ArticleNucleic acids research2018
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 28 citations in OpenAlex.
- A viral circular RNA in Kaposi's sarcoma-associated herpesvirus modulates viral and host gene expression during latent and lytic replication.Exploration of targeted anti-tumor therapy · 2025Article
- Review
- Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods.Bioinformatics (Oxford, England) · 2023Article
- Construction of a risk model and prediction of prognosis and immunotherapy based on cuproptosis-related LncRNAs in the urinary system pan-cancer.European journal of medical research · 2023Article
- Long noncoding RNAs (lncRNAs) in HIV-mediated carcinogenesis: Role in cell homeostasis, cell survival processes and drug resistance.Non-coding RNA research · 2022Review
- Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis).Scientific reports · 2022Article
- Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) to Identify MicroRNA Targets.Current protocols · 2021Article
- A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor.RNA (New York, N.Y.) · 2021Article
- Long non-coding RNAs in Epstein-Barr virus-related cancer.Cancer cell international · 2021Review
- Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells.Cancers · 2021Article
- Integrative approaches for analysis of mRNA and microRNA high-throughput data.Computational and structural biotechnology journal · 2021Review
- Long noncoding RNAs involvement in Epstein-Barr virus infection and tumorigenesis.Virology journal · 2020Review
- Long Non-coding RNAs in Gammaherpesvirus Infections: Their Roles in Tumorigenic Mechanisms.Frontiers in microbiology · 2020Review
- A Review of the Pharmacological Properties of Psoralen.Frontiers in pharmacology · 2020Review
- Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots.International journal of molecular sciences · 2019Article
- Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery.PLoS pathogens · 2019Article
- Genome-wide methods for investigating long noncoding RNAs.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2019Review
- Contemporary Ribonomics Methods for Viral microRNA Target Analysis.Non-coding RNA · 2018Review
- Connivance, Complicity, or Collusion? The Role of Noncoding RNAs in Promoting Gammaherpesvirus Tumorigenesis.Trends in cancer · 2018Review
- The Structure-To-Function Relationships of Gammaherpesvirus-Encoded Long Non-Coding RNAs and Their Contributions to Viral Pathogenesis.Non-coding RNA · 2018Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi's Sarcoma-associated herpes virus (KSHV) and Epstein-Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA-miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA-lncRNA interactions broadly contribute to the regulation of gene expression.
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