FUCHS-towards full circular RNA characterization using RNAseq

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Abstract

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA thatemerge during RNA maturation through a process called back-splicing. A downstream50 splice site is linked to an upstream 30 splice site to form a circular transcript insteadof a canonical linear transcript. Recent advances in next-generation sequencing (NGS)have brought circRNAs back into the focus of many scientists. Since then, severalstudies reported that circRNAs are differentially expressed across tissue types anddevelopmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs couldact as miRNA-sponges, the function of most circRNAs remains unknown. To expandour understanding of possible roles of circular RNAs, we propose a new pipeline thatcould fully characterizes candidate circRNA structure from RNAseq data- FUCHS:FUll CHaracterization of circular RNA using RNA-Sequencing. Currently, mostcomputational prediction pipelines use back-spliced reads to identify circular RNAs.FUCHS extends this concept by considering all RNA-seq information from long reads(typically>150 bp) to learn more about the exon coverage, the number of double breakpoint fragments, the different circular isoforms arising from one host-gene, and thealternatively spliced exons within the same circRNA boundaries. This new knowledgewill enable the user to carry out differential motif enrichment and miRNA seed analysisto determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-usePython based pipeline that contributes a new aspect to the circRNA research.

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Metge, F., Czaja-Hasse, L. F., Reinhardt, R., & Dieterich, C. (2017). FUCHS-towards full circular RNA characterization using RNAseq. PeerJ, 2017(2). https://doi.org/10.7717/peerj.2934

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