used to predict the sequenced hybrids.ResultsGrouping reference loci on the basis of aligned common reads and quantification improved the handling of the multi-mapped reads in contrast to common strategies such as the selection of the longest hit or a random choice among all hits. On benchmark data ChiRA improved the number of correct alignments to the reference up to 3-fold. It is shown that the genes that belong to the common read loci share the same protein families or similar pathways. In published data, ChiRA could detect 3 times more new interactions compared to existing approaches. In addition, ChiRAViz can be used to visualize and filter large chimeric datasets intuitively.Conclusion ChiRA tool suite provides a complete analysis and visualization framework along with ready-to-use Galaxy workflows and tutorials for RNA-RNA interactome and structurome datasets. Common read loci built by ChiRA can rescue multi-mapped reads on paralogous genes without requiring any information on gene relations. We showed that ChiRA is sensitive in detecting new RNA-RNA interactions from published RNA-RNA interactome datasets.
Highlights
Many non-coding RNAs regulate gene expression, post-transcriptionally, via mechanisms such as activation or inhibition of translation, destabilization, localization, and processing
The most recent line of development has been to ligate the miRNA to the site-specific interaction region of the target, selecting these interactions via cross-linking to 1 of the Argonaute proteins required for miRNA-based regulation, and to sequence the resulting chimeric RNA molecule, e.g., Cross-linking Ligation and Sequencing of Hybrids (CLASH) [6] and CLEAR-CLIP protocols [7]
There is a second set of data with the same arm lengths but a random 5-nucleotide sequence inserted either between or at the ends of the arms of each chimeric read
Summary
Many non-coding RNAs (ncRNAs) regulate gene expression, post-transcriptionally, via mechanisms such as activation or inhibition of translation, destabilization, localization, and processing. The most recent line of development has been to ligate the miRNA to the site-specific interaction region of the target, selecting these interactions via cross-linking to 1 of the Argonaute proteins required for miRNA-based regulation, and to sequence the resulting chimeric RNA molecule, e.g., CLASH [6] and CLEAR-CLIP protocols [7]. Researchers have applied the same idea to the detection of all transcriptome-wide RNA-RNA interactions This includes both inter- and intramolecular base-pairing without the necessity of choosing a specific regulatory protein for cross-linking, as done, e.g., in PARIS [8], SPLASH [9], and LIGR-Seq [10]. We showed that ChiRA is sensitive in detecting new RNA-RNA interactions from published RNA-RNA interactome datasets
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