The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes
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RESEARCH
Open Access
The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes Simon Boudreault, Victoria E. S. Armero, Michelle S. Scott, Jean-Pierre Perreault and Martin Bisaillon*
Abstract Background: Alternative splicing (AS) is an important mRNA maturation step that allows increased variability and diversity of proteins in eukaryotes. AS is dysregulated in numerous diseases, and its implication in the carcinogenic process is well known. However, progress in understanding how oncogenic viruses modulate splicing, and how this modulation is involved in viral oncogenicity has been limited. Epstein-Barr virus (EBV) is involved in various cancers, and its EBNA1 oncoprotein is the only viral protein expressed in all EBV malignancies. Methods: In the present study, the ability of EBNA1 to modulate the AS of cellular genes was assessed using a highthroughput RT-PCR approach to examine AS in 1238 cancer-associated genes. RNA immunoprecipitation coupled to RNA sequencing (RIP-Seq) assays were also performed to identify cellular mRNAs bound by EBNA1. Results: Upon EBNA1 expression, we detected modifications to the AS profiles of 89 genes involved in cancer. Moreover, we show that EBNA1 modulates the expression levels of various splicing factors such as hnRNPA1, FOX-2, and SF1. Finally, RNA immunoprecipitation coupled to RIP-Seq assays demonstrate that EBNA1 immunoprecipitates specific cellular mRNAs, but not the ones that are spliced differently in EBNA1-expressing cells. Conclusion: The EBNA1 protein can modulate the AS profiles of numerous cellular genes. Interestingly, this modulation protein does not require the RNA binding activity of EBNA1. Overall, these findings underline the novel role of EBNA1 as a cellular splicing modulator. Keywords: Alternative splicing, Epstein-Barr virus, Virus-host interaction, High-throughput RT-PCR, RIP-sequencing, EBNA1, Splicing factors
Background Alternative splicing (AS) is an important mechanism allowing higher proteome diversity in eukaryotes. In Homo sapiens, AS is nearly ubiquitous, as more than 90% of human genes undergo AS [1]. AS, as opposed to constitutive splicing, leads to different arrangement of exons, retained introns, and splice-sites for the same pre-messenger RNA (pre-mRNA). This allows the same pre-mRNA to be processed into different isoform-coding mature mRNAs, sometimes even with opposing functions at the protein level. The regulatory aspect of AS is becoming increasingly known, and changes in AS are linked with various diseases
* Correspondence: [email protected] Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
such as cancer, Parkinson’s disease, amyotrophic lateral sclerosis, and rheumatoid arthritis [2–5]. Recently obtained evidence show that viruses can disrupt the AS of cellular transcripts, although functional consequences on viral infection are still sparse. A number of studies have shown different mechanisms allowing v
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