Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals

Ji, Peifeng; Wu, Wanying; Chen, Shuai; Zheng, Yi; Zhou, Lin; Zhang, Jinyang; Cheng, Hao; Jin, Yan; Zhang, Shaogeng; Yang, Peng; Zhao, Fangqing

doi:10.1016/j.celrep.2019.02.078

Cited by 188 publications

(204 citation statements)

References 50 publications

(52 reference statements)

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“…The conservation can extend in those cases to the particular splice sites flanking the circRNA. Splice site conservation of specific circRNAs was observed in flies, mice, macaque, and humans (Westholm et al, 2014;Rybak-Wolf et al, 2015;Ji et al, 2019). While only 3% of all circRNAs share the exact splice junction in Hs68 cells and murine testis, this seems to be the exception rather than the rule (Jeck et al, 2013).…”

Section: Circrna Properties and Featuresmentioning

confidence: 98%

“…This might be related to their biogenesis, which requires longer and less efficiently spliced introns than average; both criteria are usually met with the first introns (Ashwal-Fluss et al, 2014). While circRNA biogenesis might require inefficient canonical splicing, the introns within circRNAs seem to be mostly spliced out (Westholm et al, 2014;Guo et al, 2014;Gao et al, 2016;Data ref: Rahimi et al, 2019;Ji et al, 2019). These findings suggest that the inefficient splicing of the introns flanking circularizable exons is specific and not related to a poor processing of those transcripts in general.…”

Section: The Making Of a Circrnamentioning

confidence: 99%

“…Evolutionary conservation of circRNAs circRNAs are present in most organisms, including Archaea, plants, yeast, and most metazoans (Danan et al, 2012;Wang et al, 2014;Broadbent et al, 2015;Lu et al, 2015;Sun et al, 2016;Ji et al, 2019). However, it is not clear how they have evolved, as they seem to be produced by different mechanisms.…”

Section: Circrna Properties and Featuresmentioning

confidence: 99%

“…Splice site conservation of specific circRNAs was observed in flies, mice, macaque, and humans (Westholm et al, 2014;Rybak-Wolf et al, 2015;Ji et al, 2019). The conservation can extend in those cases to the particular splice sites flanking the circRNA.…”

Section: Circrna Properties and Featuresmentioning

confidence: 99%

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Past, present, and future of circ RNA s

2019

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Exonic circular RNAs (circRNAs) are covalently closed RNA molecules generated by a process named back‐splicing. circRNAs are highly abundant in eukaryotes, and many of them are evolutionary conserved. In metazoans, circular RNAs are expressed in a tissue‐specific manner, are highly stable, and accumulate with age in neural tissues. circRNA biogenesis can regulate the production of the linear RNA counterpart in cis as back‐splicing competes with linear splicing. Recent reports also demonstrate functions for some circRNAs in trans: Certain circRNAs interact with microRNAs, some are translated, and circRNAs have been shown to regulate immune responses and behavior. Here, we review current knowledge about animal circRNAs and summarize new insights into potential circRNA functions, concepts of their origin, and possible future directions in the field.

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Section: Circrna Properties and Featuresmentioning

confidence: 98%

Section: The Making Of a Circrnamentioning

confidence: 99%

Section: Circrna Properties and Featuresmentioning

confidence: 99%

Section: Circrna Properties and Featuresmentioning

confidence: 99%

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Past, present, and future of circ RNA s

2019

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“…circAtlas [57] was a database newly established by Ji et al in 2019, which was the most abundant and comprehensive circRNAs database from normal samples. They provided many aspects of cir-cRNAs on their circRNA Atlas web server, including their expression patterns, genomic features, conservations and functional annotations.…”

Section: Circatlasmentioning

confidence: 99%

Online Databases and Non-coding RNAs in Cardiovascular Diseases

Chen

Shi

Yao

et al. 2020

Advances in Experimental Medicine and Biology

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Cardiovascular disease is characterized by its highest morbidity and mortality. One of the main pathological basis of this disease is the dysregulation of gene expression. Non-coding RNA (ncRNA) is a kind of functional RNA, which is transcript from DNA but not translated into proteins. More and more studies have established the important roles of ncRNAs, including transcription, RNA maturation, translation, protein degradation, and their involvement in the pathogenesis of diseases such as cancer and cardiovascular diseases. This chapter will focus on the biological functions of ncRNAs and their advances in cardiovascular disease. With the development of sequencing and computer technology, more and more databases can be easily obtained on the internet. In another part of this chapter, we will summarize some commonly used noncoding RNA databases, which can be easily and quickly used for relevant research.

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circVAMP3 Drives CAPRIN1 Phase Separation and Inhibits Hepatocellular Carcinoma by Suppressing c‐Myc Translation

et al. 2022

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Previous studies have identified the regulatory roles of circular RNAs (circRNAs) in human cancers. However, the molecular mechanisms of circRNAs in hepatocellular carcinoma (HCC) remain largely unknown. This study screens the expression profile of circRNAs in HCC and identifies circVAMP3 as a significantly downregulated circRNA in HCC tissues. HCC patients with low circVAMP3 expression present poor prognosis. circVAMP3 negatively regulates the proliferation and metastasis of HCC cells in vitro and in vivo by driving phase separation of CAPRIN1 and promoting stress granule formation in cells, which can downregulate the protein level of Myc proto‐oncogene protein by inhibiting c‐Myc translation. Furthermore, circVAMP3 is widely expressed in many human tissues and is downregulated in related cancers. Therefore, circVAMP3 is a potential prognostic indicator for HCC and may serve as a therapeutic target for HCC treatment.

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Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals

Cited by 188 publications

References 50 publications

Past, present, and future of circ RNA s

Past, present, and future of circ RNA s

Online Databases and Non-coding RNAs in Cardiovascular Diseases

circVAMP3 Drives CAPRIN1 Phase Separation and Inhibits Hepatocellular Carcinoma by Suppressing c‐Myc Translation

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