Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456(7221):470–6.
CAS
PubMed
PubMed Central
Google Scholar
David CJ, Manley JL. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev. 2010;24(21):2343–64.
CAS
PubMed
PubMed Central
Google Scholar
Prudencio M, Belzil VV, Batra R, Ross CA, Gendron TF, Pregent LJ, et al. Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nat Neurosci. 2015;18(8):1175–82.
CAS
PubMed
PubMed Central
Google Scholar
Soreq L, Guffanti A, Salomonis N, Simchovitz A, Israel Z, Bergman H, et al. Long non-coding RNA and alternative splicing modulations in Parkinson’s leukocytes identified by RNA sequencing. PLoS Comput Biol. 2014;10(3):e1003517.
PubMed
PubMed Central
Google Scholar
Turkkila M, Andersson KM, Amu S, Brisslert M, Erlandsson MC, Silfverswärd S, et al. Suppressed diversity of survivin splicing in active rheumatoid arthritis. Arthritis Research & Therapy. 2015;17(1):175.
Google Scholar
Barnhart MD, Moon SL, Emch AW, Wilusz CJ, Wilusz J. Changes in cellular mRNA stability, splicing, and polyadenylation through HuR protein sequestration by a cytoplasmic RNA virus. Cell Rep. 2013;5(4):909–17.
CAS
PubMed
Google Scholar
Álvarez E, Castelló A, Carrasco L, Izquierdo JM. Poliovirus 2A protease triggers a selective Nucleo-cytoplasmic redistribution of splicing factors to regulate alternative pre-mRNA splicing. PLoS One. 2013;8(9):e73723.
PubMed
PubMed Central
Google Scholar
Kneller ELP, Connor JH, Lyles DS. hnRNPs Relocalize to the cytoplasm following infection with vesicular stomatitis virus. J Virol. 2009;83(2):770–80.
CAS
Google Scholar
Boudreault S, Martenon-Brodeur C, Caron M, Garant J-M, Tremblay M-P, Armero VES, et al. Global profiling of the cellular alternative RNA splicing landscape during virus-host interactions. PLoS One. 2016;11(9):e0161914.
PubMed
PubMed Central
Google Scholar
Hu B, Huo Y, Yang L, Chen G, Luo M, Yang J, et al. ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells. Virol J. 2017;14:217.
PubMed
PubMed Central
Google Scholar
Rivera-Serrano EE, Fritch EJ, Scholl EH, Sherry BA. Cytoplasmic RNA virus alters the function of the cell splicing protein SRSF2. J Virol. 2017;91(7):e02488–16.
PubMed
PubMed Central
Google Scholar
Lindberg A, Kreivi J-P. Splicing inhibition at the level of spliceosome assembly in the presence of herpes simplex virus protein ICP27. Virology. 2002;294(1):189–98.
CAS
PubMed
Google Scholar
Sciabica KS. ICP27 interacts with SRPK1 to mediate HSV splicing inhibition by altering SR protein phosphorylation. EMBO J. 2003;22(7):1608–19.
CAS
PubMed
PubMed Central
Google Scholar
Bryant HE, Wadd SE, Lamond AI, Silverstein SJ, Clements JB. Herpes simplex virus IE63 (ICP27) protein interacts with spliceosome-associated protein 145 and inhibits splicing prior to the first catalytic step. J Virol. 2001;75(9):4376–85.
CAS
PubMed
PubMed Central
Google Scholar
Sandri-Goldin RM, Hibbard MK, Hardwicke MA. The C-terminal repressor region of herpes simplex virus type 1 ICP27 is required for the redistribution of small nuclear ribonucleoprotein particles and splicing factor SC35; however, these alterations are not sufficient to inhibit host cell splicing. J Virol. 1995;69(10):6063–76.
CAS
PubMed
PubMed Central
Google Scholar
Rutkowski AJ, Erhard F, L’Hernault A, Bonfert T, Schilhabel M, Crump C, et al. Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun. 2015;6:7126.
