[en] The aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generated in-vivo. CircRNA identification is mostly an in-silico process, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. Furthermore, for 63 of those samples we analysed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence of 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified by total RNAseq/mRNAseq comparison using two circRNA tools, 26 probable artif_circRNAs, and 65 identified by deep annotation analysis. Extensive benchmarking was performed (including analyses with CIRI2 and CIRCexplorer-2) and confirmed 94% of the 23,737 reliable exonic circRNAs. Moreover, this study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analysing the tissue specificity of the bovine circular transcriptome.
Disciplines :
Genetics & genetic processes
Author, co-author :
Robic, Annie ; GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
Hadlich, Frieder ; Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Costa Monteiro Moreira, Gabriel ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)
Louise Clark, Emily ; The Roslin Institute, University of Edinburgh, Edinburgh, UK
Plastow, Graham ; Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, AB, Canada
Charlier, Carole ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics
Kühn, Christa ; Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany ; Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany ; Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
Language :
English
Title :
Innovative construction of the first reliable catalogue of bovine circular RNAs.
H2020 - 815668 - BovReg - BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle
Funders :
EU - European Union
Funding text :
These studies are fully associated with the FAANG initiative. Data was produced by BovReg, which has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement [No 815668]. INRAE (GenPhySE and Animal Genetics division) and the Institute of Genome Biology of FBN supported studies around circular RNAs. Annie Robic acknowledges INRAE (more precisely the Animal Genetics and the M2I divisions) and the FBN (more precisely the Institute of Genome Biology), which supported her research stay in FBN in 2022\u20132023. We thank Dr Sylvain Foissac and Dr Laurence Liaubet (GenPhySE) for indirectly enriching this study through their insightful discussions.
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