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Series GSE152510 Query DataSets for GSE152510
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.
Overall design nsRBNS at 5 concentrations with one replicate (121nM), two 0 nM controls, and two input controls.
Contributor(s) Begg BE, Burge CB
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Submission date Jun 15, 2020
Last update date Jun 18, 2020
Contact name Bridget E Begg
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
Platforms (1)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (11)
GSM4616759 RBFOX2 1100nM
GSM4616760 RBFOX2 365nM
GSM4616761 RBFOX2 121nM replicate 1
BioProject PRJNA639556
SRA SRP267392

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE152510_Begg2020_mappingLibrary.fa.gz 2.2 Mb (ftp)(http) FA
GSE152510_RAW.tar 4.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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