|
| Status |
Public on Jun 16, 2020 |
| Title |
Concentration-dependent regulation by Rbfox enabled by motifs of intermediate affinity |
| Organism |
synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart, and muscle. Rbfox proteins have long been known to bind to the RNA sequence GCAUG with high affinity, but just half of Rbfox CLIP peaks contain a GCAUG motif. We incubated recombinant RBFOX2 with over 60,000 mouse and human transcriptomic sequences to reveal significant binding to several moderate-affinity, non-GCAYG sites at a physiologically relevant range of RBFOX concentrations. We find that many of these “secondary motifs” bind Rbfox robustly in cells and that several together can exert regulation comparable to a GCAUG in a trichromatic splicing reporter assay. Furthermore, secondary motifs regulate RNA splicing in neuronal development and in neuronal subtypes where cellular Rbfox concentrations are highest, enabling a second wave of splicing changes as Rbfox levels increase.
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| |
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| Overall design |
nsRBNS at 5 concentrations with one replicate (121nM), two 0 nM controls, and two input controls.
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| |
|
| Contributor(s) |
Begg BE, Burge CB |
| Citation missing |
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| |
| Submission date |
Jun 15, 2020 |
| Last update date |
Jun 18, 2020 |
| Contact name |
Bridget E Begg |
| E-mail(s) |
bebegg@mit.edu
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Biology
|
| Lab |
Burge Lab
|
| Street address |
31 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19604 |
Illumina HiSeq 2500 (synthetic construct) |
|
| Samples (11)
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|
| Relations |
| BioProject |
PRJNA639556 |
| SRA |
SRP267392 |
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