|
| Status |
Public on Oct 18, 2012 |
| Title |
The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
To uncover exon junction complex (EJC) deposition sites on cellular mRNAs, RNA footprints of EJC immuo-purified from HEK293 cells were deep sequenced. The analysis of these data revealed that major “canonical” EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions (-24 position) and that the majority of exon junctions carry an EJC. Unexpectedly, we find that many sites further upstream of -24 position are also enriched in these EJC footprints. These "non-canonical" sites are binding sites of EJC-interacting proteins with a subset being occupied by SR proteins. Thus, an EJC-SR protein nexus exists within spliced mRNPs and is revealed here.
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| |
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| Overall design |
Deep sequencing based profiling of EJC RNA footprints obtained by tandem RNA immunoprecipitation (RIPiT) of RNase I digested RNA:protein complexes.
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| |
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| Contributor(s) |
Singh G, Kucukural A, Moore MJ |
| Citation(s) |
23084401 |
| Submission date |
Sep 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Alper Kucukural |
| E-mail(s) |
alper.kucukural@umassmed.edu
|
| Phone |
508-856-2838
|
| Fax |
508-856-1002
|
| URL |
http://alper.kucukural.com
|
| Organization name |
UMass Medical School
|
| Department |
Biochemistry and Molecular Pharmacology
|
| Lab |
MooreLab
|
| Street address |
Lazare Medical Research Building, 870P
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605-4321 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL9442 |
AB SOLiD System 3.0 (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13393 |
AB SOLiD 4 System (Homo sapiens) |
|
| Samples (12)
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| Relations |
| BioProject |
PRJNA175949 |
| SRA |
SRP015888 |
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