Virally-Encoded Long and Short Non-Coding RNAs

Year 2023, Volume: 11 Issue: 4, 2209 - 2224, 24.10.2023

Mehmet Kara

https://doi.org/10.29130/dubited.1212643

Abstract

Recent advances in RNA sequencing methods have elucidated that over the last decade, regions in the mammalian genome, which was previously described as ‘junk DNA’, is actively converted to RNA. Through bioinformatic and proteomic analyses, it was shown that the majority of these transcripts do not code for protein. Identified as long non-coding RNAs, these genes exceed the number of known protein-coding genes. It is required to investigate how these RNA molecules are generated and how they function, in order to understand how the genome works at a fundamental level and to design therapies against diseases and biosensors for early prognosis. Viruses, as organisms to utilize their hosts’ mechanisms, encode for these RNA molecules which do not induce immune system-like proteins, and exploit ncRNAs to manipulate cellular pathways for their life cycles. In addition to understanding viral pathogenesis at a molecular level, it has become increasingly important to study virally encoded ncRNA function since viruses are used as vectors for gene therapy and vaccines. In this work, certain viral non-coding RNAs excluding the miRNAs and circular RNAs have been reviewed. Additionally, the methods and techniques for identification, characterization, and functional analyses for the lncRNA studies have been summarized. Understanding the key roles of these small molecules, which viruses utilize for infecting the host, is important for us to realize how commonly RNA is utilized for regulatory purposes.

Keywords

Virus, herpesvirus, long non-coding RNA, RNA-protein interactions, RNA omics technologies

Virüslerin Kodladığı Uzun ve Kısa Kodlamayan RNA’lar

Abstract

Yeni geliştirilen RNA dizileme teknolojileri ile yaklaşık son on yıldır, memeli genomlarının önceden çöp, ‘junk’ DNA olarak görülen kısımlarının aslında aktif olarak RNA’ya dönüştükleri gözlemlenmektedir. Yapılan biyoinformatik analizler ve proteomik çalışmalar, bu RNA ürünlerinin çok büyük bir kısmının proteine dönüşmediğini göstermektedir. Uzun kodlamayan RNA olarak adlandırılan bu sınıftaki genlerin, günümüzde, bilinen genlerden sayıca daha fazla olduğu ortaya çıkarılmıştır. Bu RNA moleküllerinin nasıl üretildikleri ve ne yaptıklarını incelemek, hem genomun nasıl çalıştığını temel bilim düzeyinde anlamak hem de hastalıklara karşı tedavi geliştirmek ve erken teşhiste biyosensör olarak kullanmak için elzemdir. Virüsler, konak canlının mekanizmalarını kullanan organizmalar olarak, bu tür RNA’ları kendi genomlarında barındırır ve proteinler gibi immün sistem gözetimi altında kalmadan görev yapan RNA moleküllerini, hücrenin yolaklarını kendi lehlerine manipüle etmede kullanırlar. Viral hastalıkları moleküler düzeyde anlamanın yanı sıra, virüslerin aşı geliştirmede ve gen terapide vektör olarak kullanılmalarından dolayı viral kökenli RNA’ların fonksiyonlarını araştırmak giderek önem kazanmaktadır. Bu derlemede viral mikroRNA’lar ve halkasal circRNA’lar hariç tutularak, başlıca virüslerin ürettiği kodlamayan RNA’lardan ve hücredeki etki mekanizmalarından bahsedilmiştir. Ayrıca bu tür RNA’ların keşfi, yapısının belirlenmesi, karakterizasyonu ve fonksiyonunun anlaşılması için kullanılan yöntemlere değinilmiştir. Virüslerin konak hücreyi enfekte ederken kullandıkları bu küçük moleküllerin görevlerini ve etkilerini anlamak, bize RNA moleküllerinin düzenleyici ajanlar olarak ne kadar yaygın biçimde kullanıldığını göstermesi açısından önemlidir.

