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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 25, 2018 |
| Title |
Modified cross-linking, ligation, and sequencing of hybrids (qCLASH) identifies KSHV microRNA targets in endothelial cells |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
KS lesions consist of endothelial cells latently infected with KSHV which express the KSHV miRNAs. Identifying the targets of the KSHV miRNAs will help us understand their role in viral oncogenesis. Cross-Linking and Sequencing of Hybrids (CLASH) is a method for unambiguously identifying miRNA targetomes. We developed a streamlined version of CLASH, called quick CLASH (qCLASH). qCLASH requires a lower initial input of cells than its parent protocol. Additionally, a new fast-growing KSHV-negative endothelial cell line, named TIVE-EX-LTC cells, was established. qCLASH was performed on TIVE-EX-LTC cells latently infected with WT KSHV or a mutant virus lacking miR-K12-11/11*. A number of novel targets of the KSHV miRNAs were identified, including targets of miR-K12-11, the ortholog of cellular oncomiR miR-155. Many of the miRNA targets were involved in processes related to oncogenesis, such as glycolysis, angiogenesis, and cell cycle control.
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| Overall design |
Cells were infected with WT KSHV or KSHV ΔmiR-K12-11. Argonaute was crosslinked to bound RNAs in living cells with UV irradiation. Argonaute was immunoprecipitated and bound RNAs were ligated to one another and then isolated.
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| Contributor(s) |
Gay LA, Sethuraman S, Jain V, Thomas M, Riva A, Turner PC, Renne R |
| Citation(s) |
29386283, 29846699, 38006335 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA119917 |
Studying the role of KSHV-encoded miRNAs |
UNIVERSITY OF FLORIDA |
ROLF F RENNE |
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| Submission date |
Jul 27, 2017 |
| Last update date |
Dec 14, 2023 |
| Contact name |
Rolf Renne |
| Organization name |
University of Florida
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| Street address |
2033 Mowry Road
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| City |
Gainesville |
| ZIP/Postal code |
32608 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA396057 |
| SRA |
SRP113726 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE101978_RAW.tar |
240.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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