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SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

Kristopher W Brannan, Wenhao Jin, Stephanie C Huelga, Charles A S Banks, Joshua M Gilmore, Laurence Florens, Michael P Washburn, Eric L Van Nostrand, Gabriel A Pratt, Marie K Schwinn, Danette L Daniels, Gene W Yeo

Molecular cell · 2016 · Vol. 64 (2) · pp. 282-293

PubMed ↗ DOI ↗ PMC full text ↗

Abstract

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 12 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 1,923 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.

Linked datasets 1

GSE86035 GSE · via ncbi_elink
GEO ↗

SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

Homo sapiens

60 data files
FileTypeSize
KB10_293_CLIP_NUMA_2_IP_ATTACTCG-CCTATCCT_L008_R1.A01_KB10_… RIP-Seq 108.5 MB
KB10_293_CLIP_NUMA_2_IP_ATTACTCG-CCTATCCT_L008_R1.B06_KB10_… RIP-Seq 191.8 MB
KB10_293_CLIP_NUMA_2_IP_ATTACTCG-CCTATCCT_L008_R2.B06_KB10_… RIP-Seq 191.8 MB
KB11_293_CLIP_NUMA_1_input_TCCGGAGA-AGGCGAAG_L008_R1.unassi… RIP-Seq 652.7 MB
KB12_293_CLIP_AIFM_1_IP_ATTACTCG-CCTATCCT_L006_R1.unassigne… RIP-Seq 377.3 MB
KB16_293_CLIP_RNF219_3_GAATTCGT-AGGCGAAG_L007_R1.C01_KB16_R… RIP-Seq 136.2 MB
KB16_293_CLIP_RNF219_3_GAATTCGT-AGGCGAAG_L007_R1.D08fixed_K… RIP-Seq 178.3 MB
KB20_293_CLIP_VIM_1_GAATTCGT-ATAGAGGC_L007_R1.C01_KB20_VIM_… RIP-Seq 215.8 MB
KB20_293_CLIP_VIM_1_GAATTCGT-ATAGAGGC_L007_R1.D08fixed_KB20… RIP-Seq 89.3 MB
KB21_293_CLIP_VIM_2_CGCTCATT-ATAGAGGC_L007_R1.C01_KB21P_VIM… RIP-Seq 256.4 MB
KB21_293_CLIP_VIM_2_CGCTCATT-ATAGAGGC_L007_R1.D08fixed_KB21… RIP-Seq 112.0 MB
KB22_293_CLIP_VIM_input_CGCTCATT-TAATCTTA_L007_R1.unassigne… RIP-Seq 682.3 MB
KB2_293_CLIP_AIFM_1_IP_TCCGGAGA-TATAGCCT_L008_R1.A01_KB2_AI… RIP-Seq 131.6 MB
KB2_293_CLIP_AIFM_1_IP_TCCGGAGA-TATAGCCT_L008_R1.B06_KB2_AI… RIP-Seq 130.8 MB
KB23_293_INPUT_ZNF184_S70_L008_R1_001.unassigned.randomer.f… RIP-Seq 1.3 GB
KB24_293_CLIP_ZNF184_S71_L008_R1_001.A01_KB24_ZNF184_1_ZNF1… RIP-Seq 433.9 MB
KB24_293_CLIP_ZNF184_S71_L008_R1_001.B06_KB24_ZNF184_1_ZNF1… RIP-Seq 551.0 MB
KB25_293_CLIP_ZNF184_S72_L008_R1_001.C01_KB25_ZNF184_2_ZNF1… RIP-Seq 770.5 MB
KB25_293_CLIP_ZNF184_S72_L008_R1_001.D08fixed_KB25_ZNF184_2… RIP-Seq 337.9 MB
KB3_293_CLIP_AIFM_2_IP_TCCGGAGA-ATAGAGGC_L008_R1.C01_KB3_AI… RIP-Seq 343.0 MB
KB3_293_CLIP_AIFM_2_IP_TCCGGAGA-ATAGAGGC_L008_R1.D08fixed_K… RIP-Seq 261.6 MB
KB5_293_CLIP_RNF219_1_input_ATTACTCG-AGGCGAAG_L008_R1.unass… RIP-Seq 656.7 MB
