From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs

Robic, Annie; Cerutti, Chloé; Demars, Julie; Kühn, Christa

doi:10.1016/j.bbagrm.2022.194815

Cited by 4 publications

(5 citation statements)

References 68 publications

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“…Intronic circRNAs are responsible for 0.37% of the global expression of circRNAs (Figure 2D). The expression of intronic circRNAs, ciRNA-ATXN2L, which was found to be the dominating ciRNA in pigs [28], was very low in most samples in the current analysis of bovine tissues, similar to a previous report [36].…”

Section: Brief Description Of Circrna Expressionsupporting

confidence: 90%

“…Finding a canonical SS may not always be sufficient for selecting the backsplicing targets. The same kind of competition can take place to choose the branch point [36]. When we looked again at the eight circRNAs from MORC3 that share their downstream boundary (end of exon7), we noted that they all were detected in the 63 total-RNAseq datasets, but not in any of the 63 mRNAseq datasets (Figure 4A).…”

Section: Resultsmentioning

confidence: 96%

“…Several studies have demonstrated the value of excluding such events [32; 41]. The 117 output files generated by CD [27; 36] were concatenated, resulting in the detection of 66,299 circRNAs. After discarding circRNAs with genomic size less than 70 nucleotides 61,083 circRNAs were retained.…”

Section: Resultsmentioning

confidence: 99%

“…Our approach to characterize circRNAs is described in Figure 1 (see M&M_Adoc-1-4 for details). The chosen circRNA tool, CD (CircDetector, [27; 36]), works in two steps. The initial step involves identifying reads that contain a circular junction, referred to as circular chimeric reads (CCRs), and generating two output files (Figure 1).…”

Section: Methodsmentioning

confidence: 99%

“…This circRNA tool was specifically designed for intronic circRNA characterization [Robic et al 2022 ;]. The identification of the reads supporting the circular junction is performed from the single end alignments of the PE reads, and the compatibility of the second read with this characterization is not verified.…”

Section:  Presentations Of CDmentioning

confidence: 99%

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Polyadenylated RNA sequencing analysis helps establish a reliable catalog of circular RNAs – a bovine example

Robic,

Hadlich,

Monteiro Moreira

et al. 2024

Preprint

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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. We suggested in-vivo copying of specific exonic circRNAs by an RNA-dependent RNA polymerase (RdRP) to explain the 20 identified circRNAs with reverse-complement exons. Furthermore, for 63 of those samples we analyzed 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 that there were 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified through comparison of total-RNAseq/mRNAseq using two circRNA tools, 26 probable artif_circRNAs, and 65 identified through deep annotation analysis. This study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analyzing the diversity of the bovine circular transcriptome.

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Section: Brief Description Of Circrna Expressionsupporting

confidence: 90%

Section: Resultsmentioning

confidence: 96%