Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA97943 | ENA |
REPOSITORIES: ENA
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Project description:Semen-derived extracellular vesicles (SEVs) have been shown to inhibit the human immunodeficiency virus type 1 (HIV-1) LTR transactivation through the blockade of the interaction of transactivator of transcription (Tat) and host transcription factors NF-kB and Sp1 (Tat•NF-ᴋB p65 and Tat•Sp1). The ability of SEVs to regulate the activities of transcription factors suggests that SEVs may contain transcription activators and repressors. In this present study, we used orthogonal SEVs-based screens, including pull-downs, mobility shift assays, and electrophoretic protein binding assays coupled with mass spectrometry (MS) to identify host proteins in SEVs that interact with the different transcription factors (SEVs•Tat and SEVs•NF-ᴋB p65 binding proteins). Protein network analysis performed on SEVs•Tat and SEVs•NF-ᴋB p65 complexes revealed interactome networks that associate with 7SK snRNA binding, mRNA Processing, P-TEFb complex, NELF complex. Additionally, Pathway enrichment analyses of SEVs•Tat and SEVs•NF-ᴋB p65 complexes identifies biological functions involved in initiation of transcription and translation elongation at the HIV LTR, formation of HIV and RNA Pol II elongation complexes, protein, nucleic acid, and chromatin binding, as well as chromatin assembly and disassembly. Finally, integrative analysis of SEVs•Tat and SEVs•NF-ᴋB p65 binding proteins identifies four proteins (AKAP9, ARHGEF28, INTS1, BRD2) to be common to both complexes. Immunoprecipitation assays suggest that SEVs-associated BRD2 and NELFB bind HIV Tat. The identification of extracellular interactome of Tat and NF-κB p65 in HIV transcription paves the way for the rational design of novel inhibitors of HIV transcription, with potential for therapeutic targeting.
2026-06-15 | PXD062816 | Pride
Project description:Semen-derived extracellular vesicles (SEVs) have been shown to inhibit the human immunodeficiency virus type 1 (HIV-1) LTR transactivation through the blockade of the interaction of transactivator of transcription (Tat) and host transcription factors NF-kB and Sp1 (Tat•NF-ᴋB p65 and Tat•Sp1). The ability of SEVs to regulate the activities of transcription factors suggests that SEVs may contain transcription activators and repressors. In this present study, we used orthogonal SEVs-based screens, including pull-downs, mobility shift assays, and electrophoretic protein binding assays coupled with mass spectrometry (MS) to identify host proteins in SEVs that interact with the different transcription factors (SEVs•Tat and SEVs•NF-ᴋB p65 binding proteins). Protein network analysis performed on SEVs•Tat and SEVs•NF-ᴋB p65 complexes revealed interactome networks that associate with 7SK snRNA binding, mRNA Processing, P-TEFb complex, NELF complex. Additionally, Pathway enrichment analyses of SEVs•Tat and SEVs•NF-ᴋB p65 complexes identifies biological functions involved in initiation of transcription and translation elongation at the HIV LTR, formation of HIV and RNA Pol II elongation complexes, protein, nucleic acid, and chromatin binding, as well as chromatin assembly and disassembly. Finally, integrative analysis of SEVs•Tat and SEVs•NF-ᴋB p65 binding proteins identifies four proteins (AKAP9, ARHGEF28, INTS1, BRD2) to be common to both complexes. Immunoprecipitation assays suggest that SEVs-associated BRD2 and NELFB bind HIV Tat. The identification of extracellular interactome of Tat and NF-κB p65 in HIV transcription paves the way for the rational design of novel inhibitors of HIV transcription, with potential for therapeutic targeting.