PubMed
PubMed Central
Google Scholar
Verma D, Bais S, Gaillard M, Swaminathan S. Epstein-Barr virus SM protein utilizes cellular splicing factor SRp20 to mediate alternative splicing. J Virol. 2010;84(22):11781–9.
CAS
PubMed
PubMed Central
Google Scholar
Verma D, Swaminathan S. Epstein-Barr virus SM protein functions as an alternative splicing factor. J Virol. 2008;82(14):7180–8.
CAS
PubMed
PubMed Central
Google Scholar
Lee N, Pimienta G, Steitz JA. AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus. RNA. 2012;18(11):2073–82.
CAS
PubMed
PubMed Central
Google Scholar
Pimienta G, Fok V, Haslip M, Nagy M, Takyar S, Steitz JA. Proteomics and transcriptomics of BJAB cells expressing the Epstein-Barr virus noncoding RNAs EBER1 and EBER2. PLoS One. 2015;10(6):e0124638.
PubMed
PubMed Central
Google Scholar
Frappier L. The Epstein-Barr Virus EBNA1 Protein. Scientifica (Cairo). 2012;438204.
Fischer N, Voß MD, Mueller-Lantzsch N, Grässer FA. A potential NES of the Epstein-Barr virus nuclear antigen 1 (EBNA1) does not confer shuttling. FEBS Lett. 1999;447(2–3):311–4.
CAS
PubMed
Google Scholar
Lu F, Wikramasinghe P, Norseen J, Tsai K, Wang P, Showe L, et al. Genome-wide analysis of host-chromosome binding sites for Epstein-Barr virus nuclear antigen 1 (EBNA1). Virol J. 2010;7:262.
PubMed
PubMed Central
Google Scholar
Saridakis V, Sheng Y, Sarkari F, Holowaty MN, Shire K, Nguyen T, et al. Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein-Barr nuclear antigen 1 implications for EBV-mediated immortalization. Mol Cell. 2005;18(1):25–36.
CAS
PubMed
Google Scholar
Valentine R, Dawson CW, Hu C, Shah KM, Owen TJ, Date KL, et al. Epstein-Barr virus-encoded EBNA1 inhibits the canonical NF-kappaB pathway in carcinoma cells by inhibiting IKK phosphorylation. Mol Cancer. 2010;9:1.
PubMed
PubMed Central
Google Scholar
Wood VHJ, O’Neil JD, Wei W, Stewart SE, Dawson CW, Young LS. Epstein-Barr virus-encoded EBNA1 regulates cellular gene transcription and modulates the STAT1 and TGFbeta signaling pathways. Oncogene. 2007;26(28):4135–47.
CAS
PubMed
Google Scholar
Schulz TF, Cordes S. Is the Epstein–Barr virus EBNA-1 protein an oncogen? PNAS. 2009;106(7):2091–2.
CAS
PubMed
Google Scholar
Armero VES, Tremblay M-P, Allaire A, Boudreault S, Martenon-Brodeur C, Duval C, et al. Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas. PLoS One. 2017;12(5):e0176880.
PubMed
PubMed Central
Google Scholar
Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, et al. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 2012;487(7408):491–5.
CAS
PubMed
PubMed Central
Google Scholar
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucl Acids Res. 2015;43(D1):D447–52.
CAS
PubMed
Google Scholar
Jiao X, Sherman BT, Huang DW, Stephens R, Baseler MW, Lane HC, et al. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics. 2012;28(13):1805–6.
CAS
PubMed
PubMed Central
Google Scholar
Patry C, Bouchard L, Labrecque P, Gendron D, Lemieux B, Toutant J, et al. Small interfering RNA-mediated reduction in heterogeneous nuclear Ribonucleoparticule A1/A2 proteins induces apoptosis in human Cancer cells but not in Normal mortal cell lines. Cancer Res. 2003;63(22):7679–88.
CAS
PubMed
Google Scholar
Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucl Acids Res. 2002;30(1):207–10.
CAS
PubMed
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(5):358–64.