Keywords

Virüs, Herpesvirüs, Uzun kodlamayan RNA, RNA protein etkileşimi, RNA omik teknikleri

References

• [1] T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, D. G. Knowles, J. Lagarde, L. Veeravalli, X. Ruan, Y. Ruan, T. Lassmann, P. Carninci, J. B. Brown, L. Lipovich, J. M. Gonzalez, M. Thomas, C. A. Davis, R. Shiekhattar, T. R. Gingeras, T. J. Hubbard, C. Notredame, J. Harrow, and R. Guigó, “The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression,” Genome Res, vol. 22, no. 9, pp. 1775–1789, Sep. 2012.
• [2] S. Djebali, C. A. Davis, A. Merkel, A. Dobin, T. Lassmann, A. Mortazavi, A. Tanzer, J. Lagarde, W. Lin, F. Schlesinger, C. Xue, G. K. Marinov, J. Khatun, B. A. Williams, C. Zaleski, J. Rozowsky, M. Röder, F. Kokocinski, R. F. Abdelhamid, T. Alioto, I. Antoshechkin, M. T. Baer, N. S. Bar, P. Batut, K. Bell, I. Bell, S. Chakrabortty, X. Chen, J. Chrast, J. Curado, T. Derrien, J. Drenkow, E. Dumais, J. Dumais, R. Duttagupta, E. Falconnet, M. Fastuca, K. Fejes-Toth, P. Ferreira, S. Foissac, M. J. Fullwood, H. Gao, D. Gonzalez, A. Gordon, H. Gunawardena, C. Howald, S. Jha, R. Johnson, P. Kapranov, B. King, C. Kingswood, O. J. Luo, E. Park, K. Persaud, J. B. Preall, P. Ribeca, B. Risk, D. Robyr, M. Sammeth, L. Schaffer, L.-H. See, A. Shahab, J. Skancke, A. M. Suzuki, H. Takahashi, H. Tilgner, D. Trout, N. Walters, H. Wang, J. Wrobel, Y. Yu, X. Ruan, Y. Hayashizaki, J. Harrow, M. Gerstein, T. Hubbard, A. Reymond, S. E. Antonarakis, G. Hannon, M. C. Giddings, Y. Ruan, B. Wold, P. Carninci, R. Guigó, and T. R. Gingeras, “Landscape of transcription in human cells,” Nature, vol. 489, no. 7414, pp. 101–108, Sep. 2012.
• [3] A. M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. R. Morales, K. Thomas, A. Presser, B. E. Bernstein, A. van Oudenaarden, A. Regev, E. S. Lander, and J. L. Rinn, “Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression,” PNAS, vol. 106, no. 28, pp. 11667–11672, Jul. 2009.
• [4] J. M. Engreitz, J. E. Haines, E. M. Perez, G. Munson, J. Chen, M. Kane, P. E. McDonel, M. Guttman, and E. S. Lander, “Local regulation of gene expression by lncRNA promoters, transcription and splicing,” Nature, vol. 539, no. 7629, pp. 452–455, Nov. 2016.
• [5] K. T. Tycowski, Y. E. Guo, N. Lee, W. N. Moss, T. K. Vallery, M. Xie, and J. A. Steitz, “Viral noncoding RNAs: more surprises,” Genes Dev., vol. 29, no. 6, pp. 567–584, Mar. 2015.
• [6] C. Arias, B. Weisburd, N. Stern-Ginossar, A. Mercier, A. S. Madrid, P. Bellare, M. Holdorf, J. S. Weissman, and D. Ganem, “KSHV 2.0: A Comprehensive Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features,” PLOS Pathog, vol. 10, no. 1, p. e1003847, Jan. 2014.
• [7] B. Y. H. Cheng, J. Zhi, A. Santana, S. Khan, E. Salinas, J. C. Forrest, Y. Zheng, S. Jaggi, J. Leatherwood, and L. T. Krug, “Tiled microarray identification of novel viral transcript structures and distinct transcriptional profiles during two modes of productive murine gammaherpesvirus 68 infection,” J. Virol., vol. 86, no. 8, pp. 4340–4357, Apr. 2012.
• [8] T. Tagawa, A. Serquiña, I. Kook, and J. Ziegelbauer, “Viral Non-coding RNAs: Stealth Strategies in the Tug-of-war between Humans and Herpesviruses,” Semin Cell Dev Biol, vol. 111, pp. 135–147, Mar. 2021.
