Henderson E, Hardin CC, Walk SK, Tinoco Jr I, Blackburn EH. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine · guanine base pairs. Cell. 1987;51:899–908.
Article
CAS
PubMed
Google Scholar
Balagurumoorthy P, Brahmachari SK. Structure and stability of human telomeric sequence. J Biol Chem. 1994;269:21858–69.
CAS
PubMed
Google Scholar
Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci. 2002;99:11593–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bugaut A, Balasubramanian S. 5′-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res. 2012;40:4727–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arora A, Suess B. An RNA G-quadruplex in the 3′UTR of the proto-oncogene PIM1 represses translation. RNA Biol. 2011;8:802–5.
Article
CAS
PubMed
Google Scholar
Sanders PGT, Cotterell J, Sharpe J, Isalan M. Transfecting RNA quadruplexes results in few transcriptome perturbations. RNA Biol. 2013;10:205–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fisette J, Montagna DR, Mihailescu M, Wolfe MS. AG‐Rich element forms a G‐quadruplex and regulates BACE1 mRNA alternative splicing. J Neurochem. 2012;121:763–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kejnovsky E, Lexa M. Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators. Mob Genet Elements. 2014;4:e28084.
Article
PubMed
PubMed Central
Google Scholar
Kejnovsky E, Tokan V, Lexa M. Transposable elements and G-quadruplexes. Chromosom Res. 2015;23:615–23.
Article
CAS
Google Scholar
Huppert JL, Balasubramanian S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 2007;35:406–13.
Article
CAS
PubMed
Google Scholar
Verma A, Halder K, Halder R, Yadav VK, Rawal P, Thakur RK, et al. Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species. J Med Chem. 2008;51:5641–9.
Article
CAS
PubMed
Google Scholar
Rawal P, Kummarasetti VBR, Ravindran J, Kumar N, Halder K, Sharma R, et al. Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res. 2006;16:644–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perrone R, Nadai M, Poe JA, Frasson I, Palumbo M, Palù G, et al. Formation of a unique cluster of G-Quadruplex Structures in the HIV-1 nef coding region: implications for antiviral activity. PLoS One. 2013;8:e73121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perrone R, Nadai M, Frasson I, Poe JA, Butovskaya E, Smithgall TE, et al. A dynamic G-quadruplex region regulates the HIV-1 long terminal repeat promoter. J Med Chem. 2013;56:6521–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Murat P, Zhong J, Lekieffre L, Cowieson NP, Clancy JL, Preiss T, et al. G-quadruplexes regulate Epstein-Barr virus–encoded nuclear antigen 1 mRNA translation. Nat Chem Biol. 2014;10:358–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang S-R, Min Y-Q, Wang J-Q, Liu C-X, Fu B-S, Wu F, et al. A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti–hepatitis C target. Sci Adv American Association for the Advancement of Science. 2016;2:e1501535.
Google Scholar
Artusi S, Nadai M, Perrone R, Biasolo MA, Palù G, Flamand L, et al. The Herpes Simplex Virus-1 genome contains multiple clusters of repeated G-quadruplex: Implications for the antiviral activity of a G-quadruplex ligand. Antiviral Res. 2015;118:123–31.
Article
CAS
PubMed
Google Scholar
Tlučková K, Marušič M, Tóthová P, Bauer L, Šket P, Plavec J, et al. Human papillomavirus G-quadruplexes. Biochemistry. 2013;52:7207–16.
Article
PubMed
Google Scholar
Shackelton LA, Holmes EC. The evolution of large DNA viruses: combining genomic information of viruses and their hosts. Trends Microbiol. 2004;12:458–65.
Article
CAS
PubMed
Google Scholar
Kropp KA, Angulo A, Ghazal P. Viral enhancer mimicry of host innate-immune promoters. PLoS Pathog. 2014;10:e1003804.
Article
PubMed
PubMed Central
Google Scholar
Holzerlandt R, Orengo C, Kellam P, Alba MM. Identification of new herpesvirus gene homologs in the human genome. Genome Res. 2002;12:1739–48.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cogoi S, Xodo LE. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res. 2006;34:2536–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Agrawal P, Lin C, Mathad RI, Carver M, Yang D. The major G-quadruplex formed in the human BCL-2 proximal promoter adopts a parallel structure with a 13-nt loop in K+ solution. J Am Chem Soc. 2014;136:1750–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fields BN, Knipe DM, Howley PM. Fields virology. 5th. Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins; 2007.
