The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes.
Alternative Splicing
Cell Line, Tumor
Epstein-Barr Virus Nuclear Antigens
/ genetics
Gene Expression Profiling
Genes, Neoplasm
Genes, Viral
HEK293 Cells
Herpesvirus 4, Human
/ genetics
High-Throughput Nucleotide Sequencing
Host Microbial Interactions
/ genetics
Humans
RNA, Messenger
/ genetics
Real-Time Polymerase Chain Reaction
Viral Proteins
/ genetics
Alternative splicing
EBNA1
Epstein-Barr virus
High-throughput RT-PCR
RIP-sequencing
Splicing factors
Virus-host interaction
Journal
Virology journal
ISSN: 1743-422X
Titre abrégé: Virol J
Pays: England
ID NLM: 101231645
Informations de publication
Date de publication:
04 03 2019
04 03 2019
Historique:
received:
22
11
2018
accepted:
25
02
2019
entrez:
6
3
2019
pubmed:
6
3
2019
medline:
30
4
2019
Statut:
epublish
Résumé
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. In the present study, the ability of EBNA1 to modulate the AS of cellular genes was assessed using a high-throughput 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. 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. 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.
Sections du résumé
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 high-throughput 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.
Identifiants
pubmed: 30832682
doi: 10.1186/s12985-019-1137-5
pii: 10.1186/s12985-019-1137-5
pmc: PMC6399920
doi:
Substances chimiques
Epstein-Barr Virus Nuclear Antigens
0
RNA, Messenger
0
Viral Proteins
0
EBV-encoded nuclear antigen 1
O5GA75RST7
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
29Subventions
Organisme : NCI NIH HHS
ID : P01 CA174439
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA171979
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA177423
Pays : United States
Références
FEBS Lett. 1999 Mar 26;447(2-3):311-4
pubmed: 10214968
J Virol. 2000 Feb;74(3):1061-8
pubmed: 10627515
Jpn J Cancer Res. 2000 May;91(5):459-63
pubmed: 10835488
J Virol. 2001 May;75(9):4376-85
pubmed: 11287586
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
pubmed: 11752295
Virology. 2002 Mar 1;294(1):189-98
pubmed: 11886277
EMBO J. 2003 Apr 1;22(7):1608-19
pubmed: 12660167
Cancer Res. 2003 Nov 15;63(22):7679-88
pubmed: 14633690
J Gen Virol. 2004 Oct;85(Pt 10):2755-65
pubmed: 15448336
Mol Cell. 2005 Apr 1;18(1):25-36
pubmed: 15808506
Oncogene. 2007 Jun 14;26(28):4135-47
pubmed: 17486072
Cancer Res. 2008 Feb 1;68(3):657-63
pubmed: 18245464
J Virol. 2008 Jul;82(14):7180-8
pubmed: 18463151
Nature. 2008 Nov 27;456(7221):470-6
pubmed: 18978772
J Virol. 2009 Jan;83(2):770-80
pubmed: 19004954
Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2091-2
pubmed: 19211802
J Virol. 2009 Oct;83(20):10336-46
pubmed: 19656898
Mol Cancer. 2010 Jan 05;9:1
pubmed: 20051109
J Virol. 2010 Nov;84(22):11781-9
pubmed: 20810723
Virol J. 2010 Oct 07;7:262
pubmed: 20929547
Genes Dev. 2010 Nov 1;24(21):2343-64
pubmed: 21041405
Bioinformatics. 2011 Jun 15;27(12):1653-9
pubmed: 21543442
Bioinformatics. 2012 Jul 1;28(13):1805-6
pubmed: 22543366
Nature. 2012 Jul 26;487(7408):491-5
pubmed: 22810586
RNA. 2012 Nov;18(11):2073-82
pubmed: 23012480
Nucleic Acids Res. 2013 Apr;41(8):e94
pubmed: 23455476
PLoS One. 2013 Sep 16;8(9):e73723
pubmed: 24066065
Cell Rep. 2013 Nov 27;5(4):909-17
pubmed: 24210824
Scientifica (Cairo). 2012;2012:438204
pubmed: 24278697
Nat Chem Biol. 2014 May;10(5):358-64
pubmed: 24633353
PLoS Comput Biol. 2014 Mar 20;10(3):e1003517
pubmed: 24651478
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52
pubmed: 25352553
Nat Commun. 2015 May 20;6:7126
pubmed: 25989971
PLoS One. 2015 Jun 29;10(6):e0124638
pubmed: 26121143
Arthritis Res Ther. 2015 Jul 10;17:175
pubmed: 26160473
Nat Neurosci. 2015 Aug;18(8):1175-82
pubmed: 26192745
J Virol. 2016 May 12;90(11):5353-5367
pubmed: 27009953
PLoS One. 2016 Sep 06;11(9):e0161914
pubmed: 27598998
J Virol. 2017 Mar 13;91(7):
pubmed: 28077658
Intervirology. 1988;29(2):77-85
pubmed: 2842274
PLoS One. 2017 May 11;12(5):e0176880
pubmed: 28493890
J Gen Virol. 2017 Aug;98(8):2128-2142
pubmed: 28758620
Virol J. 2017 Nov 7;14(1):217
pubmed: 29116029
J Virol Methods. 1986 Jul;13(4):323-32
pubmed: 3018021
Gene. 1986;43(1-2):41-50
pubmed: 3019836
Proc Natl Acad Sci U S A. 1983 Sep;80(18):5665-9
pubmed: 6310587
J Virol. 1995 Oct;69(10):6063-76
pubmed: 7666511
EMBO J. 1994 Oct 17;13(20):4840-7
pubmed: 7957053
Arch Biochem Biophys. 1999 Feb 1;362(1):22-31
pubmed: 9917325