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Series GSE230717 Query DataSets for GSE230717
Status Public on Aug 14, 2023
Title Large-scale map of RNA binding protein interactomes across the mRNA life-cycle
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary RNA-binding proteins (RBPs) target RNA in a context-dependent manner to regulate gene expression. Protein-protein interaction (PPI) maps of RBP complexes and networks are critical for defining RBP function and RNA targeting. Yet, PPI networks under-represent RBP baits and need more information about RNA-driven interactions. Therefore, we generated an RNA-aware, RBP-interactome map combining two strategies that use systematic proteomic methods to identify 1) protein interactions using co-immunoprecipitation in the presence or absence of RNase treatment of a ~100 RBPs across the RNA life-cycle and 2) RNA-dependent complexes using Size Exclusion Chromatography. Together, this dataset provides proteome-wide, cell-type specific, and quantitative identification of RNA-protein interactions across multiple RNA processing events. In the resulting PPI network, several hundred database-supported interactions establish many complexes operating at each of these mRNA life-cycle stages. Nearly a thousand novel interactions imply new functions for RBPs across multiple steps of the RNA life cycle. Overlapping our network with eCLIP data, we find RNA targets between interactors and uncover complex-driven binding signatures. Betweenness-centrality scores identify multi-functional RBPs that participate across multiple mRNA life-cycle steps. We characterize the novel interactions and functions of different classes of multi-functional proteins. We find the scaffolding protein, ERH, interacts with numerous nuclear speckle proteins and facilitates splicing and mRNA export. Finally, we show that the splicing factor, SNRNP200, interacts with nuclear export, localization, and translation proteins and is an essential factor of RNA granule formation during stress. Our large-scale RBP interaction network provides new insights and a valuable resource for exploring new RBP complexes operating to control gene expression.
 
Overall design eCLIP-seq of human SNRNP200, CAPRIN, and G3BP1
eCLIP of RBP of interest. Each sample has an input and IP sample
 
Contributor(s) Rothamel K, Street L, Abdou A, Jin W, Dong K, Rhine K, Madrigal A, Al-Azzam N, Brannan K, Jovanovic M, Yeo G
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Submission date Apr 27, 2023
Last update date Aug 14, 2023
Contact name Brian Yee
E-mail(s) brian.alan.yee@gmail.com
Organization name UCSD
Department Health
Lab Yeo
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (24)
GSM7232996 SNRNP200 whole cell eCLIP rep 1 (input)
GSM7232997 SNRNP200 whole cell eCLIP rep 2 (input)
GSM7232998 SNRNP200 cytoplasmic eCLIP rep 1 (input)
Relations
BioProject PRJNA962448

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
GSE230717_CAPRIN.reproducible_enriched_windows.tsv.gz.bed.gz 1.1 Mb (ftp)(http) BED
GSE230717_KR_G3BP1_HEK.reproducible_enriched_windows.tsv.gz.bed.gz 255.1 Kb (ftp)(http) BED
GSE230717_SNRNP200_HEK.reproducible_enriched_windows.tsv.gz.bed.gz 13.0 Mb (ftp)(http) BED
GSE230717_SNRNP200_HEKstress.reproducible_enriched_windows.tsv.gz.bed.gz 8.6 Mb (ftp)(http) BED
GSE230717_SNRNP200_cyto.reproducible_enriched_windows.tsv.gz.bed.gz 317.5 Kb (ftp)(http) BED
GSE230717_SNRNP200_stress.reproducible_enriched_windows.tsv.gz.bed.gz 567.7 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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