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Identification of c-Rel and RelA binding regions in stimulated EL4 cells

ABSTRACT: c-Rel and RelA are members of the NF-kappaB family of transcription factors. They both have important roles in T cell activation. To discover where in the genome c-Rel and RelA bind and hence which genes they may directly target, we used ChIP-chip with EL4 cells stimulated with phorbol ester (PMA) and Ionomycin. We have identified regions in EL4 cells (background strain: C57BL/6N) activated for 2h or 8h by PMA and Ionomycin, that bind the transcription factors c-Rel and RelA.

ORGANISM(S): Mus musculus

PROVIDER: GSE42818 | GEO | 2013/12/29

SECONDARY ACCESSION(S): PRJNA183490

REPOSITORIES: GEO

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Identification of c-Rel and RelA binding regions in stimulated EL4 cells

Project description:c-Rel and RelA are members of the NF-kappaB family of transcription factors. They both have important roles in T cell activation. To discover where in the genome c-Rel and RelA bind and hence which genes they may directly target, we used ChIP-chip with EL4 cells stimulated with phorbol ester (PMA) and Ionomycin. We have identified regions in EL4 cells (background strain: C57BL/6N) activated for 2h or 8h by PMA and Ionomycin, that bind the transcription factors c-Rel and RelA. Immunoprecipitated samples from EL4 cells stimulated with PMA and ionomycin for 2 h and 8 h with antibodies against RelA or c-Rel respectively were used for ChIP-on-chip experiments. In addition, samples from total input and mock immunoprecipitation were used as controls. Biological triplicates were used.

2013-12-29 | E-GEOD-42818 | biostudies-arrayexpress

Transcriptional profiling of NF-kB's Rel and RelA proteins

Project description:Rel and RelA proteins were stably expressed in the chicken DT40 pre-B cell line and analyzed by transcription profiling to identify transformation-impacting genes regulated by NF-kB’s oncogenic v-Rel and c-Rel proteins. This analysis uncovered both common and differential gene expression profiles in cells expressing Rel vs. RelA proteins, and revealed that Rel protein expression can lead to gene-specific transcriptional repression, as seen for key B-cell receptor (BCR) components and signaling molecules like B-cell linker (BLNK), the B-cell adaptor for PI3K (BCAP) and Igλ. These were also downregulated in cells expressing a transformation-competent chimeric RelA/v-Rel protein, suggesting a correlation with the capacity of Rel proteins to transform lymphocytes. DNA binding, ChIP and transformation assays indicate that downregulation of BLNK and BCAP is an important contributing factor to the malignant transformation of lymphocytes by Rel and suggest that gene repression may be as important as transcriptional activation for the transforming activity of Rel proteins. Keywords: Comparative transcriptional profiling

2008-02-14 | GSE9544 | GEO

Expression analysis to identify inducible genes in T cells

Project description:Expression microarrays were employed to identify genes induced by phorbol ester and ionomycin stimulation of EL4 cells. EL4 is a murine T cell line. To identify induced genes that were independent of new protein synthesis cells were pre-treated with cycloheximide. This expression study was used in conjunction with histone acetylation ChIP-chip to determine if inducible genes had a specific histone acetylation profile and whether the acetylation profile differed for genes with different kinetics of induction. Keywords: drug treatment comparison Cells were pre-treated with either DMSO or cylcoheximide in DMSO, then they were stimulated with PMA and Ionomycin for either 0h or 4h. 3 biological replicates were used for each treatment-stimulation combination.

2010-04-09 | E-GEOD-13278 | biostudies-arrayexpress

Analysis of gene expression in the rel- + relA+ and rel- + relAE335Q strains of Synechococcus elongatus PCC7942 with RNA sequencing during constant light conditions

Project description:We investigated the role of the basal levels of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using the rel- + relA+ and rel- + relAE335Q strains and show that basal levels of ppGpp are required for regulation of global transcription in light.

2017-12-12 | GSE103463 | GEO

NF-κB transcription factors RelA and c-Rel selectively control CD4+ T-cell function in multiple sclerosis and cancer [bulk_mouse]

Project description:The outcome of cancer and autoimmunity is dictated by the recruitment and effector functions of CD4+ conventional T cells (Tconv cells). The NF-kappaB (NF-κB) family of transcription factors is implicated in different aspects of Tconv cell biology, but the cell-autonomous roles of NF-κB subunits are elusive. Here, we explored the contributions of canonical RelA and c-Rel subunits to Tconv function in health and disease. We found that RelA, rather than c-Rel, shaped the transcriptome of mouse and human Tconv cells at steady-state and was required for Tconv polarization toward the TH17 lineage in vitro. RelA-deficient mice were fully protected against neuro-inflammation in a mouse model of multiple sclerosis (MS), because of defective transition to a pathogenic TH17 gene expression program. In contrast, Tconv-restricted ablation of c-Rel, but not RelA, impaired their function in the microenvironment of transplanted tumors, resulting in enhanced cancer burden. c-Rel in Tconv cells was required for the response to PD-1-blockade therapy, and a c-Rel-dependent gene signature was correlated with better response and prognosis in anti-PD-1-treated patients. Our data demonstrate a division of labor between different subunits of the NF-κB pathway, paving the way for subunit-targeted immunotherapies.

2024-03-28 | GSE239700 | GEO

NF-κB transcription factors RelA and c-Rel selectively control CD4+ T-cell function in multiple sclerosis and cancer [sc_rna]

2024-03-28 | GSE239703 | GEO

NF-κB transcription factors RelA and c-Rel selectively control CD4+ T-cell function in multiple sclerosis and cancer [bulk_human]

2024-03-28 | GSE239698 | GEO

Analysis of gene expression in the rel- relA+ and the rel- relAE335Q strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

Project description:We investigated the role of basal ppGpp levels in Synechococcus elongatus PCC7942 in adaptation to darkness. We performed RNA-seq experiments using the rel- relA+ and the rel- relAE335Q strain at dusk and during exposure to 12 h of darkness. We show that basal ppGpp levels is not sufficient for restoration of appropriate transcriptional shutdown in response to darkness.

2017-12-12 | GSE105774 | GEO

Expression analysis to identify inducible genes in T cells

2009-06-01 | GSE13278 | GEO

Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution (RNA-Seq)

Project description:Adaptive immunity and the five vertebrate NF-kB/Rel family members first appeared in cartilaginous fish, suggesting that NF-kB family expansion allowed the acquisition of new functions to regulate adaptive immune responses. Transcriptome profiling revealed that, even in macrophages, the NF-kB family member, c-Rel, most potently regulates a cytokine gene linked to adaptive immunity, Il12b, with limiting roles at key regulators of innate immunity. Neofunctionalization of c-Rel to regulate Il12b depends on its unique DNA-binding properties, which we examined using structural, biochemical, functional, and genomic approaches. Among our findings was functional c-Rel homodimer binding to motifs with little resemblance to canonical NF-kB motifs. To determine whether c-Rel’s unique binding properties drove c-Rel-RelA divergence, we compared binding properties in various vertebrate species. c-Rel-RelA binding properties diverged in mammals and amphibians but were comparable in earlier vertebrates, suggesting that divergent DNA binding emerged relatively late during vertebrate evolution to support increasing complexity of adaptive immune regulation.

2024-03-11 | GSE243011 | GEO

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