|
| Status |
Public on Apr 26, 2013 |
| Title |
hsa-miR-92a knock down in Flp-in T-REx 293-PTH-AGO1 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
transcriptome profiling of miR-92a inhibitor treated and control cells with the aim of measuring miR-92a influence on its mRNA targets
Abstract: MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human Ago1. Here we report datasets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, non-seed basepairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA basepairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
|
| |
|
| Overall design |
In total 10 samples were analyzed, 5 repeats for each experimental condition.
|
| |
|
| Contributor(s) |
Helwak A, Kudla G, Tollervey D |
| Citation(s) |
23622248 |
| Submission date |
Apr 13, 2013 |
| Last update date |
Jul 10, 2014 |
| Contact name |
Grzegorz Kudla |
| E-mail(s) |
gkudla@gmail.com
|
| Phone |
+44 (0) 131 332 2471
|
| Organization name |
University of Edinburgh
|
| Department |
MRC HGU
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL5188 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version] |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA197206 |
Less...
More...