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| Status |
Public on May 21, 2015 |
| Title |
New non-coding lytic transcripts derived from the Epstein Barr virus latency origin of replication oriP are hyper-edited, bind the paraspeckle protein, NONO/p54nrb, and support lytic viral transcription |
| Organism |
human gammaherpesvirus 4 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long non-coding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward transcripts (oriPtRs) are largely localized in the nucleus. While the oriPtLs are most likely non-coding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5’UTRs may partially serve non-coding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics and their expression is inhibited by phosphonoacetic acid. RNA-seq analysis showed that oriPtLs and oriPtRs exhibited extensive “hyper-editing” at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The double-stranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts suggesting that oriPts interacts with the paraspeckle-based innate anti-viral immune pathway. Knock-down and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade.
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| Overall design |
RNA-seq analysis for oriPtL knockdown and overexpression experiments
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| Contributor(s) |
Cao S, Moss W, O’Grady T, Concha M, Strong MJ, Wang X, Yu Y, Baddoo M, Zhang K, Fewell C, Lin Z, Dong Y, Flemington EK |
| Citation(s) |
25926645 |
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| Submission date |
Apr 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Erik K Flemington |
| Organization name |
Tulane University
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| Department |
Tulane Cancer Center/Pathology and Laboratory Medicine
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| Lab |
8th Floor LCRC
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| Street address |
1430 Tulane Avenue, SL-79
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| City |
New Orleans |
| State/province |
Louisiana |
| ZIP/Postal code |
70112 |
| Country |
USA |
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| Platforms (1) |
| GPL20090 |
Illumina HiSeq 2000 (Human herpesvirus 4) |
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| Samples (16)
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| GSM1664127 |
RNA-seq of induced control Akata cells (using CNTL GapmeR)_1 |
| GSM1664128 |
RNA-seq of induced control Akata cells (using CNTL GapmeR)_2 |
| GSM1664129 |
RNA-seq of induced control Akata cells (using CNTL GapmeR)_3 |
| GSM1664130 |
RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 1 for knockdown)_1 |
| GSM1664131 |
RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 1 for knockdown)_2 |
| GSM1664132 |
RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 1 for knockdown)_3 |
| GSM1664133 |
RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 2 for knockdown)_1 |
| GSM1664134 |
RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 2 for knockdown)_2 |
| GSM1664135 |
RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 2 for knockdown)_3 |
| GSM1664136 |
RNA-seq of control Mutu cells_1 |
| GSM1664137 |
RNA-seq of control Mutu cells_2 |
| GSM1664138 |
RNA-seq of oriPtL overexpressing Mutu cells_1 |
| GSM1664139 |
RNA-seq of oriPtL overexpressing Mutu cells_2 |
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| Relations |
| SRA |
SRP057529 |
| BioProject |
PRJNA281881 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68122_RPKM_values_of_EBV_genes.xls.gz |
42.8 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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