Identification of virus-encoded circular RNA

Huang, Junting; Chen, Jianning; Gong, Li‐ping; Bi, Yanlan; Liang, Jinyan; Zhou, Lu; He, Dan; Shao, Chun-Kui

doi:10.1016/j.virol.2019.01.014

Cited by 72 publications

(62 citation statements)

References 31 publications

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“…Among the over 30 candidates of unique EBV circRNAs, two circRNAs generated from the RPMS1 locus, circular RPMS1_E4_E3a and circular RPMS1_E4_E2, were detected in two EBV-positive stomach tumor samples, suggesting their potential role in the cancer environment [184]. Studies have suggested that circular RPMS1_ E4_E2 (named ebv-circRPMS1 in Huang et al's work [185] and circBART_2.2 in Toptan et al's work [183]) is located in both the cytoplasm and nuclei of EBV-infected NPC cell lines, including the C666-1 cell line [185] and HK1 EBV cells [183]. Circular RPMS1_ E4_E2 was also shown to exist in EBV-positive NPC xenografts [183].…”

Section: Circrnas In Npcmentioning

confidence: 99%

“…Considering the common "miRNA sponge" of circRNAs in the cytoplasm, the potential miRNAs targeted by circular RPMS1_E4_E2 were predicted and then validated by the downregulation of target miRNAs after introducing the circular RPMS1_ E4_E2 overexpression plasmid. Notably, exogenous circular RPMS1_E4_E2 improved the migration of cells, indicating their essential role in the progression of tumors [185]. However, the underlying mechanisms and their roles in nuclei are still unknown.…”

Section: Circrnas In Npcmentioning

confidence: 99%

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Circular RNAs and their roles in head and neck cancers

et al. 2019

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Circular RNAs are abundant endogenous non-coding RNA with no 5′ cap and 3′ polyadenylation tail that modify liner mRNAs and have no terminal structures. Our knowledge of the biogenesis of circular RNAs has been expanded, and circular RNAs were shown to be key regulators of various diseases, especially cancers. Head and neck cancers are the sixth most popular cancers worldwide, and the overall survival rates remain unsatisfactory. Recent studies have indicated that circular RNAs are involved in the tumorigenesis, progression, invasion and chemosensitivity of head and neck cancers and that some circular RNAs could serve as diagnostic and prognostic biomarkers. In this study, we summarize research advances in the regulation of circular RNA biogenesis, their characteristics and functions, the involvement of circular RNAs in the pathophysiology of head and neck cancers and their potential clinical utilization, as well as the likely directions of future studies.

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Section: Circrnas In Npcmentioning

confidence: 99%

Section: Circrnas In Npcmentioning

confidence: 99%

Circular RNAs and their roles in head and neck cancers

et al. 2019

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“…Several evidences indicated the existence of viral circRNAs encoded in gammaherpesvirus EBV, KSHV and murine gammaherpesvirus 68 (MHV68) [132][133][134][135]. In EBV, more than 30 circRNAs were detected, and these derived from one viral gene that encode for several circRNAs by back-splicing mechanisms [132,134,135].…”

Section: Viral Circular Rnamentioning

confidence: 99%

Non-Coding RNAs: Strategy for Viruses’ Offensive

Gallo

Bulati

Miceli

et al. 2020

ncRNA

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The awareness of viruses as a constant threat for human public health is a matter of fact and in this resides the need of understanding the mechanisms they use to trick the host. Viral non-coding RNAs are gaining much value and interest for the potential impact played in host gene regulation, acting as fine tuners of host cellular defense mechanisms. The implicit importance of v-ncRNAs resides first in the limited genomes size of viruses carrying only strictly necessary genomic sequences. The other crucial and appealing characteristic of v-ncRNAs is the non-immunogenicity, making them the perfect expedient to be used in the never-ending virus-host war. In this review, we wish to examine how DNA and RNA viruses have evolved a common strategy and which the crucial host pathways are targeted through v-ncRNAs in order to grant and facilitate their life cycle.

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“…CircRNAs are relatively poorly studied members of the non-coding RNA family. These unique single-stranded molecules are generated through back-splicing of pre-mRNAs in a wide range of eukaryotic and prokaryotic taxa (Danan et al, 2012;Holdt, Kohlmaier & Teupser, 2018), and even viruses (Huang et al, 2019). CircRNAs play a significant role in the regulation of the molecular pathways not only through modulating of microRNA and protein activity, but also by the affecting transcription or splicing (Holdt, Kohlmaier & Teupser, 2018).…”

Section: Introductionmentioning

confidence: 99%

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms

Nedoluzhko

Sharko

Rbbani

et al. 2020

PeerJ

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Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. These regulatory molecules can modulate microRNA activity and are involved in different molecular pathways as indirect regulators of gene expression. Thousands of circRNAs have been described in diverse taxa due to the recent advances in high throughput sequencing technologies, which led to a huge variety of total RNA sequencing being publicly available. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations. Here, we present CircParser, a simple and fast Unix/Linux pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumptive host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also, this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using a genome annotation file.

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Identification of virus-encoded circular RNA

Cited by 72 publications

References 31 publications

Circular RNAs and their roles in head and neck cancers

Circular RNAs and their roles in head and neck cancers

Non-Coding RNAs: Strategy for Viruses’ Offensive

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms

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