FUCHS - Towards full circular RNA characterization using RNAseq

• DOI: 10.7287/peerj.preprints.2418v1
• Publication Date: 2018-01-13T10:03:08Z
• Authors: Franziska Metge; Lisa F Czaja-Hasse; Richard Reinhardt; Chistoph Dieterich
• Keywords: Circular RNA; Pseudoknot

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during maturation through process called back-splicing. A downstream 5’ splice site is linked an upstream 3’ form circular transcript instead canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus many scientists. Since then, several studies reported are differentially expressed across tissue types and developmental stages, implying they actively regulated not merely by-product splicing. Though functional shown some could act as miRNA-sponges, function most remains unknown. To expand our understanding possible roles RNAs, we propose new pipeline fully characterizes candidate circRNA structure from RNAseq data – FUCHS: FU ll CH aracterization using RNA- S equencing. Currently, computational prediction pipelines use back-spliced reads identify RNAs. FUCHS extends this concept by considering all RNA-seq information long (typically > 150 bp) learn more about exon coverage, number double break point fragments, different isoforms arising one host-gene, alternatively spliced exons within same boundaries. This knowledge will enable user carry out differential-motif enrichment miRNA-seed analysis determine potential regulators biogenesis. easy-to-use Python based contributes aspect research. The available git repository: https://github.com/dieterich-lab/FUCHS