|
| Status |
Public on Nov 16, 2011 |
| Title |
microRNA Targetome Analysis of Latently KSHV-infected Primary Effusion Lymphoma Cell lines Using PAR-CLIP [Illumina] |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and, often, EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in viral latency and lymphomagenesis. Here we report the direct and transcriptome-wide identification of miRNA target sites for all miRNAs expressed in PEL cell lines. The resulting dataset revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs encoding proteins that function in pathways with relevance to KSHV pathogenesis. Moreover, ~50% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, these experiments identify an extensive list of mRNAs targeted by KSHV miRNAs and indicate that these are likely to strongly influence viral replication and pathogenesis.
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| |
|
| Overall design |
small RNA sequencing, 3 samples
Ago2 (EIF2C2) PAR-CLIP, 2 samples
|
| |
|
| Contributor(s) |
Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR |
| Citation(s) |
22100165 |
| |
| Submission date |
Sep 14, 2011 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Eva Gottwein |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University
|
| Department |
Microbiology-Immunology
|
| Street address |
320 E Superior St., Tarry building, Room 6-752
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
|
| Samples (6)
|
|
| This SubSeries is part of SuperSeries: |
| GSE32113 |
microRNA Targetome Analysis of Latently KSHV-infected Primary Effusion Lymphoma Cell lines Using PAR-CLIP |
|
| Relations |
| SRA |
SRP008216 |
| BioProject |
PRJNA154855 |
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