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| Status |
Public on Dec 21, 2011 |
| Title |
MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Illumina expression beadchip) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. We isolated polyribosome-associated mRNA, and captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally synergistic partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur with predominantly non-specific miRNA-mRNA interactions.
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| Overall design |
HEK293T cells were transfected with biotinylated miRNAs (either mir-10a-iso, mir-10a, mir-10b-iso or mir-10b) or a mock control. The miRNAs and target mRNA were pulled down with streptavidin. The pulled down RNA was hybridised to Illumina microarrays.
The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043
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| Contributor(s) |
Cloonan N |
| Citation(s) |
22208850 |
| Submission date |
May 03, 2011 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Nic Waddell |
| Organization name |
Queensland Centre for Medical Genomics
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| Street address |
St Lucia
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| City |
Brisbane |
| ZIP/Postal code |
4072 |
| Country |
Australia |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE29101 |
MicroRNAs and their isomiRs function cooperatively to target common biological pathways |
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| Relations |
| BioProject |
PRJNA142907 |
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