Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AP-MS analysis of IFIT1 and 5 interactions in interferon-stimulated human cells

ABSTRACT: This project sought to identify interactions of InterFeron Induced Tetratricopeptide repeat (IFIT) proteins 1 ad 5 in human cells. SILAC-labelled human HEK293T cells were transfected with FLAG-tagged human IFIT1 and IFIT5 pulldowns. After transfection, the cells were treated with human interferon 2-alpha and FLAG-immunoprecipitations performed to identify IFIT-binding proteins. Cells were then subject to LS/MS-MS analysis on a Orbitrap Fusion and data analysed in Maxquant v1.5.7.4

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hek-293et Cell

SUBMITTER: Edward Emmott

LAB HEAD: Trevor Sweeney

PROVIDER: PXD007584 | Pride | 2018-03-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	010216HEK293TIFIT.zip	Other
	Howtoviewspectra.txt	Txt
	Humanuniprot-proteome_UP000005640dl20160919.fasta	Fasta
	IFIT_R1.raw	Raw
	IFIT_R2.raw	Raw

Items per page:

1 - 5 of 6

Publications

IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA.

Fleith Renata C RC Mears Harriet V HV Leong Xin Yun XY Sanford Thomas J TJ Emmott Edward E Graham Stephen C SC Mansur Daniel S DS Sweeney Trevor R TR

Nucleic acids research 20180601 10

Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed during the cell-intrinsic immune response to viral infection. IFIT1 inhibits translation by binding directly to the 5' end of foreign RNAs, particularly those with non-self cap structures, precluding the recruitment of the cap-binding eukaryotic translation initiation factor 4F and ribosome recruitment. The presence of IFIT1 imposes a requirement on viruses that replicate in the cytoplasm to maintain mechanis ...[more]

PMID: 29554348

Similar Datasets

Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins

Project description:Evaluating the identity of ubiquitinated and ubiquitin-associated proteins tandem co-purifying non-covalently with wild-type (17 glutamine) human Huntingtin fragment, amino acids 1-502 C-terminally tagged with the HA peptide epitope, basally expressed from the CMV promoter within vector pcDNA3.1 transiently transfected into striatal precursor cell line St14A, significantly elevated above cells transfected with empty pcDNA3.1 vector negative control, in cells co-transfected with human FLAG-ubiquitin.

2024-07-31 | PXD053980 | Pride

Interactome analysis of ACAD11 in HEK293 cells

Project description:Affinity purification - mass spectrometry analysis of N-terminally FLAG-tagged ACAD11 transietly expressed in HEK293 cells.

2019-03-14 | PXD010788 | Pride

The hypoxia-inducible transcription factor ZNF395 is controlled by I-kappaB kinase and activates genes involved in the innate immune response and cancer

Project description:Activation of the hypoxia inducible transcription factor HIF-alpha and the NF-kappaB pathway promotes inflammation mediated tumor progression. The cellular transcription factor ZNF395 was repeatedly found over expressed in various human cancers and particularly in response to hypoxia, implying a functional relevance. To understand the biological activity of ZNF395, we identified target genes of ZNF395 by a genome-wide expression screen. Induced ZNF395 expression let to up-regulation of a subset of interferon (IFN)-responsive genes such as IFIT1/ISG56 and IFI44 as well as genes known to be involved in cancer progression including MEF2C and MACC1. ZNF395 requires its DNA binding domain and the two IFN-sensitive-response elements within the IFIT1/ISG56 promoter to activate. We provide evidence that IkBa kinase-mediated phosphorylation is required to allow activation of transcription by ZNF395 but simultaneously accelerates it for proteolytic degradation to keep the activity of ZNF395 transient and weak. We further confirm that ZNF395 is induced by hypoxia. Thus, two crucial pathways contributing to cancers progression, i.e. hypoxia and inflammation cooperate in activation of ZNF395 at the level of transcription and post-translational modification. Increased amounts of transcriptional active ZNF395 in cancers may support carcinogenesis by activating its target genes associated with the innate immune response and cancer. 4 samples treated with doxycycline-induced ZNF395 were compared to 4 untreated controls

2014-03-01 | E-GEOD-44327 | biostudies-arrayexpress

RNA immunoprecipitation to identify RHA-binding transcripts in HEK293 cells

Project description:Given that RHA regulates translation by binding a PCE located at the 5’ UTR of the target transcripts a genome-wide screen was performed to identify mRNAs that bind RHA in vivo. The results from four experiments with samples obtained in four independent RNA immunoprecipitations identified 375 transcripts that co-immunoprecipitate with FLAG RHA. Since N-terminal FLAG tagged RHA specifically co-immunoprecipitates PCE-containing mRNAs HEK293 cells were transfected with a CMV-FLAG-RHA construct. Cytoplasmic lysates were immunoprecipitated with anti-FLAG beads. RNA was extracted from the immunoprecipitate and used to probe a human Agilent expression arrays. An immunoprecipitation with cells transfected with empty FLAG plasmid was used as negative control.

