Circular RNAs: analysis, expression and potential functions

Barrett, Steven P.; Salzman, Julia

doi:10.1242/dev.128074

Cited by 739 publications

(624 citation statements)

References 67 publications

(131 reference statements)

Supporting

Mentioning

617

Contrasting

Unclassified

Order By: Relevance

“…Current biochemical methods are mainly aimed at proving the circularity of putative circRNAs and include RT-PCR followed by inverse PCR, Northern Blotting with probes designed to target the circularised junction sequences, and RNaseR sensitivity tests 25 . Another validation method takes advantage of the high processivity and strand displacement capabilities of reverse transcriptases which can yield cDNAs consisting of concatemers of circRNAs, a phenomenon known as rolling-circle RT.…”

Section: /17mentioning

confidence: 99%

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

Chong

Sauka‐Spengler

2017

Preprint

View full text Add to dashboard Cite

Circular RNAs are a puzzling class of RNAs with covalently closed loop structure, lacking 5' and 3' ends. Present in all cells, no unifying theme has emerged regarding their function. Here, we use transcriptional data obtained by biotagging in zebrafish to uncover a high-resolution cohort of embryonic circRNAs expressed in nuclear and polysomal subcellular compartments in three developmental cell types. The ample presence of embryonic circRNAs on polysomes contradicts previous reports suggesting predominant nuclear localisation. We uncover a novel class of circRNAs, significantly enriched at tandem duplicated genes. Using newly-developed NGS-based approach, we simultaneously resolve the full sequence of putative "tandem-circRNAs" and their underlying mRNAs. These form by long-range cis-splicing events often between distant tandem duplicated genes, resulting in chimaeric mRNA transcripts and circRNAs containing their supernumerary excised exons, integrated from multiple tandem loci. Taken together, our results suggest that circularisation events rather than circRNAs themselves are functionally important.

show abstract

Section: /17mentioning

confidence: 99%

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

Chong

Sauka‐Spengler

2017

Preprint

View full text Add to dashboard Cite

show abstract

“…In particular, thousands of circular RNAs with little or no protein-coding capacity are generated from genes in a variety of eukaryotes, including humans, mice, C. elegans, D. melanogaster, S. pombe, and plants (For a review see refs. [6][7][8][9][10][11][12] ). Some of these circular RNAs are expressed at much higher levels than their associated linear mRNAs, 13,14 suggesting that the main function of some protein-coding genes may be to produce circular noncoding RNAs rather than proteins.…”

Section: Introductionmentioning

confidence: 99%

Circular RNAs: Unexpected outputs of many protein-coding genes

Wilusz

2016

RNA Biology

111

View full text Add to dashboard Cite

Pre-mRNAs from thousands of eukaryotic genes can be non-canonically spliced to generate circular RNAs, some of which accumulate to higher levels than their associated linear mRNA. Recent work has revealed widespread mechanisms that dictate whether the spliceosome generates a linear or circular RNA. For most genes, circular RNA biogenesis via backsplicing is far less efficient than canonical splicing, but circular RNAs can accumulate due to their long half-lives. Backsplicing is often initiated when complementary sequences from different introns base pair and bring the intervening splice sites close together. This process is further regulated by the combinatorial action of RNA binding proteins, which allow circular RNAs to be expressed in unique patterns. Some genes do not require complementary sequences to generate RNA circles and instead take advantage of exon skipping events. It is still unclear what most mature circular RNAs do, but future investigations into their functions will be facilitated by recently described methods to modulate circular RNA levels.

show abstract

“…However, authors of an earlier study observed and sequenced the rolling RT products of circRNA in cDNA [8]. This phenomenon, known as rolling-circle RT, can lead to a laddering effect on a gel after PCR but can also result in an overestimation of circRNA by qPCR [18].…”

Section: Introductionmentioning

confidence: 99%

Application of droplet digital PCR in quantitative detection of the cell-free circulating circRNAs

Chen

Zhang

Tan

et al. 2017

Biotechnology & Biotechnological Equipment

View full text Add to dashboard Cite

Diagnostics based on circulating circular RNA (circRNA) is an emerging field for noninvasive molecular diagnosis, owing to the stable circular structure of circRNA. However, the uniquely circular structure still poses a challenge for circRNA quantification in the research community. Here, we verified the discrepancy in the circRNA quantification by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription-droplet digital polymerase chain reaction (RT-ddPCR), which is caused by the rolling reverse transcription (RT) product originating from the circular structure. In addition, we detected the stability of cell-free circRNA in serum/ plasma and determined the pre-analysis sampling procedure that will compromise the quantification of circRNA. Our results showed that prolonged RT incubation time resulted in multiple PCR products from circular RNA, which will reduce the accuracy of circRNA quantification by RT-qPCR technology, whereas ddPCR can address this limitation and could be a good alternative to qPCR for circRNA quantification. CircRNA showed a high stability in promptly separated serum/ plasma but not in delay-separated samples.

show abstract

Circular RNAs: analysis, expression and potential functions

Cited by 739 publications

References 67 publications

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

Circular RNAs: Unexpected outputs of many protein-coding genes

Application of droplet digital PCR in quantitative detection of the cell-free circulating circRNAs

Contact Info

Product

Resources

About