Circular RNAs: Identification, biogenesis and function

Ebbesen, Karoline K; Kjems, Jørgen; Hansen, Thomas B.

doi:10.1016/j.bbagrm.2015.07.007

Cited by 461 publications

(387 citation statements)

References 41 publications

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“…For a long time, circular RNA molecules (circRNAs) lacking 3 0 or 5 0 termini were considered an unusual form of nucleic acids found in few viroids or viruses using a single-stranded RNA molecule as genetic material, participating in maturation of some tRNA genes, or, alternatively, a result of aberrant RNA splicing (for recent reviews, see [1][2][3] ). However, numerous recent genome-wide experimental and computational studies (RNAseq analyses) tailored toward detection of circRNAs have revealed this class of RNA molecules as abundant in eukarya, including humans.…”

Section: Introductionmentioning

confidence: 99%

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

et al. 2017

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It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules.

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Section: Introductionmentioning

confidence: 99%

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

et al. 2017

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“…CircRNAs are expressed in tissue‐specific and developmental stage‐dependent manners 3. The dysregulations of circRNAs contribute to many diseases because they act as microRNA target decoys, RNA binding protein sponges, and transcriptional regulators 4. Additionally, circRNAs are highly stable because of a resistance to debranching enzymes and RNA exonucleases.…”

Section: Introductionmentioning

confidence: 99%

Plasma Circular RNAs, Hsa_circRNA_025016, Predict Postoperative Atrial Fibrillation After Isolated Off‐Pump Coronary Artery Bypass Grafting

Zhang

Shu

et al. 2018

JAHA

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BackgroundCircular RNAs (circRNAs) are pervasively expressed in highly divergent eukaryotes and are stable in body fluids. However, the link between circRNAs and onset of atrial fibrillation (AF) has not previously been investigated. We aimed to identify plasma circRNAs that are able predict AF after cardiac surgery.Methods and ResultsPlasma circRNA expression profiles were investigated in a total of 769 patients with or without AF after isolated off‐pump coronary artery bypass grafting. First, a circRNA microarray was used to screen 13 617 human circRNAs in plasma samples from patients in the discovery cohort (n=30). A quantitative polymerase chain reaction assay was then applied to evaluate the expression of 9 selected circRNAs in the training cohort (n=365). This approach revealed that hsa_circRNA_025016 was upregulated in patients with new‐onset AF with a high diagnostic accuracy as assessed by the area under the receiver operating characteristic curve (=0.802). Additionally, a satisfactory diagnostic performance of hsa_circRNA_025016 was found in the validation cohort (n=284). Furthermore, Kyoto Encyclopedia of Genes and Genomes biological pathway analysis indicated that hsa_circ_025016 participated in melanogenesis, insulin secretion, and the thyroid hormone signaling pathway. A positive correlation between hsa_circ_025016 and fasting blood glucose was also identified in both cohorts.ConclusionsHsa_circ_025016 is a potential biomarker for predicting new‐onset AF after isolated off‐pump coronary artery bypass grafting.

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“…CircRNAs are a novel class of ncRNAs characterized by the presence of a covalent bond linking the 3' and 5' ends generated by back-splicing (88). They have previously demonstrated substantial capabilities as gene regulators in human cell progression, including in tumor development, and have been revealed to be abundant, conserved and stable in the cytoplasm (89,90).…”

Section: Gastric Cancermentioning

confidence: 99%

“…At present, there is no study that specifically investigates the association between circRNAs and the Notch signaling pathway. However, considering that circRNAs are believed to act as inhibitors of miRNA function by binding to a specific miRNA (88), this may indicate a potential association with the Notch signaling pathway similar to miRNAs (47).…”

Section: Gastric Cancermentioning

confidence: 99%

Crosstalk between the Notch signaling pathway and non‑coding RNAs in gastrointestinal cancers (Review)

2017

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Abstract. The Notch signaling pathway is one of the main signaling pathways that mediates direct contact between cells, and is essential for normal development. It regulates various cellular processes, including cell proliferation, apoptosis, migration, invasion, angiogenesis and metastasis. It additionally serves an important function in tumor progression. Non-coding RNAs mainly include small microRNAs, long non-coding RNAs and circular RNAs. At present, a large body of literature supports the biological significance of non-coding RNAs in tumor progression. It is also becoming increasingly evident that cross-talk exists between Notch signaling and non-coding RNAs. The present review summarizes the current knowledge of Notch-mediated gastrointestinal cancer cell processes, and the effect of the crosstalk between the three major types of non-coding RNAs and the Notch signaling pathway on the fate of gastrointestinal cancer cells.

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Circular RNAs: Identification, biogenesis and function

Cited by 461 publications

References 41 publications

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

Plasma Circular RNAs, Hsa_circRNA_025016, Predict Postoperative Atrial Fibrillation After Isolated Off‐Pump Coronary Artery Bypass Grafting

Crosstalk between the Notch signaling pathway and non‑coding RNAs in gastrointestinal cancers (Review)

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