2010-08-19 | E-GEOD-23688 | biostudies-arrayexpress

Real-time quantitative PCR analysis of miRNA expression in human melanoma MMRU cell line after Sox4 knockdown

Project description:We used Applied Biological Materials (ABM)’s miRNA profiling platform to quantitate expression of miRNAs in a human melanoma cell line (MMRU) in Sox4 siRNA treated cells (siSox4) compared with the control siRNA treated cells (siCTR) or after overexpression of Flag-Dicer in Sox4 knockdown cells (siSox4=F-Dicer) compared with control cells. 72 hours after transfection, Total RNA from siCTR, siCTR+empty Flag-vector (CTR), siSox4 or siSox4+-F-Dicer transfected MMRU cells was prepared with Qiazol extraction followed by Poly-A Tailing reactions and miRNA cDNA synthesis (ABM C204). Real-time qPCR reactions and instrumental analysis was performed using Roche LightCycler480.

2012-05-31 | E-GEOD-36715 | biostudies-arrayexpress

Aberrant BAF57 Signaling Facilitates Pro-metastatic Phenotypes

Project description:BAF57, a component of the SWI/SNF chromatin remodeling complex conglomerate,modulates androgen receptor activity to promote prostate cancer. However the molecular consequences of tumor associated BAF57 elevation have remianed undefined in advanced disease such as castration resistant prostate cancer and/or metastasis Global gene expression analyses were performed in models mimicking tumor-associated BAF57 expression. These analyses demonstrated that BAF57 deregulation circumvented androgen mediated signaling and elicited upregulation of M-NM-12 integrin and other migration and metastasis related gene signatures. LNCaP cells were transfected to overexpress BAF57 and validated for BAF57 transcript induction. Appropriate vector control transfected cells were also used. Vector and BAF57 transfected samples were treated with 0.1% vehicle with a 1nM DHT vector control. Gene expression analyses were performed on biological duplicates.

2013-06-04 | E-GEOD-44418 | biostudies-arrayexpress

Identification of proteins that interacted with ESCO2

Project description:The Flag–ESCO2 plasmids were transfected into HEK293T cells, Flag–ESCO2 complexes were co-immunoprecipitated using an anti-Flag antibody. The Flag–ESCO2 complexes was separated using SDS PAGE, and then was identified by combining silver staining and mass spectrometry.

2021-09-10 | PXD023527 | Pride

Screening of host proteins interacting with African swine fever virus MGF360-9L

Project description:To identify the potential host protein binding to African swine fever virus MGF360-9L, the 3 × FLAG tag MGF360-9L plasmid and empty FLAG were transfected into PK-15 cells for co-immunoprecipitation and LC-MS analysis. The cell lysates were immunoprecipitated using anti-FLAG antibody. Immunoprecipitation samples of cells transfected with empty FLAG were used as negative controls to eliminate non-specific interactions. LC-MS identified the interaction between MGF360-9L and PK-15 cell proteome. The final MGF360-9L binding protein data eliminated the nonspecific interaction through empty FLAG control. The interactions that remained were analyzed by significance analysis of interactome. Finally, 268 cellular proteins interacting with MGF360-9L were identified.

2022-02-17 | PXD027260 | Pride

Mass spectrometry identification data for the interactomics of SMYD3

Project description:SMYD3, a member of the SET and MYND domain-containing (SMYD) family, is a histone methyltransferase (HMT) and transcription factor that plays an important role in transcriptional regulation in human carcinogenesis.In an effort to better understanding the mechanistic role of SMYD3, affinity purification and mass spectrometry assays were used to identify proteins associated with SMYD3 in vivo. In these experiments, FLAG-tagged SMYD3 or an empty vector was stably expressed in LM3 cells. Cellular extracts were prepared and subjected to affinity purification using an anti-FLAG affinity gel. Immunocomplexed proteins were separated using SDS–PAGE and silver stained. Immunoprecipitated proteins in specific bands in comparison to the vector were gel extracted, trypsin digested and identified using liquid chromatography tandem mass spectrometry.

2023-03-11 | PXD031971 | Pride

Identification of serine/threonine-specific phosphatases that dephosphorylate the co-chaperone BAG3 to mediate protein-protein interactions

Project description:Targeted phosphoproteomics of the human flag-tagged co-chaperone BAG3 to quantify phosphosite regulation by PP5.

2024-11-05 | PXD050035 | Pride