KB6_293_CLIP_RANGAP_3_IP_CGCTCATT-TATAGCCT_L008_R1.C01_KB6_… RIP-Seq 219.5 MB
KB6_293_CLIP_RANGAP_3_IP_CGCTCATT-TATAGCCT_L008_R1.D08fixed… RIP-Seq 230.1 MB
KB7_293_CLIP_RANGAP_4_IP_CGCTCATT-TAATCTTA_L008_R1.C01_KB7_… RIP-Seq 229.1 MB
KB7_293_CLIP_RANGAP_4_IP_CGCTCATT-TAATCTTA_L008_R1.D08fixed… RIP-Seq 175.2 MB
KB7_293_CLIP_RANGAP_4_IP_CGCTCATT-TAATCTTA_L008_R2.C01_KB7_… RIP-Seq 229.1 MB
KB8_293_CLIP_RANGAP_2_input_ATTCAGAA-CCTATCCT_L008_R1.unass… RIP-Seq 704.3 MB
KB9_293_CLIP_NUMA_1_IP_GAATTCGT-GGCTCTGA_L008_R1.A01_KB9_NU… RIP-Seq 139.5 MB
KB9_293_CLIP_NUMA_1_IP_GAATTCGT-GGCTCTGA_L008_R1.B06_KB9_NU… RIP-Seq 219.8 MB
SRR4063765_GSM2291979 RIP-Seq 131.0 MB
SRR4063766_GSM2291979 RIP-Seq 130.0 MB
SRR4063767_GSM2291980 RIP-Seq 342.0 MB
SRR4063768_GSM2291980 RIP-Seq 261.0 MB
SRR4063769_GSM2291981 RIP-Seq 656.0 MB
SRR4063770_GSM2291982 RIP-Seq 219.0 MB
SRR4063771_GSM2291982 RIP-Seq 230.0 MB
SRR4063772_GSM2291983 RIP-Seq 229.0 MB
SRR4063773_GSM2291983 RIP-Seq 175.0 MB
SRR4063774 RIP-Seq 704.3 MB
SRR4063774_GSM2291984 RIP-Seq 704.0 MB
SRR4063775_GSM2291985 RIP-Seq 139.0 MB
SRR4063776_GSM2291985 RIP-Seq 219.0 MB
SRR4063777_GSM2291986 RIP-Seq 108.0 MB
SRR4063778_GSM2291986 RIP-Seq 191.0 MB
SRR4063779_GSM2291987 RIP-Seq 652.0 MB
SRR4063780_GSM2291988 RIP-Seq 377.0 MB
SRR4063781_GSM2291989 RIP-Seq 136.0 MB
SRR4063782_GSM2291989 RIP-Seq 178.0 MB
SRR4063783_GSM2291990 RIP-Seq 215.0 MB
SRR4063784_GSM2291990 RIP-Seq 89.0 MB
SRR4063785_GSM2291991 RIP-Seq 256.0 MB
SRR4063786_GSM2291991 RIP-Seq 112.0 MB
SRR4063787_GSM2291992 RIP-Seq 682.0 MB
SRR4063788_GSM2291993 RIP-Seq 1.3 GB
SRR4063789 RIP-Seq 433.9 MB
SRR4063789_GSM2291994 RIP-Seq 433.0 MB
SRR4063790_GSM2291994 RIP-Seq 551.0 MB
SRR4063791_GSM2291995 RIP-Seq 770.0 MB
SRR4063792_GSM2291995 RIP-Seq 337.0 MB

Potentially related datasets 5

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
MSV000079668 MASSIVE · MassIVE No title in the index
MSV000079669 MASSIVE · MassIVE No title in the index
PXD004000 PXD · PRIDE No title in the index
PXD003999 PXD · PRIDE No title in the index
GSE86035 GSE · GEO GEO ↗ SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

Analysis pipelines 1

Pipeline Assay Steps Dataset
GSE86035 eCLIP Data Processing geo_data_processing eCLIP 32 GSE86035
Funding 5 grants
Grant Funder
R01 HG004659 NHGRI NIH HHS (United States)
P30 CA023100 NCI NIH HHS (United States)
T32 GM008666 NIGMS NIH HHS (United States)
U54 HG007005 NHGRI NIH HHS (United States)
R01 NS075449 NINDS NIH HHS (United States)