Universität zu Köln

Metge, Franziska ORCID: 0000-0003-1192-421X (2018). Exon-intron chain reconstruction of circular RNA using RNA-Seq. PhD thesis, Universität zu Köln.

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Abstract

Circular RNAs (circRNAs) are a class of RNA forming a covalently closed loop through back-splicing. A few well studied circRNAs indicate miRNA sponging and regulation of host gene transcription. CircRNAs can be identified in rRNA depleted RNA-Seq by detecting reads, which span a back-splice junction. CircRNA detection tools exist but none are able to summarize or characterize circRNAs. To perform accurate downstream analyses it is crucial to know the exact exon-intron structure of circRNAs. Here, I am presenting FUCHS and FUCHSdenovo to summarize circRNAs and reconstruct their exon-intron chain. In short: I developed a pipeline called FUCHS : FUll CHaracterization of circular RNA using RNA-Sequencing; that summarizes circRNAs, detects skipped exons, finds double-breakpoint fragments, generates coverage profiles, and clusters these profiles. I developed an additional module, FUCHSdenovo, to reconstruct the exon-intron structure based on linear-splice signals of back-spliced reads. I ran both programs on a dataset of young and old murine hearts and young and old murine livers. FUCHS revealed that heart circRNAs are less diverse but more abundant than liver circRNAs. From the obtained coverage profiles, I concluded that annotated gene models were not all matching the exon-intron structure of circRNAs. A de-novo reconstruction of circle structures using FUCHSdenovo showed a gain of information of 15%. Furthermore, FUCHSdenovo identified alternative splicing (AS) in 10% of circRNAs. Performing a differential motif enrichment analysis of the flanking introns of circRNAs with AS over circRNAs without AS identified FOXO as a potential transcription factor driving AS in circRNAs. Comparing the seed density of circRNAs and mRNAs showed that circRNAs were more densely populated with both. This suggests that circRNAs could form an additional layer in the gene-regulatory network by competing with their host genes for miRNA or RBP binding. https://github.com/dieterich-lab/FUCHS.git

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Metge, Franziska franziska.metge@age.mpg.de orcid.org/0000-0003-1192-421X UNSPECIFIED
URN:	urn:nbn:de:hbz:38-84837
Date:	2018
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > MPI for Biology of Ageing
Subjects:	Data processing Computer science Life sciences
Uncontrolled Keywords:	Keywords Language circRNA, circRNA detection, de-novo recontruction, mouse heart, mouse liver, RNA-seq English
Date of oral exam:	6 October 2017
Referee:	Name Academic Title Valenzano, Dario R. Dr. Beyer, Andreas Prof. Dr.
Funders:	DFG Priority Program SPP1738, MPI Biology of Ageing
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/8483