2026-06-15 | PXD062784 | Pride
Project description:NF-kB p65 ChIPseq revealed differential binding of p65 in Treg vs Tconv upon TCR stimulation
2017-09-13 | GSE99319 | GEO
Project description:The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-?B subunit p65 in relation to active enhancers and promoters of transcribed genes by ChIP-seq experiments. Out of 35,000 active enhancer regions, 410 H3K4me1-positive enhancers show interleukin (IL)-1-induced H3K27ac and p65 binding. Inhibition of TAK1, IKK2 or depletion of p65 blocked inducible enhancer activation and gene expression. As exemplified by the CXC chemokine cluster located on chromosome 4, the TAK1-p65 pathway also regulates the recruitment kinetics of the histone acetyltransferase CBP, of NF-?B p50 and of AP-1 transcription factors to both, promoters and enhancers. This study provides a high resolution view of epigenetic changes occurring during the IL-1 response and allows the first genome-wide identification of a novel class of inducible p65 NF-?B-dependent enhancers in epithelial cells. RNA-seq of KB cells either untreated or treated with IL-1 alpha
2014-12-16 | E-GEOD-64185 | biostudies-arrayexpress
Project description:The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-κB subunit p65 in relation to active enhancers and promoters of transcribed genes by ChIP-seq experiments. Out of 35,000 active enhancer regions, 410 H3K4me1-positive enhancers show interleukin (IL)-1-induced H3K27ac and p65 binding. Inhibition of TAK1, IKK2 or depletion of p65 blocked inducible enhancer activation and gene expression. As exemplified by the CXC chemokine cluster located on chromosome 4, the TAK1-p65 pathway also regulates the recruitment kinetics of the histone acetyltransferase CBP, of NF-κB p50 and of AP-1 transcription factors to both, promoters and enhancers. This study provides a high resolution view of epigenetic changes occurring during the IL-1 response and allows the first genome-wide identification of a novel class of inducible p65 NF-κB-dependent enhancers in epithelial cells. ChIP-seq in KB cells with 5 different antibodies under different treatment conditions
2014-12-16 | E-GEOD-64223 | biostudies-arrayexpress
Project description:Metastasis suppressor 1 (MTSS1) is a 755 amino acid protein found in the cell cytoplasm which binds to actin and promotes cytoskeleton organization and is a known suppressor of lung adenocarcinoma metastasis This study demonstrated that preservation of MTSS1 protein expression in lung adenocarcinoma was associated with a 20% 5-year survival advantage in patients. Furthermore, overexpression of MTSS1 was found to reduce metastasis and disease progression in an in-vivo orthotopic lung adenocarcinoma mouse model. Nuclear factor kappa B (NF-kB), an important nuclear transcription factor, has been shown to be constitutively active in lung adenocarcinoma and strongly associated with the development of metastasis. The NF-kB RelA/p65 subunit is involved in NF-kB heterodimer formation and subsequent nuclear translocation leading to activation of NF-kB responsive gene transcription. Phosphorylation and acetylation of p65 are critical post-translational modifications required for NF-kB activation. In this study, we demonstrate that MTSS1 expression leads to decreased NF-κB mediated gene transcription through inhibition of p65 phosphorylation. These findings uncover a novel mechanism through which MTSS1 may regulate lung adenocarcinoma metastasis by impairment of NF-κB regulated gene transcription.
2024-07-07 | GSE179644 | GEO
Project description:T cell activation following antigen binding to the T cell receptor (TCR) involves the mobilization of intracellular calcium (Ca2+) to activate the key transcription factors NFAT and NF-κB. The mechanism of NFAT activation by Ca2+ has been determined; however, the role of Ca2+ in controlling NF-κB signaling is poorly understood and the source of Ca2+ required for NF-κB activation is unknown. We demonstrate that TCR- but not TNF- induced NF-κB signaling upstream of IκB kinase (IKK) activation absolutely requires the influx of extracellular Ca2+ via STIM1-dependent CRAC/Orai channels. We further show that Ca2+ influx controls phosphorylation of the NF-κB protein p65 on Ser536 and that this post- translational modification controls its nuclear localization and transcriptional activation. Notably our data reveal that this role for Ca2+ is entirely separate from its upstream control of IκBα degradation, thereby identifying a novel Ca2+- dependent distal step in TCR-induced NF-κB activation. Finally, we demonstrate that this control of distal signaling occurs via Ca2+-dependent PKCk-mediated phosphorylation of p65. Thus, we establish the source of Ca2+ required for TCR induced NF-kB activation and we define a new distal Ca2+-dependent checkpoint in TCR-induced NF-kB signaling that has broad implications for the control of immune cell development and T cell functional specificity. 3 treatments were analyzed, with biological replicates for each treatment. In addition, three timepoints (1 hour, 4 hour, and 8 hour) were examined for each treatment, as well as an untreated control. In total 19 samples were analyzed