Google Scholar
Mullen MA, Olson KJ, Dallaire P, Major F, Assmann SM, Bevilacqua PC. RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Res. 2010;38:8149–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dheekollu J, Chen H-S, Kaye KM, Lieberman PM. Timeless-dependent DNA replication-coupled recombination promotes Kaposi’s sarcoma-associated herpesvirus episome maintenance and terminal repeat stability. J Virol. 2013;87:3699–709.
Article
CAS
PubMed
PubMed Central
Google Scholar
White RE, Carline L, Allday MJ. Mutagenesis of the herpesvirus saimiri terminal repeat region reveals important elements for virus production.J Virol. 2007;81:6765–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takemoto M, Shimamoto T, Isegawa Y, Yamanishi K. The R3 region, one of three major repetitive regions of human herpesvirus 6, is a strong enhancer of immediate-early gene U95. J Virol. 2001;75:10149–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gomez-Marquez J, Puga A, Notkins AL. Regions of the terminal repetitions of the herpes simplex virus type 1 genome. Relationship to immunoglobulin switch-like DNA sequences. J Biol Chem. 1985;260:3490–5.
CAS
PubMed
Google Scholar
Lagunoff M, Ganem D. The structure and coding organization of the genomic termini of Kaposi’s sarcoma-associated herpesvirus (human herpesvirus 8). Virology. 1997;236:147–54.
Article
CAS
PubMed
Google Scholar
Stow ND, Mcmonagle EC, Davison AJ. Fragments from both termini of the herpes simplex virus type 1 genome contain signals required for the encapsidation of viral DNA. Nucleic Acids Res. 1983;11:8205–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zimmermann J, Hammerschmidt W. Structure and role of the terminal repeats of Epstein-Barr virus in processing and packaging of virion DNA.J Virol. 1995;69:3147–55.
CAS
PubMed
PubMed Central
Google Scholar
McVoy MA, Nixon DE, Adler SP, Mocarski ES. Sequences within the Herpesvirus-Conservedpac1 and pac2 Motifs Are Required for Cleavage and Packaging of the Murine Cytomegalovirus Genome. J Virol. 1998;72:48–56.
CAS
PubMed
PubMed Central
Google Scholar
Mani P, Yadav VK, Das SK, Chowdhury S. Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination. PLoS One. 2009;4:e4399.
Article
PubMed
PubMed Central
Google Scholar
Ohye T, Inagaki H, Ihira M, Higashimoto Y, Kato K, Oikawa J, et al. Dual roles for the telomeric repeats in chromosomally integrated human herpesvirus-6. Sci Rep. 2014;4.
Kumari S, Bugaut A, Huppert JL, Balasubramanian S. An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat Chem Biol. 2007;3:218–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gomez D, Guedin A, Mergny JL, Salles B, Riou JF, Teulade-Fichou MP, et al. A G-quadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells. Nucleic Acids Res. 2010;38:7187–98.
McGeoch DJ. The genomes of the human herpesviruses: contents, relationships, and evolution. Annu Rev Microbiol. 1989;43:235–65.
Article
CAS
PubMed
Google Scholar
Mocarski Jr ES. Comparative analysis of herpesvirus-common proteins. In: 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.
Secchiero P, Nicholas J, Deng H, Xiaopeng T, van Loon N, Ruvolo VR, et al. Identification of human telomeric repeat motifs at the genome termini of human herpesvirus 7: structural analysis and heterogeneity. J Virol. 1995;69:8041–5.
CAS
PubMed
PubMed Central
Google Scholar
Marsh TC, Henderson E. G-wires: self-assembly of a telomeric oligonucleotide, d (GGGGTTGGGG), into large superstructures. Biochemistry. 1994;33:10718–24.
Article
CAS
PubMed
Google Scholar
Weir JP. Regulation of herpes simplex virus gene expression. Gene. 2001;271:117–30.
