[en] Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity than is captured by existing annotation. The pervasive nature of overlapping transcription throughout herpesvirus genomes, however, poses substantial problems in resolving transcript structures using these methods alone. We present an approach that combines the unique attributes of Pacific Biosciences Iso-Seq long-read, Illumina short-read and deepCAGE (Cap Analysis of Gene Expression) sequencing to globally resolve polyadenylated isoform structures in replicating Epstein-Barr virus (EBV). Our method, Transcriptome Resolution through Integration of Multi-platform Data (TRIMD), identifies nearly 300 novel EBV transcripts, quadrupling the size of the annotated viral transcriptome. These findings illustrate an array of mechanisms through which EBV achieves functional diversity in its relatively small, compact genome including programmed alternative splicing (e.g. across the IR1 repeats), alternative promoter usage by LMP2 and other latency-associated transcripts, intergenic splicing at the BZLF2 locus, and antisense transcription and pervasive readthrough transcription throughout the genome.
Disciplines :
Human health sciences: Multidisciplinary, general & others
Author, co-author :
O'Grady, Tina ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et biologie moléculaires animales
Wang, Xia
Honer Zu Bentrup, Kerstin
Baddoo, Melody
Concha, Monica
Flemington, Erik K.
Language :
English
Title :
Global transcript structure resolution of high gene density genomes through multi-platform data integration.
Publication date :
2016
Journal title :
Nucleic Acids Research
ISSN :
0305-1048
eISSN :
1362-4962
Publisher :
Oxford University Press, United Kingdom
Volume :
44
Issue :
18
Pages :
e145
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
(c) The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
Pattle, S.B., and Farrell, P.J. (2006). The role of Epstein-Barr virus in cancer. Expert Opin. Biol. Ther., 6, 1193-1205
Henle, W., and Henle, G. (1974). Epstein-Barr virus, and human malignancies. Cancer, 34(Suppl. S4), 1368-1374
Kang, M.S., and Kieff, E. (2015). Epstein-Barr virus latent genes. Exp. Mol. Med., 47, e131
Longnecker, R., Kieff, E., and Cohen, J.I. (2013). Epstein-Barr Virus. In: Knipe, DM, and Howley, PM (eds). Fields Virology. 6th edn., Wolters Kluwer Health/LippincottWIlliams & Wilkins, Philadelphia, pp. 1898-1959
Baer, R., Bankier, A.T., Biggin, M.D., Deininger, P.L., Farrell, P.J., Gibson, T.J., Hatfull, G., Hudson, G.S., Satchwell, S.C., Seguin, C., et al. (1984). DNA sequence, and expression of the B95-8 Epstein-Barr virus genome. Nature, 310, 207-211
Johnson, L.S., Willert, E.K., and Virgin, H.W. (2010). Redefining the genetics of murine gammaherpesvirus 68 via transcriptome-based annotation. Cell Host Microbe, 7, 516-526
Gatherer, D., Seirafian, S., Cunningham, C., Holton, M., Dargan, D.J., Baluchova, K., Hector, R.D., Galbraith, J., Herzyk, P., Wilkinson, G.W., et al. (2011). High-resolution human cytomegalovirus transcriptome. Proc. Natl. Acad. Sci. U.S.A., 108, 19755-19760
Arias, C., Weisburd, B., Stern-Ginossar, N., Mercier, A., Madrid, A.S., Bellare, P., Holdorf, M., Weissman, J.S., and Ganem, D. (2014). 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., 10, e1003847
O'Grady, T., Cao, S., Strong, M.J., Concha, M., Wang, X., Splinter Bondurant, S., Adams, M., Baddoo, M., Srivastav, S.K., Lin, Z., et al. (2014). Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J. Virol., 88, 1604-1616
Murata, M., Nishiyori-Sueki, H., Kojima-Ishiyama, M., Carninci, P., Hayashizaki, Y., and Itoh, M. (2014). Detecting expressed genes using CAGE. Methods Mol. Biol., 1164, 67-85
Tilgner, H., Grubert, F., Sharon, D., and Snyder, M.P. (2014). Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc. Natl. Acad. Sci. U.S.A., 111, 9869-9874
Concha, M., Wang, X., Cao, S., Baddoo, M., Fewell, C., Lin, Z., Hulme, W., Hedges, D., McBride, J., and Flemington, E.K. (2012). Identification of new viral genes, and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. J. Virol., 86, 1458-1467