CAS
PubMed
PubMed Central
Google Scholar
Dheekollu J, Wiedmer A, Sentana-Lledo D, Cassel J, Messick T, Lieberman PM. HCF1 and OCT2 cooperate with EBNA1 to enhance OriP-dependent transcription and Episome maintenance of latent Epstein-Barr virus. J Virol. 2016;90(11):5353–67.
CAS
PubMed
PubMed Central
Google Scholar
Ayoubian H, Fröhlich T, Pogodski D, Flatley A, Kremmer E, Schepers A, et al. Antibodies against the mono-methylated arginine-glycine repeat (MMA-RG) of the Epstein–Barr virus nuclear antigen 2 (EBNA2) identify potential cellular proteins targeted in viral transformation. J Gen Virol. 2017;98(8):2128–42.
CAS
PubMed
Google Scholar
Wang SC, Hammarskjöld ML, Klein G. Immunoprecipitation of Epstein-Barr virus EBNA1 protein using human polyclonal serum. J Virol Methods. 1986;13(4):323–32.
CAS
PubMed
Google Scholar
Hammarskjöld M-L, Shih-Chung W, Klein G. High-level expression of the Epstein-Barr virus EBNA1 protein in CV1 cells and human lymphoid cells using a SV40 late replacement vector. Gene. 1986;43(1):41–50.
PubMed
Google Scholar
Hennessy K, Kieff E. One of two Epstein-Barr virus nuclear antigens contains a glycine-alanine copolymer domain. Proc Natl Acad Sci U S A. 1983;80(18):5665–9.
CAS
PubMed
PubMed Central
Google Scholar
Sculley TB, Sculley DG, Pope JH, Bornkamm GW, Lenoir GM, Rickinson AB. Epstein-Barr virus nuclear antigens 1 and 2 in Burkitt lymphoma cell lines containing either ‘a’- or ‘B’-type virus. Intervirology. 1988;29(2):77–85.
CAS
PubMed
Google Scholar
Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Gervais-Bird J, Madden R, et al. Multiple alternative splicing markers for ovarian Cancer. Cancer Res. 2008;68(3):657–63.
CAS
PubMed
Google Scholar
Lu C-C, Wu C-W, Chang SC, Chen T-Y, Hu C-R, Yeh M-Y, et al. Epstein–Barr virus nuclear antigen 1 is a DNA-binding protein with strong RNA-binding activity. J Gen Virol. 2004;85(10):2755–65.
CAS
PubMed
Google Scholar
Norseen J, Johnson FB, Lieberman PM. Role for G-Quadruplex RNA binding by Epstein-Barr virus nuclear antigen 1 in DNA replication and metaphase chromosome attachment. J Virol. 2009;83(20):10336–46.
CAS
PubMed
PubMed Central
Google Scholar
Li Y, Zhao DY, Greenblatt JF, Zhang Z. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res 2013;41(8):e94-e94.
Snudden DK, Hearing J, Smith PR, Grässer FA, Griffin BE. EBNA-1, the major nuclear antigen of Epstein-Barr virus, resembles « RGG » RNA binding proteins. EMBO J. 1994;13(20):4840–7.
CAS
PubMed
PubMed Central
Google Scholar
Lee H-J, Tomioka S, Kinbara K, Masumoto H, Jeong S-Y, Sorimachi H, et al. Characterization of a human digestive tract-specific Calpain, nCL-4, expressed in the Baculovirus system. Arch Biochem Biophys. 1999;362(1):22–31.
CAS
PubMed
Google Scholar
Yoshikawa Y, Mukai H, Hino F, Asada K, Kato I. Isolation of two novel genes, Down-regulated in gastric Cancer. Jpn J Cancer Res. 2000;91(5):459–63.
CAS
PubMed
PubMed Central
Google Scholar
Zhang L, Pagano JS. Interferon regulatory factor 7 is induced by Epstein-Barr virus latent membrane protein 1. J Virol. 2000;74(3):1061–8.
CAS
PubMed
PubMed Central
Google Scholar
Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27(12):1653–9.
CAS
PubMed
PubMed Central
Google Scholar