• [9] A. A. Nash, B. M. Dutia, J. P. Stewart, and A. J. Davison, “Natural history of murine gamma-herpesvirus infection.,” Philos Trans R Soc Lond B Biol Sci, vol. 356, no. 1408, pp. 569–579, Apr. 2001.
• [10] J. P. Simas and S. Efstathiou, “Murine gammaherpesvirus 68: a model for the study of gammaherpesvirus pathogenesis,” Trends in Microbiology, vol. 6, no. 7, pp. 276–282, Jul. 1998.
• [11] T. Minamitani, D. Iwakiri, and K. Takada, “Adenovirus virus-associated RNAs induce type I interferon expression through a RIG-I-mediated pathway,” Journal of Virology, vol. 85, no. 8, pp. 4035–4040, Apr. 2011.
• [12] J. G. Howe and M. D. Shu, “Epstein-Barr virus small RNA (EBER) genes: unique transcription units that combine RNA polymerase II and III promoter elements,” Cell, vol. 57, no. 5, pp. 825–834, Jun. 1989.
• [13] K. W. Diebel, A. L. Smith, and L. F. van Dyk, “Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters,” RNA, vol. 16, no. 1, pp. 170–185, Jan. 2010.
• [14] I. W. Boss and R. Renne, “Viral miRNAs: tools for immune evasion,” Curr Opin Microbiol, vol. 13, no. 4, pp. 540–545, Aug. 2010.
• [15] I. Jurak, A. Griffiths, and D. M. Coen, “Mammalian Alphaherpesvirus miRNAs,” Biochim Biophys Acta, vol. 1809, no. 11–12, pp. 641–653, 2011.
• [16] R. Mishra, A. Kumar, H. Ingle, and H. Kumar, “The Interplay Between Viral-Derived miRNAs and Host Immunity During Infection,” Front Immunol, vol. 10, p. 3079, Jan. 2020.
• [17] B. R. Cullen, “Viruses and microRNAs: RISCy interactions with serious consequences,” Genes Dev., vol. 25, no. 18, pp. 1881–1894, Sep. 2011.
• [18] R. P. Kincaid and C. S. Sullivan, “Virus-Encoded microRNAs: An Overview and a Look to the Future,” PLOS Pathog, vol. 8, no. 12, p. e1003018, Dec. 2012. [19] H. L. Cook, H. E. Mischo, and J. A. Steitz, “The Herpesvirus saimiri Small Nuclear RNAs Recruit AU-Rich Element-Binding Proteins but Do Not Alter Host AU-Rich Element-Containing mRNA Levels in Virally Transformed T Cells,” Mol. Cell. Biol., vol. 24, no. 10, pp. 4522–4533, May 2004.
• [20] S. I. Lee and J. A. Steitz, “Herpesvirus saimiri U RNAs are expressed and assembled into ribonucleoprotein particles in the absence of other viral genes.,” J Virol, vol. 64, no. 8, pp. 3905–3915, Aug. 1990.
• [21] G. Chavez-Calvillo, S. Martin, C. Hamm, and J. Sztuba-Solinska, “The Structure-To-Function Relationships of Gammaherpesvirus-Encoded Long Non-Coding RNAs and Their Contributions to Viral Pathogenesis,” Non-Coding RNA, vol. 4, no. 4, p. 24, Dec. 2018.
• [22] H. Täuber, S. Hüttelmaier, and M. Köhn, “POLIII-derived non-coding RNAs acting as scaffolds and decoys,” Journal of Molecular Cell Biology, vol. 11, no. 10, pp. 880–885, Oct. 2019.
• [23] R. J. White, “Transcription by RNA polymerase III: more complex than we thought,” Nat Rev Genet, vol. 12, no. 7, pp. 459–463, Jul. 2011.
• [24] V. K. Vachon and G. L. Conn, “Adenovirus VA RNA: An essential pro-viral non-coding RNA,” Virus Res, vol. 212, pp. 39–52, Jan. 2016.
