An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and associated RNA species identified by Northern blot, RT-PCR, affinity labeling, sequencing, or microarray analysis.

Publication

Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs.

Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM

Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) ... [more]

J Proteome Res Jan. 05, 2024; 23(1);149-160 [Pubmed: 38043095]

Throughput

High Throughput

Additional Notes

24 hrs PI
viral RNAs used to isolate proteins which were then identified through mass spec

Related interactions

Interaction	Experimental Evidence Code	Dataset	Throughput	Score	Curated By	Notes
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Armstrong SD (2024)	High	-	BioGRID	3730801
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Chen X (2024)	High	-	BioGRID	3753598
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Chen Z (2021)	High	-	BioGRID	2893656
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Ciccosanti F (2021)	High	-	BioGRID	-
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Min YQ (2023)	High	-	BioGRID	3739635
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Ren J (2024)	High	-	BioGRID	-
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Somasekharan SP (2021)	High	-	BioGRID	3325637
N YBX1	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Yang Z (2024)	High	-	BioGRID	-
N YBX1	Affinity Capture-RNA Affinity Capture-RNA An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and associated RNA species identified by Northern blot, RT-PCR, affinity labeling, sequencing, or microarray analysis.	Whitworth IT (2023)	High	-	BioGRID	3559067
N YBX1	Affinity Capture-Western Affinity Capture-Western An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.	Chen X (2024)	Low	-	BioGRID	-
N YBX1	Co-localization Co-localization Interaction inferred from two proteins that co-localize in the cell by indirect immunofluorescence only when in addition, if one gene is deleted, the other protein becomes mis-localized. Also includes co-dependent association of proteins with promoter DNA in chromatin immunoprecipitation experiments.	Chen X (2024)	Low	-	BioGRID	-
N YBX1	Protein-RNA Protein-RNA An interaction is detected between and protein and an RNA in vitro.	Jiang L (2023)	High	-	BioGRID	3748993
N YBX1	Proximity Label-MS Proximity Label-MS An interaction is inferred when a bait-enzyme fusion protein selectively modifies a vicinal protein with a diffusible reactive product, followed by affinity capture of the modified protein and identification by mass spectrometric methods.	Meyers JM (2021)	High	-	BioGRID	3577580

Curated By

BioGRID

Interaction Summary

N

YBX1

Gene Ontology Biological Process

Gene Ontology Molecular Function

Gene Ontology Cellular Component