Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775-89. https://doi.org/10.1101/gr.132159.111

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See L-H, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature. 2012;489(7414):101-8. https://doi.org/10.1038/nature11233

Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Morales DR, Thomas K, Presser A, Bernstein BE, Oudenaarden A van, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009;106(28):11667-72. https://doi.org/10.1073/pnas.0904715106

Kamel M, El-Sayed A. Utilization of herpesviridae as recombinant viral vectors in vaccine development against animal pathogens. Virus Res. 2019;270:197648. https://doi.org/10.1016/j.virusres.2019.197648

Guh C-Y, Hsieh Y-H, Chu H-P. Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs. J Biomed Sci. 2020;27(1):44. https://doi.org/10.1186/s12929-020-00640-3

Schlub TE, Holmes EC. Properties and abundance of overlapping genes in viruses. Virus Evol. 2020;6(1):veaa009. https://doi.org/10.1093/ve/veaa009

Boldogkői Z, Moldován N, Balázs Z, Snyder M, Tombácz D. Long-Read Sequencing - A Powerful Tool in Viral Transcriptome Research. Trends Microbiol. 2019;27(7):578-92 https://doi.org/10.1016/j.tim.2019.01.010

Tombácz D, Csabai Z, Szűcs A, Balázs Z, Moldován N, Sharon D, Snyder M, Boldogkői Z. Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1. Front Microbiol. 2017;8:1079. https://doi.org/10.3389/fmicb.2017.01079

O'Grady T, Wang X, Höner Zu Bentrup K, Baddoo M, Concha M, Flemington EK. Global transcript structure resolution of high gene density genomes through multi-platform data integration. Nucleic Acids Res. 2016;44(18):e145. https://doi.org/10.1093/nar/gkw629

Arvin A, Campadelli-Fiume G, Mocarski E, Moore PS, Roizman B, Whitley R, Yamanishi K, editors. Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis. Cambridge: Cambridge University Press; 2007. https://doi.org/10.1017/CBO9780511545313

Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, Holdorf M, Weissman JS, Ganem D. 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. 2014;10(1):e1003847. https://doi.org/10.1371/journal.ppat.1003847

Canny SP, Reese TA, Johnson LS, Zhang X, Kambal A, Duan E, Liu CY, Virgin HW. Pervasive Transcription of a Herpesvirus Genome Generates Functionally Important RNAs. mBio. 2014;5(2):e01033-13. https://doi.org/10.1128/mBio.01033-13

O'Grady T, Feswick A, Hoffman BA, Wang Y, Medina EM, Kara M, van Dyk LF, Flemington EK, Tibbetts SA. Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68. Cell Rep. 2019;27(13):3988. https://doi.org/10.1016/j.celrep.2019.05.086

Elfman J, Li H. Detection and Measurement of Chimeric RNAs by RT-PCR. In: Li H, Elfman J, editors. Chimeric RNA: Methods and Protocols. New York, NY: Springer US; 2020. p. 83-94. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9904-0_6

Shi X, Qin F, Li H. Confirmation of Transcriptional Read-Through Events by RT-PCR. Methods Mol Biol. 2020;2079:177-86. https://doi.org/10.1007/978-1-4939-9904-0_14

Su W-C, Lai MMC. Quantitative RT-PCR Analysis of Influenza Virus Endocytic Escape. Methods Mol Biol. 2018;1836:185-94. https://doi.org/10.1007/978-1-4939-8678-1_9

Cheng BYH, Zhi J, Santana A, Khan S, Salinas E, Forrest JC, Zheng Y, Jaggi S, Leatherwood J, Krug LT. Tiled microarray identification of novel viral transcript structures and distinct transcriptional profiles during two modes of productive murine gammaherpesvirus 68 infection. J Virol. 2012;86(8):4340-57. https://doi.org/10.1128/JVI.05892-11

Virgin HW, Presti RM, Li XY, Liu C, Speck SH. Three distinct regions of the murine gammaherpesvirus 68 genome are transcriptionally active in latently infected mice. J Virol. 1999;73(3):2321-32. https://doi.org/10.1128/JVI.73.3.2321-2332.1999

