Abstract
DNA sequencing approaches originally developed in two directions, the chemical degradation method and the chain-termination method. The latter one became more widespread and a huge amount of sequencing data including whole genome sequences accumulated, based on the use of capillary sequencer systems and the application of a modified chain-termination method which proved to be relatively easy, fast, and reliable. In addition, relatively long, up to 1000 bp sequences could be obtained with a single read with high per-base accuracy. Although the recent appearance of next-generation DNA sequencing (NGS) technologies enabled high-throughput and low cost analysis of DNA, the modified chain-terminating methods are often applied in research until now. In the following, we shall present the application of capillary sequencing for the sequence characterization of viral genomes in case of partial and whole genome sequencing, and demonstrate it on the BARF1 promoter of Epstein Barr virus (EBV).
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References
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A 74:560–564
Mueller PR, Wold B (1989) In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246:780–786
Garrity PA, Wold BJ (1992) Effects of different DNA polymerases in ligation-mediated PCR: Enhanced genomic sequencing and in vivo footprinting. Proc Natl Acad Sci U S A 89:1021–1025
Niller HH, Glaser G, Knüchel R et al (1995) Nucleoprotein complexes and DNA 5′-ends at oriP of Epstein-Barr virus. J Biol Chem 270:12864–12868
Szenthe K, Koroknai A, Banati F et al (2013) The 5′ regulatory sequences of active miR-146a promoters are hypomethylated and associated with euchromatic histone modification marks in B lymphoid cells. Biochem Biophys Res Commun 433:489–495
Szenthe K, Koroknai A, Banati F et al (2013) The role of DNA hypomethylation, histone acetylation and in vivo protein-DNA binding in Epstein-Barr virus-induced CD23 upregulation. Biochem Biophys Res Commun 435:8–15
Prober JM, Trainor GL, Dam RJ et al (1987) A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238:336–341
Huang XC, Quesada MA, Mathies RA (1992) DNA sequencing using capillary array electrophoresis. Anal Chem 64:2149–2154
Dolnik V (1999) DNA sequencing by capillary electrophoresis (review). J Biochem Biophys Methods 41:103–119
Ausubel FM, Albright LM, Ju J (1999) DNA sequencing. Curr Protoc Mol Biol 7:1–7.0.15
Baer R, Bankier AT, Biggin MD et al (1984) DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310:207–211
Cheung A, Kieff E (1982) Long internal direct repeat in Epstein-Barr virus DNA. J Virol 44:286–294
Dambaugh TR, Kieff E (1982) Identification and nucleotide sequences of two similar tandem direct repeats in Epstein-Barr virus DNA. J Virol 44:823–833
Jones MD, Foster L, Sheedy T et al (1984) The EB virus genome in Daudi Burkitt’s lymphoma cells has a deletion similar to that observed in a non-transforming strain (P3HR-1) of the virus. EMBO J 3:813–821
Hatfull G, Bankier AT, Barrell BG et al (1988) Sequence analysis of Raji Epstein-Barr virus DNA. Virology 164:334–340
de Jesus O, Smith PR, Spender LC et al (2003) Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST, BARF0) RNAs of EBV. J Gen Virol 84:1443–1450
Lin Z, Wang X, Strong MJ et al (2013) Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol 87:1172–1182
Tso KK, Yip KY, Mak CK et al (2013) Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1. Infect Agent Cancer 8:29
Palser AL, Grayson NE, White RE et al (2015) Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection. J Virol 89:5222–5237
Hoebe EK, Wille C, Hopmans ES et al (2012) Epstein-Barr virus transcription activator R upregulates BARF1 expression by direct binding to its promoter, independent of methylation. J Virol 86:11322–11332
Fiorini S, Ooka T (2008) Secretion of Epstein-Barr Virus-encoded BARF1 oncoprotein from latently infected B cells. Virol J 5:70
Hoebe EK, Le Large TY, Greijer AE et al (2013) BamHI-A rightward frame 1, an Epstein-Barr virus-encoded oncogene and immune modulator. Rev Med Virol 23:367–383
Ernberg I, Falk K, Minarovits J et al (1989) The role of methylation in the phenotype dependent modulation of Epstein–Barr nuclear antigen 2 and latent membrane protein genes in cells latently infected with Epstein–Barr virus. J Gen Virol 70:2989–3002
Altiok E, Minarovits J, Hu LF et al (1992) Host-cell-phenotype-dependent control of the BCR2/BWR1 promoter complex regulates the expression of Epstein-Barr virus nuclear antigens 2-6. Proc Natl Acad Sci U S A 89:905–909
Gregory CD, Rowe M, Rickinson AB (1990) Different Epstein–Barr virus–B cell interactions in phenotypically distinct clones of a Burkitt’s lymphoma cell line. J Gen Virol 71:1481–1495
Epstein MA, Achong BG, Barr YM et al (1966) Morphological and virological investigations on cultured Burkitt tumor lymphoblasts (strain Raji). J Natl Cancer Inst 37:547–559
Cailleau R, Young R, Olive M et al (1974) Breast tumor cell lines from pleural effusions. J Natl Cancer Inst 53:661–674
Wakisaka N, Kondo S, Yoshizaki T et al (2004) Epstein-Barr virus latent membrane protein 1 induces synthesis of hypoxia-inducible factor 1 alpha. Mol Cell Biol 24:5223–5234
Cheung ST, Huang DP, Hui AB et al (1999) Nasopharyngeal carcinoma cell line (C666-1) consistently harboring Epstein-Barr virus. Int J Cancer 83:121–126
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Szenthe, K., Bánáti, F. (2017). Characterization of EBV Promoters and Coding Regions by Sequencing PCR-Amplified DNA Fragments. In: Minarovits, J., Niller, H. (eds) Epstein Barr Virus. Methods in Molecular Biology, vol 1532. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6655-4_13
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DOI: https://doi.org/10.1007/978-1-4939-6655-4_13
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