• [25] G. D. Ghadge, S. Swaminathan, M. G. Katze, and B. Thimmapaya, “Binding of the adenovirus VAI RNA to the interferon-induced 68-kDa protein kinase correlates with function.,” Proc Natl Acad Sci U S A, vol. 88, no. 16, pp. 7140–7144, Aug. 1991.
• [26] N. Xu, B. Segerman, X. Zhou, and G. Akusjärvi, “Adenovirus virus-associated RNAII-derived small RNAs are efficiently incorporated into the rna-induced silencing complex and associate with polyribosomes,” J Virol, vol. 81, no. 19, pp. 10540–10549, Oct. 2007.
• [27] E. Carnero, J. D. Sutherland, and P. Fortes, “Adenovirus and miRNAs,” Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol. 1809, no. 11–12, pp. 660–667, Nov. 2011.
• [28] J. R. Arrand and L. Rymo, “Characterization of the major Epstein-Barr virus-specific RNA in Burkitt lymphoma-derived cells.,” J Virol, vol. 41, no. 2, pp. 376–389, Feb. 1982.
• [29] W. Ahmed, S. Tariq, and G. Khan, “Tracking EBV-encoded RNAs (EBERs) from the nucleus to the excreted exosomes of B-lymphocytes,” Sci Rep, vol. 8, no. 1, p. 15438, Oct. 2018.
• [30] T. V. Sharp, M. Schwemmle, I. Jeffrey, K. Laing, H. Mellor, C. G. Proud, K. Hilse, and M. J. Clemens, “Comparative analysis of the regulation of the interferon-inducible protein kinase PKR by Epstein-Barr virus RNAs EBER-1 and EBER-2 and adenovirus VAI RNA,” Nucleic Acids Res, vol. 21, no. 19, pp. 4483–4490, Sep. 1993.
• [31] M. Samanta, D. Iwakiri, T. Kanda, T. Imaizumi, and K. Takada, “EB virus-encoded RNAs are recognized by RIG-I and activate signaling to induce type I IFN,” EMBO J, vol. 25, no. 18, pp. 4207–4214, Sep. 2006.
• [32] N. Lee, W. N. Moss, T. A. Yario, and J. A. Steitz, “EBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA,” Cell, vol. 160, no. 4, pp. 607–618, Feb. 2015.
• [33] E. J. Usherwood, J. P. Stewart, and A. A. Nash, “Characterization of tumor cell lines derived from murine gammaherpesvirus-68-infected mice.,” J Virol, vol. 70, no. 9, pp. 6516–6518, Sep. 1996.
• [34] H. W. Virgin, P. Latreille, P. Wamsley, K. Hallsworth, K. E. Weck, A. J. D. Canto, and S. H. Speck, “Complete sequence and genomic analysis of murine gammaherpesvirus 68.,” J. Virol., vol. 71, no. 8, pp. 5894–5904, Aug. 1997.
• [35] J. Y. Zhu, M. Strehle, A. Frohn, E. Kremmer, K. P. Höfig, G. Meister, and H. Adler, “Identification and Analysis of Expression of Novel MicroRNAs of Murine Gammaherpesvirus 68,” J. Virol., vol. 84, no. 19, pp. 10266–10275, Oct. 2010.
• [36] T. A. Reese, J. Xia, L. S. Johnson, X. Zhou, W. Zhang, and H. W. Virgin, “Identification of Novel MicroRNA-Like Molecules Generated from Herpesvirus and Host tRNA Transcripts,” J. Virol., vol. 84, no. 19, pp. 10344–10353, Oct. 2010.
• [37] D. P. Bartel, “MicroRNAs: target recognition and regulatory functions,” Cell, vol. 136, no. 2, pp. 215–233, Jan. 2009.
• [38] H. P. Bogerd, H. W. Karnowski, X. Cai, J. Shin, M. Pohlers, and B. R. Cullen, “A mammalian herpesvirus uses non-canonical expression and processing mechanisms to generate viral microRNAs,” Mol Cell, vol. 37, no. 1, p. 135, Jan. 2010.
• [39] E. R. Feldman, M. Kara, L. M. Oko, K. R. Grau, B. J. Krueger, J. Zhang, P. Feng, L. F. van Dyk, R. Renne, and S. A. Tibbetts, “A Gammaherpesvirus Noncoding RNA Is Essential for Hematogenous Dissemination and Establishment of Peripheral Latency,” mSphere, vol. 1, no. 2, Apr. 2016.
