Virus-encoded Small RNA Research Articles

Systematic identification and characterization of viral small RNAs from small RNA-Seq data.

Virus-encoded small RNAs (vsRNAs) have been reported to play an important role in viral infections. Unfortunately, there is still a lack of a systematic characterization and resource of vsRNAs. Herein, we identified a total of 19 734 high-confidence vsRNAs including 2746 microRNAs (miRNAs) in 64 viral species from more than 800 samples of public small RNA-Seq data. The number of vsRNAs identified in viruses varied from 1 to 2489 with a median of 170. The length distribution of vsRNAs peaked at 21 and 22 nt. Plant viruses were found to express larger number and higher levels of vsRNAs than those of animal viruses. Besides, the number of vsRNAs identified increased as the viral infection persisted. Interestingly, the vsRNA showed strong expression specificity as little overlap was observed among vsRNAs identified in different strains of a virus, or in different hosts, cells, or tissues infected by the same virus. Little conservation was observed among vsRNAs of different viruses. The viral miRNAs were found to interact with host genes involved in multiple biological processes related to organization, development, action potential, polarity establishment, methylation, immune response, gene regulation, localization, and so on. To facilitate the usage of vsRNAs, a database named vsRNAdb was built for organizing and storing vsRNAs which is available at http://www.computationalbiology.cn/vsRNAdb/#/vsRNAdb/#/. Overall, the study deepens our understanding about the diversity and complexity of vsRNAs and provides a rich resource for further studies of vsRNAs.

VsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data.

Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is publicly available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. vsRNAfinder would greatly facilitate effective identification of vsRNAs from sRNA-Seq data.

Identification and Expression Analysis of Herpes B Virus-Encoded Small RNAs

Herpes B virus (BV) naturally infects macaque monkeys and is genetically similar to herpes simplex virus (HSV). Zoonotic infection of humans can cause encephalitis and if untreated has a fatality rate of ∼80%. The frequent use of macaques in biomedical research emphasizes the need to understand the molecular basis of BV pathogenesis with a view toward improving safety for those working with macaques. MicroRNAs (miRNAs) are small noncoding RNAs that regulate the expression of mRNAs bearing complementary target sequences and are employed by viruses to control viral and host gene expression. Using deep sequencing and validation by expression in transfected cells, we identified 12 novel BV-encoded miRNAs expressed in lytically infected cells and 4 in latently infected trigeminal ganglia (TG). Using quantitative reverse transcription-PCR (RT-qPCR), we found that most of the miRNAs exhibited a high level of abundance throughout infection. Further analyses showed that some miRNAs could be generated from multiple transcripts with different kinetic classes, possibly explaining detection throughout infection. Interestingly, miRNAs were detected at early times in the absence of viral gene expression and were present in purified virions. In TG, despite similar amounts of viral DNA per ganglion, it was notable that the relative amount of each miRNA varied between ganglia. The majority of the miRNAs are encoded by the regions that exhibit the most sequence differences between BV and HSV. Additionally, there is no sequence conservation between BV- and HSV-encoded miRNAs, which may be important for the differences in the human diseases caused by BV and HSV.

Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV, HHV-8)

Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV or human herpesvirus 8, HHV-8) are members of gamma-herpes virus family. Both viruses infect to B cells and cause malignancies such as lymphoma. Since EBV and HHV-8 are so-called 'oncovirus', their oncogenecities have been focused in the researches on EBV and KSHV for a long time. EBV was discovered in 1964, whereas KSHV was identified in 1994. However, KSHV was analyzed rapidly in these fifteen years. One of the recent progresses in the research on EBV and KSHV is that virus-encoded small RNAs were identified in their genomes and characterized. EBV is the first human virus in whose genome microRNA was identified. The oncogenecity of EBV and KSHV remains unclear. Here, I discuss the pathogenesis by EBV and KSHV with special reference to recent progress in this field.

Expression of Epstein-Barr Virus-encoded Small Nuclear RNA 1 in Japanese Nasopharyngeal Carcinomas

An examination was made of the incidence of the Epstein -Barr virus (EBV) genome and its exact localization in 39 cases of nasopharyngeal carcinoma (NPC) in Japanese patients by means of in situ hybridization (ISH) with a digoxigeninlabeled Epstein -Barr virus-encoded small nuclear RNA 1 (EBER1) oligonucleotide probe. Hybridization signals were observed in the nucleus of tumor cells in all 39 NPCs, including keratinizing carcinomas. The signals varied greatly in intensity from case to case and even from cell to cell in the same tumor, but were recognized in most tumor cells in each case. Signals could occasionally be seen in limiting number of infiltrating small lymphocytes but were absent in all tumors of the tongue, midpharynx and hypopharynx. Combined immunohistochemistry-ISH studies indicated that EBER1 signals were restricted to tumor cells positive for cytokeratin. As a result of this study, it is now possible to perform large-scale retrospective analyses using routine formalin-fixed, paraffin-embedded tissue sections and to combine ISH for the EBV genome with immunohistochemistry for cytokeratin to determine the epithelial features of EBV genome-possessing cells. All NPCs were clearly shown to be EBV-infected, thus indicating that EBV is essential for the oncogenesis of NPCs.