2016-01-14 | E-GEOD-76804 | biostudies-arrayexpress
Project description:NF-kB has been linked to doxorubicin-based chemotherapy resistance in breast cancer patients. NF-kB nuclear translocation and DNA binding in doxorubicin treated-breast cancer cells have been extensively examined, however its functional consequences in terms the spectrum of NF-kB -dependent genes expressed and, thus, the impact on tumour cell behaviour are unclear. We hypothesized that NF-kB gene expression profile induced by doxorubicin might be different among breast cancer cells and tumors. Doxorubicin treatment in the p53-mutated MDA-MB-231 cells resulted in NF-kB driven-gene transcription demonstrated by gene expression microarrays. Selected genes (ICAM-1, CXCL1, IL8) related with invasion, metastasis and chemoresistance expression were confirmed by RT-PCR in a subset of additional doxorubicin-treated cells and fresh primary human breast tumors. In both systems, p53-deficient background correlated with the activation of these NF-kB targeted genes. Overexpression of p53WT in the mutant p53 MDA-MB-231 cells impaired NF-kB driven transcription induced by doxorubicin. Moreover, tumors with a p53 deficient background and nuclear NF-kB /p65 expression correlated with reduced disease free-survival. This study supports that tumor molecular profiles for doxorubicin driven NF-kB-response are likely to exist. A link between p53 deficiency and the presence of active transcriptionally NF-kB could favour an aggressive behaviour and might have implications for doxorubicin-based chemotherapy in breast tumors exhibiting aberrant p53 activity 12 samples were analyzed: controls (n=3); Doxorubicin treated (n=3); MLN120B treated (n=3); MLN120B + Doxorubicin treated (n=3)
2013-12-31 | E-GEOD-47013 | biostudies-arrayexpress
Project description:Nuclear factor kappaB (NF-kB) is a transcription factor that regulates various aspects of immune response, cell death and differentiation as well as cancer. In this study we introduce the Py-Im polyamide 1 that binds preferentially to the sequences 5'-WGGWWW-3' and 5' GGGWWW-3'. The compound is capable of binding to kB sites and reducing the expression of various NF-kB driven genes including IL6 and IL8 by qRT-PCR. Chromatin immunoprecipitation experiments demonstrate a reduction of p65 occupancy within the proximal promoters of those genes. Genome-wide expression analysis by RNA-seq compares the DNA-binding polyamide with the well-characterized NF-kB inhibitor PS1145, identifying overlaps and differences in affected gene groups and showing that both affect comparable numbers of TNFa inducible genes. Inhibition of NF-kB DNA binding via direct displacement of the transcription factor is a potential alternative to the existing antagonists. A549 cells were treated with either a Py-Im polyamide or PS1145, subsequently induced with TNFa and compared with the untreated TNFa induced and the basal state by RNAseq. The NF-kB binding motif was derived by ChIP-seq
2011-12-12 | E-GEOD-34329 | biostudies-arrayexpress
Project description:Purpose: In this study we employed unbiased, genome-wide techniques to investigate how inflammation-induced NF-kB activation by acute (LPS vs. saline) and chronic (high-fat diet vs. regular chow) environmental stimuli leads to circadian disruption. Methods: We performed ChIP-seq with antibodies directed against the p65 subunit of NF-kB, CLOCK, BMAL1, H3K27Ac and RNA Poll II in livers from mice treated with LPS or saline. ChIP-seq analysis was also performed in livers from mice that were fed high-fat diet for 4 weeks or regular chow. In addition, we performed ChIP-seq with BMAL1 in mouse embryonic fibroblast deficient in p65. Results: Induction of NF-kB reconfigures the genome-wide position of core clock transcription factors. Acute (i.e. LPS) and chronic (e.g. high-fat diet) inflammation-induced NF-kB re-localizes components of the forward limb of clock (CLOCK/BMAL1) to sites convergent with NF-kB and acetylated H3K27 and enriched in RNA POL II in liver. In addition, NF-kB activation leads to higher p65 binding specific to E-box elements within the negative limb of the clock with both acute and chronic stimuli. Conclusions: Our findings cast new light on NF-kB as a pivotal genomic control node integrating metabolic inflammation and circadian systems at both the cellular and organismal levels. In particular, NF-kB directly regulates the expression of the negative limb of the clock while at the same time the clock activator TFs CLOCK/BMAL1 co-localize with NF-kB at new sites to regulate transcription following inflammatory stimuli. In addition, our data indicate significant overlap between NF-kB activation following both acute and chronic inflammatory challenges in liver.
2018-11-20 | GSE117488 | GEO