Lin, Z., Puetter, A., Coco, J., Xu, G., Strong, M.J., Wang, X., Fewell, C., Baddoo, M., Taylor, C., and Flemington, E.K. (2012). Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES. J. Virol., 86, 2970-2977
Wu, T.D., and Watanabe, C.K. (2005). GMAP: a genomic mapping, and alignment program for mRNA, and EST sequences. Bioinformatics, 21, 1859-1875
Lin, Z., Wang, X., Strong, M.J., Concha, M., Baddoo, M., Xu, G., Baribault, C., Fewell, C., Hulme, W., Hedges, D., et al. (2013). Whole-genome sequencing of the Akata, and Mutu Epstein-Barr virus strains. J. Virol., 87, 1172-1182
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15-21
Li, B., and Dewey, C.N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323-339
Frith, M.C., Valen, E., Krogh, A., Hayashizaki, Y., Carninci, P., and Sandelin, A. (2008). A code for transcription initiation in mammalian genomes. Genome Res., 18, 1-12
Wang, L., Park, H.J., Dasari, S., Wang, S., Kocher, J.P., and Li, W. (2013). CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res., 41, e74
Feng, L., Lintula, S., Ho, T.H., Anastasina, M., Paju, A., Haglund, C., Stenman, U.H., Hotakainen, K., Orpana, A., Kainov, D., et al. (2012). Technique for strand-specific gene-expression analysis, and monitoring of primer-independent cDNA synthesis in reverse transcription. Biotechniques, 52, 263-270
Takada, K., and Ono, Y. (1989). Synchronous, and sequential activation of latently infected Epstein-Barr virus genomes. J. Virol., 63, 445-449
Pacific Bio Sciences of California, I., Vol. 2015, http://www.pacb.com/
Tang, D.T., Plessy, C., Salimullah, M., Suzuki, A.M., Calligaris, R., Gustincich, S., and Carninci, P. (2013). Suppression of artifacts, and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic Acids Res., 41, e44
Kurosawa, J., Nishiyori, H., and Hayashizaki, Y. (2011). Deep cap analysis of gene expression. Methods Mol. Biol., 687, 147-163
Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M., Arakawa, T., et al. (2003). Cap analysis gene expression for high-throughput analysis of transcriptional starting point, and identification of promoter usage. Proc. Natl. Acad. Sci. U.S.A., 100, 15776-15781
Carninci, P., Kvam, C., Kitamura, A., Ohsumi, T., Okazaki, Y., Itoh, M., Kamiya, M., Shibata, K., Sasaki, N., Izawa, M., et al. (1996). High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics, 37, 327-336
Chenchik, A., Zhu, Y.Y., Diatchenko, L., Li, R., Hill, J., and Siebert, P.D. (1998). Generation, and use of high-quality cDNA from small amounts of total RNA by SMART PCR. In: Siebert, PD, and Larrick, JW (eds). Gene cloning, and analysis by RT-PCR. Biotechniques Books, Natick, pp. 305-319
Lu, C.C., Jeng, Y.Y., Tsai, C.H., Liu, M.Y., Yeh, S.W., Hsu, T.Y., and Chen, M.R. (2006). Genome-wide transcription program, and expression of the Rta responsive gene of Epstein-Barr virus. Virology, 345, 358-372
Yuan, J., Cahir-McFarland, E., Zhao, B., and Kieff, E. (2006). Virus, and cell RNAs expressed during Epstein-Barr virus replication. J. Virol., 80, 2548-2565
Cao, S., Strong, M.J., Wang, X., Moss, W.N., Concha, M., Lin, Z., O'Grady, T., Baddoo, M., Fewell, C., Renne, R., et al. (2015). High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project. J. Virol., 89, 713-729
Edwards, R.H., Marquitz, A.R., and Raab-Traub, N. (2008). Epstein-Barr virus BART microRNAs are produced from a large intron prior to splicing. J. Virol., 82, 9094-9106
Sadler, R.H., and Raab-Traub, N. (1995). Structural analyses of the Epstein-Barr virus BamHI A transcripts. J. Virol., 69, 1132-1141
Smith, P.R., de Jesus, O., Turner, D., Hollyoake, M., Karstegl, C.E., Griffin, B.E., Karran, L., Wang, Y., Hayward, S.D., and Farrell, P.J. (2000). Structure, and coding content of CST (BART) family RNAs of Epstein-Barr virus. J. Virol., 74, 3082-3092
Dresang, L.R., Teuton, J.R., Feng, H., Jacobs, J.M., Camp, D.G. 2nd, Purvine, S.O., Gritsenko, M.A., Li, Z., Smith, R.D., Sugden, B., et al. (2011). Coupled transcriptome, and proteome analysis of human lymphotropic tumor viruses: insights on the detection, and discovery of viral genes. BMC Genomics, 12, 625-640
