Transcription Factor Binding in CD8+ DCs

A wild-type CD8⁺ dendritic cell line (MuTu1940) was established and cultured as described previously (22 (link),39 (link)). For ChIP-seq and ChIP-qPCR experiments, CD8⁺ dendritic cells (DCs) were treated for 90 min with 5 μg/ml of high molecular weight polyinosinic–polycytidylic acid (pIC, InvivoGen), 1 mM class B CpG oligonucleotide 1826 (CpG, InvivoGen) or 100 U/ml interferon-β (IFN-β, Millipore) or a combination of these ligands. The binding sites of IRF3, IRF5 and IRF9 were determined in DCs stimulated by pIC, CpG and IFN-β, respectively. The binding of cRel and Junb was determined in CpG-stimulated and unstimulated DCs. For gene expression qPCR experiments, CD8⁺ DCs were treated for 1.5, 3, 6 or 12 h with 5 μg/ml pIC, 1 mM CpG or 100 U/ml IFN-β.

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Csumita M., Csermely A., Horvath A., Nagy G., Monori F., Göczi L., Orbea H.A., Reith W, & Széles L. (2019). Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5′ and 3′ flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion. Nucleic Acids Research, 48(2), 589-604.

Publication 2019

IFN-β

Binding sites Cd8 cells Cell line Chip Chip seq Cpg oligonucleotide Dendritic Dendritic cells Gene expression Interferon β Irf3 Irf5 Irf9 Ligands Polyinosinic polycytidylic acid

Corresponding Organization :

Other organizations : University of Debrecen, University of Lausanne, University of Geneva

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Variable analysis

independent variables

Treatment with 5 μg/ml of high molecular weight polyinosinic–polycytidylic acid (pIC, InvivoGen)
Treatment with 1 mM class B CpG oligonucleotide 1826 (CpG, InvivoGen)
Treatment with 100 U/ml interferon-β (IFN-β, Millipore)
Combination of pIC, CpG, and IFN-β treatments

dependent variables

Binding sites of IRF3, IRF5, and IRF9 in DCs
Binding of cRel and Junb in CpG-stimulated and unstimulated DCs
Gene expression of DCs treated with pIC, CpG, or IFN-β for 1.5, 3, 6, or 12 hours

control variables

CD8+ dendritic cell line (MuTu1940) cultured as described previously

controls

Unstimulated DCs (used as a control for CpG-stimulated DCs)

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