Zobrazit v EDS

Innovative construction of the first reliable catalogue of bovine circular RNAs

Uloženo v:
Podrobná bibliografie
Název: Innovative construction of the first reliable catalogue of bovine circular RNAs
Autoři: Robic, Annie, Hadlich, Frieder, Costa Monteiro Moreira, Gabriel, Louise Clark, Emily, Plastow, Graham, Charlier, Carole, Kühn, Christa
Přispěvatelé: EU - European Union, robic, annie, Génétique Physiologie et Systèmes d'Elevage (GenPhySE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute for Farm Animal Biology (FBN), Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED), École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-Research), Université de Liège, Université de Liège - Gembloux, The Roslin Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Alberta, University of Rostock, INRAE (GenPhySE and Animal Genetics division) and Institute of Genome Biology of FBN, European Project: 815668,H2020,H2020-EU.3.2.1.1., H2020-EU.3.2.3.1.,BovReg(2019), Research Institute for Farm Animal Biology (FBN), Université de Liège = University of Liège = Universiteit van Luik = Universität Lüttich (ULiège), Gembloux Agro-Bio Tech Faculté universitaire des sciences agronomiques de Gembloux ( FUSAGx ), University of Rostock = Universität Rostock, Friedrich-Loeffler-Institut (FLI)
Zdroj: RNA Biol
RNA Biology, Vol 21, Iss 1, Pp 716-738 (2024)
Informace o vydavateli: Informa UK Limited, 2024.
Rok vydání: 2024
Témata: lariat-derived circRNA, [SDV]Life Sciences [q-bio], circular transcriptome, Genetics & genetic processes, bovine circRNAs, Sequence Analysis, RNA/methods, QH426-470, intron circle, Génétique & processus génétiques, Genetics, Animals, Molecular Biology, artificial annotation, Sequence Analysis, RNA, Gene Expression Profiling, Computational Biology, Cell Biology, RNA, Circular, Exons, Computational Biology/methods, Life sciences, artificial circRNA, Introns, 3. Good health, [SDV] Life Sciences [q-bio], RNA, Circular/genetics, Exonic circRNA, backsplicing, Sciences du vivant, Cattle, Gene Expression Profiling/methods, Transcriptome, Research Paper
Popis: 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.
Druh dokumentu: Article
Other literature type
Popis souboru: application/pdf
Jazyk: English
ISSN: 1555-8584
1547-6286
DOI: 10.1080/15476286.2024.2375090
DOI: 10.57745/iuj40p
DOI: 10.57745/xorqhk
Přístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/38989833
https://doaj.org/article/eb86ff58292c434c83d3a7ca3858587e
Rights: CC BY NC
URL: http://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (http://creativecommons.org/licenses/by-nc/4.0/) ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.
Přístupové číslo: edsair.doi.dedup.....a6a0f454ba806b2b63ba9bbaf1ddbfc6
Databáze: OpenAIRE
Popis
Abstrakt: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.
ISSN:15558584
15476286
DOI:10.1080/15476286.2024.2375090