Article
CAS
PubMed
Google Scholar
Roizman B, Pellett PE. The family Herpesviridae: a brief introduction. Fields Virol Lippincott Williams & Wilkins Philadelphia. 2001;2:2381–97.
Google Scholar
Bugaut A, Balasubramanian S. A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry. 2008;47:689–97.
Article
CAS
PubMed
Google Scholar
Mullaney J, Moss HWM, McGeoch DJ. Gene UL2 of herpes simplex virus type 1 encodes a uracil-DNA glycosylase. J Gen Virol. 1989;70:449–54.
Article
CAS
PubMed
Google Scholar
Bertrand L, Leiva-Torres GA, Hyjazie H, Pearson A. Conserved residues in the UL24 protein of herpes simplex virus 1 are important for dispersal of the nucleolar protein nucleolin. J Virol. 2010;84:109–18.
Article
CAS
PubMed
Google Scholar
Wong EL, Damania B. Transcriptional regulation of the Kaposi’s sarcoma-associated herpesvirus K15 gene. J Virol. 2006;80:1385–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hayward GS. KSHV strains: the origins and global spread of the virus. Semin Cancer Biol. 1999;9:187–99.
Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D. Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res. 2006;34:2723–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perrone R, Butovskaya E, Daelemans D, Palù G, Pannecouque C, Richter SN. Anti-HIV-1 activity of the G-quadruplex ligand BRACO-19. J Antimicrob Chemother. 2014;69:3248–58.
Article
CAS
PubMed
Google Scholar
Gowan SM, Harrison JR, Patterson L, Valenti M, Read MA, Neidle S, et al. A G-quadruplex-interactive potent small-molecule inhibitor of telomerase exhibiting in vitro and in vivo antitumor activity. Mol Pharmacol. 2002;61:1154–62.
Article
CAS
PubMed
Google Scholar
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, et al. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 2012;40:D593–8.
Article
CAS
PubMed
Google Scholar
Huppert JL, Balasubramanian S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 2005;33:2908–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wernersson R. FeatureExtract—extraction of sequence annotation made easy. Nucleic Acids Res. 2005;33:W567–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rossetto CC, Tarrant-Elorza M, Verma S, Purushothaman P, Pari GS. Regulation of viral and cellular gene expression by Kaposi’s sarcoma-associated herpesvirus polyadenylated nuclear RNA. J Virol. 2013;87:5540–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oh J, Sanders IF, Chen EZ, Li H, Tobias JW, Isett RB, et al. Genome Wide Nucleosome Mapping for HSV-1 Shows Nucleosomes Are Deposited at Preferred Positions during Lytic Infection. PLoS One. 2015;10:e0117471.
Article
PubMed
PubMed Central
Google Scholar
Chambers J, Angulo A, Amaratunga D, Guo H, Jiang Y, Wan JS, et al. DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression. J Virol. 1999;73:5757–66.
CAS
PubMed
PubMed Central
Google Scholar
Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, et al. 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:e1003847.
Article
PubMed
PubMed Central
Google Scholar
Davison AJ, Scott JE. The complete DNA sequence of varicella-zoster virus. J Gen Virol. 1986;67:1759–816.
Article
CAS
PubMed
Google Scholar
Dunn W, Chou C, Li H, Hai R, Patterson D, Stolc V, et al. Functional profiling of a human cytomegalovirus genome. Proc Natl Acad Sci. 2003;100:14223–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu M, Suen J, Frias C, Pfeiffer R, Tsai M-H, Chuang E, et al. Dissection of the Kaposi’s sarcoma-associated herpesvirus gene expression program by using the viral DNA replication inhibitor cidofovir. J Virol. 2004;78:13637–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arvin, A, Campadelli-Fiume, G, Mocarski, E, Moore PS, Roizman B, Whitley R, Yamanishi K. Human herpesviruses: Biology, therapy, and immunoprophylaxis. Cambridge: Cambridge University Press; 2007.
Zacny VL, Wilson J, Pagano JS. The Epstein-Barr virus immediate-early gene product, BRLF1, interacts with the retinoblastoma protein during the viral lytic cycle. J Virol. 1998;72:8043–51.
CAS
PubMed
PubMed Central
Google Scholar