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Status |
Public on Mar 28, 2017 |
Title |
Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer (Mouse RNA-Seq) |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the miR-122 target network remains incomplete. To this end, we performed Argonaute crosslinking immunoprecipitation (Ago-CLIP) sequencing in miR-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (HCC) and benign liver tissue to identify miRNA target sites transcriptome-wide in two species. We observed a majority of miR-122 binding on 3’-UTRs and coding exons followed by extensive binding to other genic and non-genic sites. Motif analysis of miR-122 dependent binding revealed a novel G-bulged motif in addition to canonical motifs. A large number of miR-122 targets were found to be species-specific. Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma.
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Overall design |
AGO CLIP-seq libraries were generated from four miR-122 KO mice and five floxed littermate controls, all at six weeks of age.
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Contributor(s) |
Luna JM, Barajas JM, Teng K, Sun H, Moore MJ, Rice CM, Darnell RB, Ghoshal K |
Citation(s) |
28735896 |
Submission date |
Mar 27, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Joseph M Luna |
E-mail(s) |
jluna@rockefeller.edu
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Organization name |
The Rockefeller University
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Lab |
Rice
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Street address |
1230 York Ave #64
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
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Platforms (1) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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Samples (9)
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This SubSeries is part of SuperSeries: |
GSE97061 |
Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer |
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Relations |
BioProject |
PRJNA380616 |
SRA |
SRP102517 |