Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Jan;21(1):52-74.
doi: 10.1080/15476286.2024.2375090. Epub 2024 Jul 11.

Innovative construction of the first reliable catalogue of bovine circular RNAs

Annie Robic  1 , Frieder Hadlich  2 , Gabriel Costa Monteiro Moreira  3 , Emily Louise Clark  4 , Graham Plastow  5 , Carole Charlier  3   6 , Christa Kühn  2   7   8
Affiliations

Innovative construction of the first reliable catalogue of bovine circular RNAs

Annie Robic et al. RNA Biol. 2024 Jan.

Abstract

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.

Keywords: Exonic circRNA; artificial annotation; artificial circRNA; backsplicing; bovine circRNAs; circular transcriptome; intron circle; lariat-derived circRNA.

PubMed Disclaimer

Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Analytical pipeline used to characterize circRNAs.
Figure 2.
Figure 2.
Overview of circRNAs detected in the 117 samples considered.
Figure 3.
Figure 3.
Analysis of circRNAs detected in mRNAseq.
Figure 4.
Figure 4.
Analysis of circRNAs detected by CIRI2.
Figure 5.
Figure 5.
Analyses of the possible presence of 23,737 exonic circRNAs in bovine tissues/samples.
Figure 6.
Figure 6.
Expression analysis of 23,737 exonic circRNAs in four samples.
Figure 7.
Figure 7.
Benchmarking of 23,737 reliable exonic circRNAs and additional exonic circRNAs.
Figure 8.
Figure 8.
Hierarchical clustering analysis (HCA).
Figure 9.
Figure 9.
Principal component analyses (PCA).
Figure 10.
Figure 10.
List and characteristics of different events leading to the formation of a circular junction.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Rosen BD, Bickhart DM, Schnabel RD, et al. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience. 2020;9(3). doi: 10.1093/gigascience/giaa021 - DOI - PMC - PubMed
    1. Goszczynski DE, Halstead MM, Islas-Trejo AD, et al. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage. Genome Res. 2021;31(4):732–744. doi: 10.1101/gr.267336.120 - DOI - PMC - PubMed
    1. Ross EM, Sanjana H, Nguyen LT, et al. Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman Cattle. Front Genet. 2022;13:784663. doi: 10.3389/fgene.2022.784663 - DOI - PMC - PubMed
    1. Salavati M, Clark R, Becker D, et al. Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using cap analysis gene expression sequencing. G3: Genes, Genomes, Genet. 2023;13(8):G3 13. doi: 10.1093/g3journal/jkad108 - DOI - PMC - PubMed
    1. Jeck WR, Sorrentino JA, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013;19(2):141–157. doi: 10.1261/rna.035667.112 - DOI - PMC - PubMed