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Critical Reviews™ in Eukaryotic Gene Expression

Published 6 issues per year

ISSN Print: 1045-4403

ISSN Online: 2162-6502

The Impact Factor measures the average number of citations received in a particular year by papers published in the journal during the two preceding years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) IF: 1.6 To calculate the five year Impact Factor, citations are counted in 2017 to the previous five years and divided by the source items published in the previous five years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) 5-Year IF: 2.2 The Immediacy Index is the average number of times an article is cited in the year it is published. The journal Immediacy Index indicates how quickly articles in a journal are cited. Immediacy Index: 0.3 The Eigenfactor score, developed by Jevin West and Carl Bergstrom at the University of Washington, is a rating of the total importance of a scientific journal. Journals are rated according to the number of incoming citations, with citations from highly ranked journals weighted to make a larger contribution to the eigenfactor than those from poorly ranked journals. Eigenfactor: 0.00058 The Journal Citation Indicator (JCI) is a single measurement of the field-normalized citation impact of journals in the Web of Science Core Collection across disciplines. The key words here are that the metric is normalized and cross-disciplinary. JCI: 0.33 SJR: 0.345 SNIP: 0.46 CiteScore™:: 2.5 H-Index: 67

Indexed in

HITS-CLIP and PAR-CLIP Advance Viral MiRNA Targetome Analysis

Volume 24, Issue 2, 2014, pp. 101-116
DOI: 10.1615/CritRevEukaryotGeneExpr.2014006367
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ABSTRACT

MiRNAs regulate gene expression by binding predominantly to the 3' untranslated region (UTR) of target transcripts to prevent their translation and/or induce target degradation. In addition to the more than 1200 human miRNAs, human DNA tumor viruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) encode miRNAs. Target predictions indicate that each miRNA targets hundreds of transcripts, many of which are regulated by multiple miRNAs. Thus, target identification is a big challenge for the field. Most methods used currently investigate single miRNA−target interactions and are not able to analyze complex miRNA−target networks. To overcome these challenges, cross-linking and immunoprecipitation (CLIP), a recently developed method to study direct RNA−protein interactions in living cells, has been successfully applied to miRNA target analysis. It utilizes Argonaute (Ago)-immunoprecipitation to isolate native Ago−miRNA−mRNA complexes. In four recent publications, two variants of the CLIP method (HITS-CLIP and PAR-CLIP) were utilized to determine the targetomes of human and viral miRNAs in cells infected with the gamma-herpesviruses KSHV and EBV, which are associated with a number of human cancers. Here, we briefly introduce herpesvirus-encoded miRNAs and then focus on how CLIP technology has largely impacted our understanding of viral miRNAs in viral biology and pathogenesis.

CITED BY
  1. Avey Denis, Brewers Brittany, Zhu Fanxiu, Recent advances in the study of Kaposi’s sarcoma-associated herpesvirus replication and pathogenesis, Virologica Sinica, 30, 2, 2015. Crossref

  2. Zhai Lihong, Wang Lin, Teng Feng, Zhou Lanting, Zhang Wenjing, Xiao Juan, Liu Ying, Deng Wenbin, Argonaute and Argonaute-Bound Small RNAs in Stem Cells, International Journal of Molecular Sciences, 17, 2, 2016. Crossref

  3. Jain Vaibhav, Plaisance-Bonstaff Karlie, Sangani Rajnikumar, Lanier Curtis, Dolce Alexander, Hu Jianhong, Brulois Kevin, Haecker Irina, Turner Peter, Renne Rolf, Krueger Brian, A Toolbox for Herpesvirus miRNA Research: Construction of a Complete Set of KSHV miRNA Deletion Mutants, Viruses, 8, 2, 2016. Crossref

  4. Thakker Suhani, Verma Subhash C., Co-infections and Pathogenesis of KSHV-Associated Malignancies, Frontiers in Microbiology, 7, 2016. Crossref

  5. Preiksaitis Jutta K., Cockfield Sandra M., Peters Anthea C., Epstein–Barr Virus Infection and Lymphoproliferative Disorders After Transplantation, in Transplant Infections, 2016. Crossref

  6. Strahan Roxanne, Uppal Timsy, Verma Subhash, Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology, Viruses, 8, 4, 2016. Crossref

  7. Paces Jan, Nic Miloslav, Novotny Tomas, Svoboda Petr, Literature review of baseline information to support the risk assessment of RNAi‐based GM plants, EFSA Supporting Publications, 14, 6, 2017. Crossref

  8. Bruce A. Gregory, Barcy Serge, Staheli Jeannette, Bielefeldt-Ohmann Helle, Ikoma Minako, Howard Kellie, Rose Timothy M., Sestak Karol, Experimental co-transmission of Simian Immunodeficiency Virus (SIV) and the macaque homologs of the Kaposi Sarcoma-Associated Herpesvirus (KSHV) and Epstein-Barr Virus (EBV), PLOS ONE, 13, 11, 2018. Crossref

  9. Gay Lauren, Turner Peter, Renne Rolf, Contemporary Ribonomics Methods for Viral microRNA Target Analysis, Non-Coding RNA, 4, 4, 2018. Crossref

  10. Sethuraman Sunantha, Thomas Merin, Gay Lauren A, Renne Rolf, Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs, Nucleic Acids Research, 46, 16, 2018. Crossref

  11. Diggins Nicole, Hancock Meaghan, HCMV miRNA Targets Reveal Important Cellular Pathways for Viral Replication, Latency, and Reactivation, Non-Coding RNA, 4, 4, 2018. Crossref

  12. Cipriano Andrea, Ballarino Monica, The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions, Frontiers in Molecular Biosciences, 5, 2018. Crossref

  13. Papadopoulos Theofilos, Klein Julie, Bascands Jean-Loup, Schanstra Joost P., miRNA Analysis, in Integration of Omics Approaches and Systems Biology for Clinical Applications, 2018. Crossref

  14. Katano Harutaka, Expression and Function of Kaposi’s Sarcoma-Associated Herpesvirus Non-coding RNAs, Current Clinical Microbiology Reports, 5, 4, 2018. Crossref

  15. Boxberger Nina, Hecker Michael, Zettl Uwe K., Dysregulation of Inflammasome Priming and Activation by MicroRNAs in Human Immune-Mediated Diseases, The Journal of Immunology, 202, 8, 2019. Crossref

  16. Girardi Erika, Pfeffer Sebastien, Baumert Thomas F., Majzoub Karim, Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell, Seminars in Cell & Developmental Biology, 111, 2021. Crossref

  17. Costa Marina C., Leitão Ana Lúcia, Gabriel André F., Enguita Francisco J., Wet-lab methods for miRNA analysis, in MicroRNA in Human Malignancies, 2022. Crossref

  18. Zhou Yiyang, Sotcheff Stephanea L., Routh Andrew L., Next-generation sequencing: A new avenue to understand viral RNA–protein interactions, Journal of Biological Chemistry, 298, 5, 2022. Crossref

  19. Qin Jie, Li Wan, Gao Shou-Jiang, Lu Chun, KSHV microRNAs: Tricks of the Devil, Trends in Microbiology, 25, 8, 2017. Crossref

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