|
| Status |
Public on Jul 12, 2018 |
| Title |
The Epstein Barr virus circleRNAome |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings of EBV encoded microRNAs, new long non-coding RNAs, and hundreds of new polyadenylated lytic transcripts. Here we report an additional layer to the EBV transcriptome through the identification of a repertoire of latent and lytic viral circRNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, and III, we identified circRNAs expressed from the latency Cp promoter involving backsplicing from the W1 and W2 exons to the C1 exon, from the EBNA BamHI U exon, and from the latency long-non-coding RPMS1 locus. We also identified circRNAs expressed during reactivation including an exon 8-to-2 backspliced LMP2 transcript and a highly expressed circRNA derived from the BHLF1 gene. Altogether we identified over 30 EBV circRNA candidates and validated and determined the structural features, expression profiles and nuclear-cytoplasmic distributions of several prominent viral circRNAs. Further, we show that two RPMS1 circRNAs are expressed in stomach cancer specimens. This study increases the known EBV latency and lytic transcriptome repertoires to include viral circRNAs and provides an essential foundation for investigations into the functions of this new class of EBV transcripts in EBV biology and disease.
|
| |
|
| Overall design |
RNase R treated, Ribodepletion, and Poly-A selection libraries of EBV+ B-cell lymphoma and gastric carcinoma cell lines were generated and RNA-sequencing was done.
|
| |
|
| Contributor(s) |
Flemington E |
| Citation(s) |
30080890 |
| |
| Submission date |
Jul 05, 2018 |
| Last update date |
Jan 15, 2020 |
| Contact name |
Erik K Flemington |
| E-mail(s) |
eflemin@tulane.edu
|
| Phone |
504 988-1167
|
| Organization name |
Tulane Health Sciences Center
|
| Department |
Pathology
|
| Street address |
1430 Tulane Ave., SL79
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (24)
|
| GSM3258253 |
Akata (uninduced) - Total RNA - RNase R treated |
| GSM3258254 |
Akata (uninduced) - Nuclear RNA - RNase R treated |
| GSM3258255 |
Akata (uninduced) - Cytoplasmic RNA - RNase R treated |
|
| Relations |
| BioProject |
PRJNA479852 |
| SRA |
SRP152310 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116675_10_Mutu_Cl14_uninduced_sites.bed.gz |
3.6 Mb |
(ftp)(http) |
BED |
| GSE116675_11_Mutu-Cl14-induced_sites.bed.gz |
4.7 Mb |
(ftp)(http) |
BED |
| GSE116675_12_SavI_sites.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE116675_13_MutuIII_sites.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE116675_14_IB4_sites.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
| GSE116675_15_Jijoye_sites.bed.gz |
3.2 Mb |
(ftp)(http) |
BED |
| GSE116675_16_JY_RNaseR_sites.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSE116675_17_JY-cytoplasmic_sites.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSE116675_18_JY-nuclear_sites.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSE116675_19_SNU719_sites.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE116675_1_Akata-60--uninduced---cr_sites.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE116675_20_YCCEL1_sites.bed.gz |
2.7 Mb |
(ftp)(http) |
BED |
| GSE116675_2_Akata-60--induced---cr_sites.bed.gz |
3.4 Mb |
(ftp)(http) |
BED |
| GSE116675_5_Akata-60--uninduced-cytoplasmic_sites.bed.gz |
3.0 Mb |
(ftp)(http) |
BED |
| GSE116675_6_Akata-60--induced-cytoplasmic_sites.bed.gz |
3.7 Mb |
(ftp)(http) |
BED |
| GSE116675_7_Akata-60--uninduced-nuclear_sites.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSE116675_8_Akata-60--induced-nuclear_sites.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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