• [40] B. A. Hoffman, Y. Wang, E. R. Feldman, and S. A. Tibbetts, “Epstein-Barr virus EBER1 and murine gammaherpesvirus TMER4 share conserved in vivo function to promote B cell egress and dissemination,” Proc Natl Acad Sci U S A, vol. 116, no. 51, pp. 25392–25394, Dec. 2019.
• [41] M. Ve, L. Si, and S. Ja, “Viral small nuclear ribonucleoproteins bind a protein implicated in messenger RNA destabilization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 4, Feb. 1992.
• [42] D. Cazalla, M. Xie, and J. A. Steitz, “A Primate Herpesvirus Uses the Integrator Complex to Generate Viral MicroRNAs,” Mol Cell, vol. 43, no. 6, pp. 982–992, Sep. 2011.
• [43] D. Cazalla, “Learning noncoding RNA biology from viruses,” Mamm Genome, vol. 33, no. 2, pp. 412–420, Jun. 2022.
• [44] D. Gatherer, S. Seirafian, C. Cunningham, M. Holton, D. J. Dargan, K. Baluchova, R. D. Hector, J. Galbraith, P. Herzyk, G. W. G. Wilkinson, and A. J. Davison, “High-resolution human cytomegalovirus transcriptome,” Proc. Natl. Acad. Sci. U.S.A., vol. 108, no. 49, pp. 19755–19760, Dec. 2011.
• [45] M. B. Reeves, A. A. Davies, B. P. McSharry, G. W. Wilkinson, and J. H. Sinclair, “Complex I Binding by a Virally Encoded RNA Regulates Mitochondria-Induced Cell Death,” Science, vol. 316, no. 5829, pp. 1345–1348, Jun. 2007.
• [46] B. Lau, K. Kerr, Q. Gu, K. Nightingale, R. Antrobus, N. M. Suárez, R. J. Stanton, E. C. Y. Wang, M. P. Weekes, and A. J. Davison, “Human Cytomegalovirus Long Non-coding RNA1.2 Suppresses Extracellular Release of the Pro-inflammatory Cytokine IL-6 by Blocking NF-κB Activation,” Front Cell Infect Microbiol, vol. 10, p. 361, Jul. 2020.
• [47] T. T. Wu, Y. H. Su, T. M. Block, and J. M. Taylor, “Evidence that two latency-associated transcripts of herpes simplex virus type 1 are nonlinear.,” J Virol, vol. 70, no. 9, pp. 5962–5967, Sep. 1996.
• [48] G.-C. Perng, C. Jones, J. Ciacci-Zanella, M. Stone, G. Henderson, A. Yukht, S. M. Slanina, F. M. Hofman, H. Ghiasi, A. B. Nesburn, and S. L. Wechsler, “Virus-Induced Neuronal Apoptosis Blocked by the Herpes Simplex Virus Latency-Associated Transcript,” Science, vol. 287, no. 5457, pp. 1500–1503, Feb. 2000.
• [49] J. L. Umbach, M. F. Kramer, I. Jurak, H. W. Karnowski, D. M. Coen, and B. R. Cullen, “MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs,” Nature, vol. 454, no. 7205, pp. 780–783, Aug. 2008.
• [50] K. Tormanen, S. Wang, H. H. Matundan, J. Yu, U. Jaggi, and H. Ghiasi, “Herpes Simplex Virus 1 Small Noncoding RNAs 1 and 2 Activate the Herpesvirus Entry Mediator Promoter,” J Virol, vol. 96, no. 3, pp. e01985-21.
• [51] W. Zhong and D. Ganem, “Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi’s sarcoma-associated herpesvirus (human herpesvirus 8).,” Journal of Virology, vol. 71, no. 2, pp. 1207–1212, Feb. 1997.
• [52] M. Campbell and Y. Izumiya, “PAN RNA: transcriptional exhaust from a viral engine,” Journal of Biomedical Science, vol. 27, no. 1, p. 41, Mar. 2020.