Kara M, Tibbetts SA. Empirical Validation of Overlapping Virus lncRNAs and Coding Transcripts by Northern Blot. In: Navarro A, editor. Long Non-Coding RNAs in Cancer. New York, NY: Springer US; 2021. p. 243-53. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-0716-1581-2_17

Nealy MS, Coleman CB, Li H, Tibbetts SA. Use of a virus-encoded enzymatic marker reveals that a stable fraction of memory B cells expresses latency-associated nuclear antigen throughout chronic gammaherpesvirus infection. J Virol. 2010;84(15):7523-34. https://doi.org/10.1128/JVI.02572-09

Forrest JC, Speck SH. Establishment of B-Cell Lines Latently Infected with Reactivation-Competent Murine Gammaherpesvirus 68 Provides Evidence for Viral Alteration of a DNA Damage-Signaling Cascade. J Virol. 2008;82(15):7688-99. https://doi.org/10.1128/JVI.02689-07

Hangauer MJ, Vaughn IW, McManus MT. Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs. PLOS Genet. 2013;9(6):e1003569. https://doi.org/10.1371/journal.pgen.1003569

Tombácz D, Balázs Z, Csabai Z, Snyder M, Boldogkői Z. Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses. Front Genet. 2018;9:259. https://doi.org/10.3389/fgene.2018.00259

Tombácz D, Csabai Z, Oláh P, Balázs Z, Likó I, Zsigmond L, Sharon D, Snyder M, Boldogkői Z. Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus. PLoS One. 2016;11(9):e0162868. https://doi.org/10.1371/journal.pone.0162868

Kolenda T, Ryś M, Guglas K, Teresiak A, Bliźniak R, Mackiewicz J, Lamperska K. Quantification of long non-coding RNAs using qRT-PCR: comparison of different cDNA synthesis methods and RNA stability. Arch Med Sci. 2021;17(4):1006-15. https://doi.org/10.5114/aoms.2019.82639

Gredmark S, Schlieker C, Quesada V, Spooner E, Ploegh HL. A Functional Ubiquitin-Specific Protease Embedded in the Large Tegument Protein (ORF64) of Murine Gammaherpesvirus 68 Is Active during the Course of Infection. J Virol. 2007;81(19):10300-9. https://doi.org/10.1128/JVI.01149-07

Sun C, Schattgen SA, Pisitkun P, Jorgensen JP, Hilterbrand AT, Wang LJ, West JA, Hansen K, Horan KA, Jakobsen MR, O'Hare P, Adler H, Sun R, Ploegh HL, Damania B, Upton JW, Fitzgerald KA, Paludan SR. Evasion of innate cytosolic DNA sensing by a gammaherpesvirus facilitates establishment of latent infection. J Immunol. 2015;194(4):1819-31. https://doi.org/10.4049/jimmunol.1402495

Xuan Y, Gong D, Qi J, Han C, Deng H, Gao G. ZAP Inhibits Murine Gammaherpesvirus 68 ORF64 Expression and Is Antagonized by RTA. J Virol. 2013;87(5):2735-43. https://doi.org/10.1128/JVI.03015-12

Kara M, O'Grady T, Feldman ER, Feswick A, Wang Y, Flemington EK, Tibbetts SA. Gammaherpesvirus Readthrough Transcription Generates a Long Non-Coding RNA That Is Regulated by Antisense miRNAs and Correlates with Enhanced Lytic Replication In Vivo. Noncoding RNA. 2019;5(1):6. https://doi.org/10.3390/ncrna5010006

Schifano JM, Corcoran K, Kelkar H, Dittmer DP. Expression of the Antisense-to-Latency Transcript Long Noncoding RNA in Kaposi's Sarcoma-Associated Herpesvirus. J Virol. 2017;91(4):e01698-16. https://doi.org/10.1128/JVI.01698-16

Perng G-C, Jones C, Ciacci-Zanella J, Stone M, Henderson G, Yukht A, Slanina SM, Hofman FM, Ghiasi H, Nesburn AB, Wechsler SL. Virus-Induced Neuronal Apoptosis Blocked by the Herpes Simplex Virus Latency-Associated Transcript. Science (1979). 2000;287(5457):1500-3. https://doi.org/10.1126/science.287.5457.1500

Cohen JI. Herpesvirus latency. J Clin Invest. 130(7):3361-9. https://doi.org/10.1172/JCI136225