ArticleBMC genomics2013
Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 86 citations in OpenAlex.
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- ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells.Cell & bioscience · 2025Article
- Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers.PLoS genetics · 2024Article
- Epstein-Barr virus noncoding RNA EBER1 promotes the expression of a ribosomal protein paralog to boost oxidative phosphorylation.Journal of medical virology · 2024Article
- Epstein-Barr virus noncoding RNA EBER1 promotes the expression of a ribosomal protein paralog to boost oxidative phosphorylation.bioRxiv : the preprint server for biology · 2024Article
- PlantIntronDB: a database for plant introns that host functional elements.Database : the journal of biological databases and curation · 2023Article
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- Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA.EMBO reports · 2023Article
- Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome.NAR genomics and bioinformatics · 2022Article
- Pseudouridylation of Epstein-Barr virus noncoding RNA EBER2 facilitates lytic replication.RNA (New York, N.Y.) · 2022Article
- Stable lariats bearing a snoRNA (slb-snoRNA) in eukaryotic cells: A level of regulation for guide RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Eukaryotic initiating factor eIF4E is targeted by EBV-encoded miR-BART11-3p and regulates cell cycle and apoptosis in EBV-associated gastric carcinoma.Virus genes · 2021Article
- Pathogenic Role of Epstein-Barr Virus in Lung Cancers.Viruses · 2021Review
- The many ways Epstein-Barr virus takes advantage of the RNA tool kit.RNA biology · 2021Review
- Viral non-coding RNAs: Stealth strategies in the tug-of-war between humans and herpesviruses.Seminars in cell & developmental biology · 2021Review
- Role of Virally Encoded Circular RNAs in the Pathogenicity of Human Oncogenic Viruses.Frontiers in microbiology · 2021Review
- New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome.Viruses · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundEpstein-Barr virus (EBV) is a human herpesvirus implicated in cancer and autoimmune disorders. Little is known concerning the roles of RNA structure in this important human pathogen. This study provides the first comprehensive genome-wide survey of RNA and RNA structure in EBV.
resultsNovel EBV RNAs and RNA structures were identified by computational modeling and RNA-Seq analyses of EBV. Scans of the genomic sequences of four EBV strains (EBV-1, EBV-2, GD1, and GD2) and of the closely related Macacine herpesvirus 4 using the RNAz program discovered 265 regions with high probability of forming conserved RNA structures. Secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. The analysis of RNA-Seq data uncovered the first observation of a stable intronic sequence RNA (sisRNA) in EBV. The abundance of this sisRNA rivals that of the well-known and highly expressed EBV-encoded non-coding RNAs (EBERs).
conclusionThis work identifies regions of the EBV genome likely to generate functional RNAs and RNA structures, provides structural models for these regions, and discusses potential functions suggested by the modeled structures. Enhanced understanding of the EBV transcriptome will guide future experimental analyses of the discovered RNAs and RNA structures.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.