• [53] C. C. Rossetto and G. S. Pari, “Kaposi’s Sarcoma-Associated Herpesvirus Noncoding Polyadenylated Nuclear RNA Interacts with Virus- and Host Cell-Encoded Proteins and Suppresses Expression of Genes Involved in Immune Modulation ▿,” J Virol, vol. 85, no. 24, pp. 13290–13297, Dec. 2011.
• [54] M. Campbell, K. Y. Kim, P.-C. Chang, S. Huerta, B. Shevchenko, D.-H. Wang, C. Izumiya, H.-J. Kung, and Y. Izumiya, “A lytic viral long noncoding RNA modulates the function of a latent protein,” J Virol, vol. 88, no. 3, pp. 1843–1848, Feb. 2014.
• [55] J. M. Schifano, K. Corcoran, H. Kelkar, and D. P. Dittmer, “Expression of the Antisense-to-Latency Transcript Long Noncoding RNA in Kaposi’s Sarcoma-Associated Herpesvirus,” Journal of Virology, vol. 91, no. 4, pp. e01698-16, Feb. 2017.
• [56] N. Chbab, A. Egerer, I. Veiga, K. W. Jarosinski, and N. Osterrieder, “Viral control of vTR expression is critical for efficient formation and dissemination of lymphoma induced by Marek’s disease virus (MDV),” Vet Res, vol. 41, no. 5, p. 56, Oct. 2010.
• [57] M. M. Hitt, M. J. Allday, T. Hara, L. Karran, M. D. Jones, P. Busson, T. Tursz, I. Ernberg, and B. E. Griffin, “EBV gene expression in an NPC-related tumour,” EMBO J, vol. 8, no. 9, pp. 2639–2651, Sep. 1989.
• [58] N. Raab-Traub, R. Hood, C. S. Yang, B. Henry, and J. S. Pagano, “Epstein-Barr virus transcription in nasopharyngeal carcinoma,” J Virol, vol. 48, no. 3, pp. 580–590, Dec. 1983. [59] R. H. Edwards, A. R. Marquitz, and N. Raab-Traub, “Epstein-Barr Virus BART MicroRNAs Are Produced from a Large Intron prior to Splicing,” J Virol, vol. 82, no. 18, pp. 9094–9106, Sep. 2008.
• [60] S. Pfeffer, M. Zavolan, F. A. Grässer, M. Chien, J. J. Russo, J. Ju, B. John, A. J. Enright, D. Marks, C. Sander, and T. Tuschl, “Identification of Virus-Encoded MicroRNAs,” Science, vol. 304, no. 5671, pp. 734–736, Apr. 2004.
• [61] A. R. Marquitz, A. Mathur, R. H. Edwards, and N. Raab-Traub, “Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region,” J Virol, vol. 89, no. 22, pp. 11256–11268, Nov. 2015.
• [62] D. H. Dreyfus, “Genetics and Molecular Biology of Epstein-Barr Virus-Encoded BART MicroRNA: A Paradigm for Viral Modulation of Host Immune Response Genes and Genome Stability,” J Immunol Res, vol. 2017, p. 4758539, 2017.
• [63] M. Kara, T. O’Grady, E. R. Feldman, A. Feswick, Y. Wang, E. K. Flemington, and S. A. Tibbetts, “Gammaherpesvirus Readthrough Transcription Generates a Long Non-Coding RNA That Is Regulated by Antisense miRNAs and Correlates with Enhanced Lytic Replication In Vivo,” Non-Coding RNA, vol. 5, no. 1, p. 6, Mar. 2019.
• [64] R. P. Kincaid, J. M. Burke, and C. S. Sullivan, “RNA virus microRNA that mimics a B-cell oncomiR,” Proc. Natl. Acad. Sci. U.S.A., vol. 109, no. 8, pp. 3077–3082, Feb. 2012.
• [65] V. R. Sanghvi and L. F. Steel, “The Cellular TAR RNA Binding Protein, TRBP, Promotes HIV-1 Replication Primarily by Inhibiting the Activation of Double-Stranded RNA-Dependent Kinase PKR▿,” J Virol, vol. 85, no. 23, pp. 12614–12621, Dec. 2011.
• [66] G. Manokaran, E. Finol, C. Wang, J. Gunaratne, J. Bahl, E. Z. Ong, H. C. Tan, O. M. Sessions, A. M. Ward, D. J. Gubler, E. Harris, M. A. Garcia-Blanco, and E. E. Ooi, “Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness,” Science, vol. 350, no. 6257, pp. 217–221, Oct. 2015.
