Circular RNAs: Characterization, cellular roles, and applications

Liu, Chu-Xiao; Chen, Lingling

doi:10.1016/j.cell.2022.04.021

Cited by 449 publications

(380 citation statements)

References 190 publications

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“…Additionally, there were 579, 135, 69 and 347 de-regulated RNA circles in the SHH, WNT, Group 3 and Group 4 subtypes, respectively, in comparison to both the remaining subtypes and to cerebellum (Figure S3, File S4). The uniquely de-regulated circles (Figure 1B) found in these lists (File S4) have a good potential as possible biomarkers for subtype-specific disease development [36].…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, the raw counts of the fusions from the circular enriched preparations were found to be comparable to those of the fusions from the poly(A) enriched preparations (Figure 2A, File S6). This is in contrast to the general observations of circular RNAs being expressed less than linear poly(A) mRNAs [36]. The 20 most abundant fusion transcripts from each of the linear and circular RNA preparations in cerebellum and medulloblastoma were selected (Figure S5, File S6).…”

Section: Fusion Rnas-cerebellummentioning

confidence: 99%

“…Increasing the read depth, currently at 25 M reads per sample, should provide the means to overcome this limitation. It is also possible that certain fusion RNAs, similarly to certain circular RNAs, may have limited impact on disease development and could simply represent "passenger" molecules, reflecting the stochasticity of the gene expression and splicing processes [22,36]. Even in such a scenario, differentially expressed circles, due to their stability, could still be effective as diagnostic markers [36,44].…”

Section: Limitationsmentioning

confidence: 99%

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Circular and Fusion RNAs in Medulloblastoma Development

Azatyan

Zaphiropoulos

2022

Cancers

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Background. The cerebellar cancer medulloblastoma is the most common childhood cancer in the brain. Methods. RNA sequencing of 81 human biospecimens of medulloblastoma using pipelines to detect circular and fusion RNAs. Validation via PCR and Sanger sequencing. Results. 27, 56, 28 and 11 RNA circles were found to be uniquely up-regulated, while 149, 7, 20 and 15 uniquely down-regulated in the SHH, WNT, Group 3, and Group 4 medulloblastoma subtypes, respectively. Moreover, linear and circular fusion RNAs containing exons from distinct genes joined at canonical splice sites were also identified. These were generally expressed less than the circular RNAs, however the expression of both the linear and the circular fusions was comparable. Importantly, the expression of the fusions in medulloblastoma was also comparable to that of cerebellum. Conclusions. A significant number of fusions in tumor may be generated by mechanisms similar to the ones generating fusions in normal tissue. Some fusions could be rationalized by read-through transcription of two neighboring genes. However, for other fusions, e.g., a linear fusion with an exon from a downstream gene joined 5′ to 3′ with an exon from an upstream gene, more complicated splicing mechanisms, e.g., trans-splicing, have to be postulated.

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Section: Discussionmentioning

confidence: 99%

Section: Fusion Rnas-cerebellummentioning

confidence: 99%

Section: Limitationsmentioning

confidence: 99%

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Circular and Fusion RNAs in Medulloblastoma Development

Azatyan

Zaphiropoulos

2022

Cancers

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“…CircRNAs perform highly specifically roles in tissues and cells, making them have the opportunity to become valuable prognostic and diagnostic biomarkers for ESCC. Furthermore, the unique properties of circRNAs on conformation, stability and immunogenicity will be of interest to explore RNA circle-based technologies, which include regulating innate immune responses, serving as sponges of cellular miRNAs and as aptamers to interfere with intracellular processes [ 132 ]. The research on those innovative technologies may open up a novel field in diagnosis and treatment of many diseases.…”

Section: Conclusion and Perspectivesmentioning

confidence: 99%

Current advances and future perspectives on the functional roles and clinical implications of circular RNAs in esophageal squamous cell carcinoma: more influential than expected

Wang

et al. 2022

Biomark Res

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Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive gastrointestinal cancers with high incidence and mortality. Therefore, it is necessary to identify novel sensitive and specific biomarkers for ESCC detection and treatment. Circular RNAs (circRNAs) are a type of noncoding RNAs featured by their covalently closed circular structure. This special structure makes circRNAs more stable in mammalian cells, coupled with their great abundance and tissue specificity, suggesting circRNAs may present enormous potential to be explored as valuable prognostic and diagnostic biomarkers for tumor. Mounting studies verified the critical roles of circRNAs in regulating ESCC cells malignant behaviors. Here, we summarized the current progresses in a handful of aberrantly expressed circRNAs, and elucidated their biological function and clinical significance in ESCC, and introduced a series of databases for circRNA research. With the improved advancement in high-throughput sequencing and bioinformatics technique, new frontiers of circRNAs will pave the path for the development of precision treatment in ESCC.

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“…The 748 E. histolytica and E. invadens circRNAs previously identified (López-Luis, 2022) were compared to the 1997 genes with introns and annotated as Iron-Sulfur (Fe-S, marked with S) metabolism in the AmoebaDB. From this set, only 162 genes with two or more exons were considered because introns are required for circRNAs biogenesis through back-splicing (Liu and Chen, 2022). The common genes of this set with those whose circRNAs were detected in the virulent (HM1-IMSS; 174) and the avirulent (Rahman; 191) amoebic strains.…”

Section: Circrnas Are Shared In Different Metabolic and Differentiati...mentioning

confidence: 99%