|
| Status |
Public on Nov 27, 2019 |
| Title |
The biochemical basis of microRNA targeting efficacy [3] |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of mRNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA–target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute–miRNA complexes and all ≤12-nucleotide sequences. This approach revealed noncanonical target sites unique to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.
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| |
|
| Overall design |
mRNA sequencing of HeLa cells serially transfected with synthetic miRNA duplexes and a massively parallel reporter library. This study consists of 12 libraries with 6 different miRNA transfected in replicate.
|
| |
|
| Contributor(s) |
McGeary SE, Lin KS, Bartel DP |
| Citation(s) |
31806698, 35191832 |
| |
| Submission date |
Nov 12, 2019 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Sean E. McGeary |
| E-mail(s) |
sean_mcgeary@hms.harvard.edu
|
| Organization name |
Whitehead Institute / MIT
|
| Department |
Biology
|
| Lab |
Bartel Lab
|
| Street address |
455 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (12)
|
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| This SubSeries is part of SuperSeries: |
| GSE140220 |
The biochemical basis of microRNA targeting efficacy |
|
| Relations |
| BioProject |
PRJNA592022 |
| SRA |
SRP235216 |
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