• [67] A. Slonchak and A. A. Khromykh, “Subgenomic flaviviral RNAs: What do we know after the first decade of research,” Antiviral Res, vol. 159, pp. 13–25, Nov. 2018.
• [68] B. E. Slatko, A. F. Gardner, and F. M. Ausubel, “Overview of Next Generation Sequencing Technologies,” Curr Protoc Mol Biol, vol. 122, no. 1, p. e59, Apr. 2018.
• [69] Z. Boldogkői, N. Moldován, Z. Balázs, M. Snyder, and D. Tombácz, “Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research,” Trends in Microbiology, vol. 27, no. 7, pp. 578–592, Jul. 2019.
• [70] T. O’Grady, S. Cao, M. J. Strong, M. Concha, X. Wang, S. S. BonDurant, M. Adams, M. Baddoo, S. K. Srivastav, Z. Lin, C. Fewell, Q. Yin, and E. K. Flemington, “Global Bidirectional Transcription of the Epstein-Barr Virus Genome during Reactivation,” J. Virol., vol. 88, no. 3, pp. 1604–1616, Feb. 2014.
• [71] T. O’Grady, X. Wang, K. Höner Zu Bentrup, M. Baddoo, M. Concha, and E. K. Flemington, “Global transcript structure resolution of high gene density genomes through multi-platform data integration,” Nucleic Acids Res., Jul. 2016.
• [72] T. O’Grady, A. Feswick, B. A. Hoffman, Y. Wang, E. M. Medina, M. Kara, L. F. van Dyk, E. K. Flemington, and S. A. Tibbetts, “Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68,” Cell Rep, vol. 27, no. 13, pp. 3988-4002.e5, Jun. 2019.
• [73] D. Tombácz, Z. Csabai, A. Szűcs, Z. Balázs, N. Moldován, D. Sharon, M. Snyder, and Z. Boldogkői, “Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1,” Front Microbiol, vol. 8, p. 1079, 2017.
• [74] D. Tombácz, Z. Balázs, Z. Csabai, M. Snyder, and Z. Boldogkői, “Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses,” Frontiers in Genetics, vol. 9, 2018.
• [75] M. Kara and S. A. Tibbetts, “Empirical Validation of Overlapping Virus lncRNAs and Coding Transcripts by Northern Blot,” in Long Non-Coding RNAs in Cancer, A. Navarro, Ed. New York, NY: Springer US, 2021, pp. 243–253.
• [76] C. Chu, J. Quinn, and H. Y. Chang, “Chromatin isolation by RNA purification (ChIRP),” J Vis Exp, no. 61, 2012.
• [77] J. Engreitz, E. S. Lander, and M. Guttman, “RNA antisense purification (RAP) for mapping RNA interactions with chromatin,” Methods Mol Biol, vol. 1262, pp. 183–197, 2015.
• [78] C. G. Simpson and J. W. Brown, “RNase A/T1 protection assay,” Methods Mol Biol, vol. 49, pp. 239–247, 1995.
• [79] P. A. Latos, F. M. Pauler, M. V. Koerner, H. B. Şenergin, Q. J. Hudson, R. R. Stocsits, W. Allhoff, S. H. Stricker, R. M. Klement, K. E. Warczok, K. Aumayr, P. Pasierbek, and D. P. Barlow, “Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing,” Science, vol. 338, no. 6113, pp. 1469–1472, Dec. 2012.
• [80] S. Tm, V. La, A. Cg, and K. Ca, “Molecular investigation of the 7.2 kb RNA of murine cytomegalovirus,” Virology journal, vol. 10, Dec. 2013.
• [81] S. L. Moon, B. J. T. Dodd, D. E. Brackney, C. J. Wilusz, G. D. Ebel, and J. Wilusz, “Flavivirus sfRNA suppresses antiviral RNA interference in cultured cells and mosquitoes and directly interacts with the RNAi machinery,” Virology, vol. 485, pp. 322–329, Nov. 2015.