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Human Ku70 WT AP-MS - Mapping the Ku interactome using proximity-dependent biotin identification in human cells

ABSTRACT: Affinity purification coupled to mass spectrometry is often used as a complementary technique to BioID experiments, and the data presented here complements another project. To infer processes involving Ku70, we used AP-MS to identify candidate proteins that may interact with Ku70 and compared these results to those acquired using BioID with Ku70.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Sanna Abbasi

LAB HEAD: Caroline Schild-Poulter

PROVIDER: PXD010930 | Pride | 2019-01-03

REPOSITORIES: Pride

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			Action	DRS
	APMS_Ku70_IP_Rep_1.raw	Raw
	APMS_Ku70_IP_Rep_2.raw	Raw
	APMS_Ku70_IP_Rep_3.raw	Raw
	APMS_Mouse_IgG_Control.raw	Raw
	Ku70_APMS_IP_Rep_1.mzid.gz	Mzid

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Publications

Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells.

Abbasi Sanna S Schild-Poulter Caroline C

Journal of proteome research 20190114 3

The Ku heterodimer, composed of Ku70 and Ku80, is best characterized for its role in repairing double-stranded DNA breaks but is also known to participate in other regulatory processes. Despite our understanding of Ku protein interplay during DNA repair, the extent of Ku's protein interactions in other processes has never been fully determined. Using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS) with wild-type Ku70, we identified ...[more]

PMID: 30585729

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HEK293 Ku70 WT BioID - Mapping the Ku interactome using proximity-dependent biotin identification in human cells

Project description:We conducted proximity-dependent biotin identification (BioID) using wild-type Ku70 in HEK293 cells. Ku70 is part of a protein complex known as Ku, which is involved in a variety of functions throughout the cell. By identifying candidate protein interactors, we can infer new cellular processes that may involve the Ku complex.

2019-01-03 | PXD010931 | Pride

Generation and Characterization of a Conditional Ku70 Knockout Cell Line

Project description:In this study we characterize and investigate the effect of the loss of Ku70 protein in a conditional Ku70 knockout TREx-293 cell system. Loss of Ku70 protein levels was directly correlated with a loss of cell viability, supporting the observation that Ku performs an essential role in human cells. Interestingly, critical loss of average telomere length was not observed in Ku70 knockouts generated. Global quantitative proteomic analysis of whole cell extracts from Ku70 knockouts following depletion of Ku70 may indicate that Ku’s essential role in humans is not at telomeres, but a non-canonical role which is not yet fully understood.

2023-07-27 | PXD036297 | Pride

Transcriptome of Yarrowia lipolytica strain E150 delta-Ku70 on glucose

Project description:batch culture of Yarrowia lipolytica strain E150 delta-Ku70

2012-12-31 | E-MTAB-940 | biostudies-arrayexpress

Ku80/Ku70 complex associated RNA in HEK293T cells

Project description:We report the Ku80/Ku70 complex associated RNA in HEK293T cells using RNA-seq following PAR-Clip.

2024-04-09 | GSE219220 | GEO

Non-classical action of Ku70 promotes Treg suppressive function through a FOXP3-dependent mechanism in lung adenocarcinoma

Project description:To explore the role of Ku70 in Treg cell biology, we isolated conventional T cells (Tconv) and regulatory T cells (Treg) from Foxp3Yfp-cre mice and performed Ku70 ChIP-seq. Furthermore, to investigate the impact of Ku70 deficiency on Foxp3 binding patterns, we sorted Treg cells from Foxp3Cre (WT) and Xrcc6fl/fl;Foxp3Cre (KO) mice and conducted Foxp3 ChIP-seq. These analyses revealed that Ku70 forms a complex with FOXP3, which supports FOXP3 transcriptional activity.

2024-11-04 | GSE278950 | GEO

Critical residues in the Ku70 von Willebrand A domain mediate Ku interaction with the LigIV-XRCC4 complex in non-homologous end-joining

Project description:Interrogated the Ku interactome in response to DNA damage with wildtype and mutant Ku70

2024-08-16 | PXD047914 | Pride

HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer’s disease pathology

Project description:DNA damage is increased in Alzheimer’s disease (AD), while the underlying mechanisms are unknown. Here, we employ comprehensive phosphoproteome analysis, and identify abnormal phosphorylation of 70 kDa subunit of Ku antigen (Ku70) at Ser77/78, which prevents Ku70-DNA interaction, in human AD postmortem brains. The abnormal phosphorylation inhibits accumulation of Ku70 to the foci of DNA double strand break (DSB), impairs DNA damage repair and eventually causes transcriptional repression-induced atypical cell death (TRIAD). Cells under TRIAD necrosis reveal senescence phenotypes. Extracellular high mobility group box 1 (HMGB1) protein, which is released from necrotic or hyper-activated neurons in AD, binds to toll-like receptor 4 (TLR4) of neighboring neurons, and activates protein kinase C alpha (PKCα) that executes Ku70 phosphorylation at Ser77/78. Administration of human anti-HMGB1 antibody to post-symptomatic AD model mice decreases neuronal DSBs, suppresses secondary TRIAD necrosis of neurons, prevents escalation of neurodegeneration, and ameliorates cognitive symptoms. TRIAD shares multiple features with senescence. These results newly unravel the HMGB1-Ku70 axis that accounts for the increase of neuronal DNA damage and secondary enhancement of TRIAD, the cell death phenotype of senescence, in AD.

2022-02-15 | PXD028089 | Pride

Screening for Ku70 phosphoS155-dependent proximal proteins

Project description:To identify Ku70 phosphoS155-specific proximal protein interactors, we used the proximity-dependent biotin identification (BioID2) technique with wild-type Ku70, Ku70 S155A, and Ku70 S155D in the doxycycline-inducible T-REx 293 cell line and compared the different datasets.

2023-05-10 | PXD025581 | Pride

Ku70/HP1g are presented at the KCl induced acutely activated enhancers [ChIP-seq]

Project description:Ku70/HP1g are serving as the marker for the KCl induced acutely enhancer activation in cortical neurons.

2022-08-04 | GSE185648 | GEO

Ku70 Is a Novel Cytosolic DNA Sensor that Induces Type-III Rather than Type-I IFN

Project description:Cytosolic foreign DNA is detected by pattern recognition receptors and mainly induces Type-I IFN production. We found that transfection of different types of DNA into various untreated cells induces Type-III IFN (IFN-lambda1) rather than Type-I IFN, indicating the presence of uncharacterized DNA sensor(s). A pull-down assay using cytosolic proteins identified that Ku70 and Ku80 are the DNA binding proteins. The knockdown studies and the reporter assay revealed that Ku70 is a novel DNA sensor inducing the IFN-lambda1 activation. The functional analysis of IFNL1 promoter revealed that PRDI and ISRE sites are predominantly involved in the DNA-mediated IFNL1 activation. A pull-down assay using nuclear proteins demonstrated that the IFN-lambda1 induction is associated with the activation of IRF-1 and IRF-7. This is the first report of a specific induction of Type-III rather than Type-I IFN and of Ku70 that plays a key role in the activation of innate immune responses. To identify the nature of the anti-HIV mediators associated with the empty vector transfection, we compared patterns of gene expression between untreated and pCMV9-transfected HEK293 cells, using DNA microarray analysis.

2011-01-29 | E-GEOD-26944 | biostudies-arrayexpress

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