Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition

Ares, Manuel; Igel, Haller; Katzman, Sol; Donohue, John P.

doi:10.1101/2024.03.26.586863

Cited by 2 publications

(1 citation statement)

References 98 publications

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“…The residue of intronic lariats can become circular RNA precursors to provide ciRNAs or lariat derived circRNAs [8; 17; 18]. In addition to these ciRNAs, intron circles resulting from circularization of the entire intron have also been described [17; 19; 20; 68].…”

Section: Introductionmentioning

confidence: 99%

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: Introductionmentioning

confidence: 99%

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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Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers

Yao

Winans

et al. 2020

Preprint

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We used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq), which gives end-to-end sequence reads of highly structured RNAs, to identify >8,000 short (≤300 nt) full-length excised intron (FLEXI) RNAs in human cells. Most FLEXI RNAs are predicted to have stable secondary structures, making them difficult to detect by other RNA-seq methods. Some FLEXI RNAs correspond to annotated mirtron pre-miRNAs (introns that are processed into functional miRNAs) or agotrons (introns that bind AGO2 and function in a miRNA-like manner), but the vast majority had not been identified or characterized previously. FLEXI RNA profiles are cell-type specific, reflecting differences in host gene transcription, alternative splicing, or intron RNA turnover, and comparisons of matched tumor and healthy tissues from breast cancer patients and cell lines revealed hundreds of differences in FLEXI RNA expression. About half of the FLEXI RNAs contained one or more experimentally identified binding sites for a spliceosomal protein, AGO1-4, DICER, or a number of different regulatory proteins, suggesting multiple ways in which FLEXIs could contribute to the regulation of gene expression. As FLEXI RNAs are linked to the expression of thousands of protein-coding and lncRNA genes, they potentially constitute a new class of broadly applicable, highly discriminatory biomarkers for human diseases.

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Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition

Cited by 2 publications

References 98 publications

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

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

Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers

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