Cao, S., Moss, W., O'Grady, T., Concha, M., Strong, M.J., Wang, X., Yu, Y., Baddoo, M., Zhang, K., Fewell, C., et al. (2015). New noncoding lytic transcripts derived from the Epstein-Barr virus latency origin of replication, oriP, are hyperedited, bind the paraspeckle protein, NONO/p54nrb, and support viral lytic transcription. J. Virol., 89, 7120-7132
Daikoku, T., Kudoh, A., Fujita, M., Sugaya, Y., Isomura, H., Shirata, N., and Tsurumi, T. (2005). Architecture of replication compartments formed during Epstein-Barr virus lytic replication. J. Virol., 79, 3409-3418
Sugimoto, A., Sato, Y., Kanda, T., Murata, T., Narita, Y., Kawashima, D., Kimura, H., and Tsurumi, T. (2013). Different distributions of Epstein-Barr virus early, and late gene transcripts within viral replication compartments. J. Virol., 87, 6693-6699
Bodescot, M., Perricaudet, M., and Farrell, P.J. (1987). A promoter for the highly spliced EBNA family of RNAs of Epstein-Barr virus. J. Virol., 61, 3424-3430
Sample, J., Hummel, M., Braun, D., Birkenbach, M., and Kieff, E. (1986). Nucleotide sequences of mRNAs encoding Epstein-Barr virus nuclear proteins: a probable transcriptional initiation site. Proc. Natl. Acad. Sci. U.S.A., 83, 5096-5100
Austin, P.J., Flemington, E., Yandava, C.N., Strominger, J.L., and Speck, S.H. (1988). Complex transcription of the Epstein-Barr virus BamHI fragment H rightward open reading frame 1 (BHRF1) in latently, and lytically infected B lymphocytes. Proc. Natl. Acad. Sci. U.S.A., 85, 3678-3682
Bodescot, M., and Perricaudet, M. (1986). Epstein-Barr virus mRNAs produced by alternative splicing. Nucleic Acids Res., 14, 7103-7114
Pearson, G.R., Luka, J., Petti, L., Sample, J., Birkenbach, M., Braun, D., and Kieff, E. (1987). Identification of an Epstein-Barr virus early gene encoding a second component of the restricted early antigen complex. Virology, 160, 151-161
FANTOM Consortium, and the RIKEN PMI, and CLST (DGT), Forrest, A.R., Kawaji, H., Rehli, M., Baillie, J.K., de Hoon, M.J., Haberle, V., Lassmann, T., et al. (2014). A promoter-level mammalian expression atlas. Nature, 507, 462-470
Mallinjoud, P., Villemin, J.P., Mortada, H., Polay Espinoza, M., Desmet, F.O., Samaan, S., Chautard, E., Tranchevent, L.C., and Auboeuf, D. (2014). Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin. Genome Res., 24, 511-521
Mayr, C., and Bartel, D.P. (2009). Widespread shortening of 3 UTRs by alternative cleavage, and polyadenylation activates oncogenes in cancer cells. Cell, 138, 673-684
Schaefer, B.C., Strominger, J.L., and Speck, S.H. (1995). The Epstein-Barr virus BamHI F promoter is an early lytic promoter: lack of correlation with EBNA 1 gene transcription in group 1 Burkitt's lymphoma cell lines. J. Virol., 69, 5039-5047
Nonkwelo, C., Skinner, J., Bell, A., Rickinson, A., and Sample, J. (1996). Transcription start sites downstream of the Epstein-Barr virus (EBV) Fp promoter in early-passage Burkitt lymphoma cells define a fourth promoter for expression of the EBV EBNA-1 protein. J. Virol., 70, 623-627
Hudson, G.S., Farrell, P.J., and Barrell, B.G. (1985). Two related but differentially expressed potential membrane proteins encoded by the EcoRI Dhet region of Epstein-Barr virus B95-8. J. Virol., 53, 528-535
Rutkowski, A.J., Erhard, F., L'Hernault, A., Bonfert, T., Schilhabel, M., Crump, C., Rosenstiel, P., Efstathiou, S., Zimmer, R., Friedel, C.C., et al. (2015). Widespread disruption of host transcription termination in HSV-1 infection. Nat. Commun., 6, 7126-7141
Vilborg, A., Passarelli, M.C., Yario, T.A., Tycowski, K.T., and Steitz, J.A. (2015). Widespread inducible transcription downstream of human genes. Mol. Cell, 59, 449-461
Cheshenko, N., Del Rosario, B., Woda, C., Marcellino, D., Satlin, L.M., and Herold, B.C. (2003). Herpes simplex virus triggers activation of calcium-signaling pathways. J. Cell Biol., 163, 283-293
Faggioni, A., Zompetta, C., Grimaldi, S., Barile, G., Frati, L., and Lazdins, J. (1986). Calcium modulation activates Epstein-Barr virus genome in latently infected cells. Science, 232, 1554-1556
Patro, R., Mount, S.M., and Kingsford, C. (2014). Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat. Biotechnol., 32, 462-464
