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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 06, 2016 |
| Title |
SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes. |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
RNA metabolism is controlled by an expanding yet incomplete catalog of RNA binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull-down of twelve nuclear and cytoplasmic RBPs followed by quantitative mass-spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1923 human, 489 fly and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.
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| Overall design |
eCLIP-seq was performed in biological replicate for AIFM1, NUMA1, RANGAP1, RNF219, VIM, ZNF184. Each sample has a size-matched input control for analysis
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| Contributor(s) |
Brannan KW, Jin W, Banks CA, Gilmore JM, Florens L, Washburn MP, Van Nostrand EL, Pratt GA, Schwinn MK, Daniels DL, Yeo GW |
| Citation(s) |
27720645 |
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| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
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| Organization name |
UCSD
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| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA340076 |
| SRA |
SRP082930 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE86035_RAW.tar |
515.6 Mb |
(http)(custom) |
TAR (of BB, BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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