Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

Legnini, Ivano; Timoteo, Gaia Di; Rossi, Francesca Maria; Morlando, Mariangela; Briganti, Francesca; Sthandier, Olga; Fatica, Alessandro; Santini, Tiziana; Andronache, Adrian; Wade, Mark; Laneve, Pietro; Rajewsky, Nikolaus; Bozzoni, Irene

doi:10.1016/j.molcel.2017.02.017

Cited by 1,735 publications

(1,768 citation statements)

References 51 publications

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“…The protein-coding potential of circZNF609 was validated with an expression vector encoding the 3FLAG tag at the COOH-terminus of the predicted protein upstream of the initiating methionine, with production of the 3×FLAG-tagged protein being possible only from the circular form of the vector. Expression of the 3×FLAG-tagged protein was induced by heat shock stress, consistent with the activation of cap-independent translation by various external stimuli (Legnini et al, 2017).…”

Section: (2) Circznf609supporting

confidence: 65%

“…Whereas circZNF609 is down-regulated during myogenesis, it is up-regulated in myoblasts of DMD patients, suggesting that overexpression of circZNF609 might contribute to the delayed myoblast differentiation phenotype of such patients (Legnini et al, 2017).…”

Section: (2) Circznf609mentioning

confidence: 99%

“…1B) ( Legnini et al, 2017;Pamudurti et al, 2017). Some circRNAs have even been found to generate proteins containing >100 amino acids (Legnini et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Hidden Peptides Encoded by Putative Noncoding RNAs

Matsumoto

Nakayama

2018

Cell Struct. Funct.

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Although the definition of a noncoding RNA (ncRNA) is an RNA molecule that does not encode a protein, recent evidence has revealed that some ncRNAs are indeed translated to give rise to small polypeptides (usually containing fewer than 100 amino acids). Despite their small size, however, these peptides are often biologically relevant in that they are required for a variety of cellular processes. In this review, we summarize the production and functions of peptides that have been recently identified as translation products of putative ncRNAs.4

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Section: (2) Circznf609supporting

confidence: 65%

Section: (2) Circznf609mentioning

confidence: 99%

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Hidden Peptides Encoded by Putative Noncoding RNAs

Matsumoto

Nakayama

2018

Cell Struct. Funct.

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“…We observed both differential splicing and circRNA increases at Calx (Supporting Information Figure S3). Two recent reports suggest that a subset of circRNAs are translated, suggesting potential regulatory roles during aging (Legnini et al, 2017; Pamudurti et al, 2017). Like the translated circRNAs identified in these studies, the Calx circRNA contains a start codon and could be a potential target for translation; however, we have not examined this possibility.…”

Section: Discussionmentioning

confidence: 99%

Proper splicing contributes to visual function in the aging Drosophila eye

et al. 2018

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Changes in splicing patterns are a characteristic of the aging transcriptome; however, it is unclear whether these age‐related changes in splicing facilitate the progressive functional decline that defines aging. In Drosophila, visual behavior declines with age and correlates with altered gene expression in photoreceptors, including downregulation of genes encoding splicing factors. Here, we characterized the significance of these age‐regulated splicing‐associated genes in both splicing and visual function. To do this, we identified differential splicing events in either the entire eye or photoreceptors of young and old flies. Intriguingly, aging photoreceptors show differential splicing of a large number of visual function genes. In addition, as shown previously for aging photoreceptors, aging eyes showed increased accumulation of circular RNAs, which result from noncanonical splicing events. To test whether proper splicing was necessary for visual behavior, we knocked down age‐regulated splicing factors in photoreceptors in young flies and examined phototaxis. Notably, many of the age‐regulated splicing factors tested were necessary for proper visual behavior. In addition, knockdown of individual splicing factors resulted in changes in both alternative splicing at age‐spliced genes and increased accumulation of circular RNAs. Together, these data suggest that cumulative decreases in splicing factor expression could contribute to the differential splicing, circular RNA accumulation, and defective visual behavior observed in aging photoreceptors.

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“…The circDeep is implemented in python using keras 1.0.4 which is found https://github.com/ fchollet/keras, with the backend of Theano (0.9.0) [30]. In order to benefit from the parallel computation of the tensors, we train our model on a NVIDIA Tesla C2050.…”

Section: Experiments Setupmentioning

confidence: 99%

End-to-end learning framework for circular RNA classiﬁcation from other long non-coding RNAs using multi-modal deep learning.

Chaabane¹

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Over the past two decades, a circular form of RNA (circular RNA) produced from splicing mechanism has become the focus of scientific studies due to its major role as a microRNA (miR) activity modulator and its association with various diseases including cancer. Therefore, the detection of circular RNAs is a vital operation for continued comprehension of their biogenesis and purpose.Prediction of circular RNA can be achieved by first distinguishing non-coding RNAs from protein coding gene transcripts, separating short and long non-coding RNAs (lncRNAs), and finally predicting circular RNAs from other lncRNAs. However, available tools to distinguish circular RNAs from other lncRNAs have only reached 80% accuracy due to the difficulty of classifying circular RNAs from other lncRNAs. Therefore, the availability of a faster, more accurate machine learning method for the identification of circular RNAs, which will take into account the specific features of circular RNA, is essential in the development of systematic annotation. Here we present an Endto-End multimodal deep learning framework, our tool, to classify circular RNA from other lncRNA.It fuses a RCM descriptor, an ACNN-BLSTM sequence descriptor, and a conservation descriptor into high level abstraction descriptors, where the shared representations across different modalities are integrated. The experiments show that our tool is not only faster compared to existing tools but also eclipses other tools by an over 12% increase in accuracy. Another interesting result found from analysis of a ACNN-BLSTM sequence descriptor is that circular RNA sequences share the characteristics of the coding sequences.iv

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Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

Cited by 1,735 publications

References 51 publications

Hidden Peptides Encoded by Putative Noncoding RNAs

Hidden Peptides Encoded by Putative Noncoding RNAs

Proper splicing contributes to visual function in the aging Drosophila eye

End-to-end learning framework for circular RNA classiﬁcation from other long non-coding RNAs using multi-modal deep learning.

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