Comparison of the PU.1 transcriptional regulome and interactome in human and mouse dendritic cells
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ABSTRACT:
PROVIDER: PRJNA662951 | ENA |
REPOSITORIES: ENA
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Project description:Dendritic cells (DCs) are key immune modulators, and are able to mount immune responses or tolerance. DC differentiation and activation imply a plethora of molecular and cellular responses, including transcriptional changes. PU.1 is a highly expressed transcription factor in DCs, and coordinates relevant aspects of DC biology. Due to their role as immune regulators, DCs pose as a promising immunotherapy tool. However, some of their functional features, such as survival, activation or migration, are compromised due to the limitations to simulate in vitro the physiological DC differentiation process. A better knowledge of transcriptional programs would allow the identification of potential targets for manipulation with the aim of obtaining “qualified” DCs for immunotherapy purposes. Most of the current knowledge regarding DC biology derives from studies using mouse models, which not always find a parallel in human. In the present study we dissect the PU.1 transcriptional regulome and interactome in mouse and human DCs, in the steady state (ST) or LPS-activated. The PU.1 transcriptional regulome was identified by performing PU.1 chromatin immunoprecipitation followed by high throughput sequencing, and pairing these data with RNA-sequencing data. The PU.1 interactome was identified by performing PU.1 immunoprecipitation followed by mass spectrometry analysis. Our results portray PU.1 as a pivotal factor that plays an important role in the regulation of genes required for proper DC activation and function, and assures the repression of non-lineage genes. The interspecies differences between human and mouse DCs are surprisingly substantial, highlighting the need to study the biology of human DCs.
2020-11-19 | GSE157844 | GEO
Project description:Comparison of the PU.1 interactome and transcriptome in human and mouse dendritic cells
| PRJNA508394 | ENA
Project description:Mouse bone marrow derived dendritic cells were generated by culturing bone marrow cells at a density of 0.5x10E6 cells/ml in RPMI-1640 supplemented with 5% FCS, 1% Pen/Strep, 5microM 2-mercaptoethanol, 20ng/ml GM-CSF. At day 7 dendritic cells were stimulated or not with 500 ng/ml LPS, and collected at day 10.
2x10E8 cells were used to prepare whole cell extracts and to perform PU.1 immunoprecipitaion with PU.1 antibody (T-21 Santa Cruz). IgG was used as control.
2018-11-30 | MSV000083176 | MassIVE
Project description:Dendritic cells (DCs) are can be broadly divided into conventional (cDC) and plasmacytoid (pDC) subsets. Despite the importance of this lineage diversity, its genetic basis is not fully understood. ChIP-seq profiling of PU.1 binding sites in cDCs and pDCs revealed a key role for PU.1 in maintaining cDC identity.
2018-10-21 | GSE121544 | GEO
Project description:Dendritic cells (DCs) are can be broadly divided into conventional (cDC) and plasmacytoid (pDC) subsets. Despite the importance of this lineage diversity, its genetic basis is not fully understood. RNA-seq gene expression analysis of wild type (WT) and PU.1 transgenic mice revealed a key role for PU.1 in maintaining cDC identity.
2018-10-20 | GSE121446 | GEO
Project description:IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by pro-inflammatory signals such as interferon gamma. Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type, and in IRF8 and IRF1 mutant primary macrophages to systematically catalog all the genes bound by (cistromes) and transcriptionally activated (regulomes) by IRF8, IRF1, PU.1 and STAT1 including modulation of epigenetic histone marks. Of seven binding combinations identified, two (cluster 1: IRF8/IRF1/STAT1/PU.1; cluster 5: IRF1/STAT1/PU.1) were found to have a major role in controlling macrophage transcriptional programs both at basal level and following IFNγ activation. They direct expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and anti-microbial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immuno-deficiencies, and with loci associated for several inflammatory diseases in humans.
2016-03-07 | GSE77885 | GEO
Project description:IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by pro-inflammatory signals such as interferon gamma. Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type, and in IRF8 and IRF1 mutant primary macrophages to systematically catalog all the genes bound by (cistromes) and transcriptionally activated (regulomes) by IRF8, IRF1, PU.1 and STAT1 including modulation of epigenetic histone marks. Of seven binding combinations identified, two (cluster 1: IRF8/IRF1/STAT1/PU.1; cluster 5: IRF1/STAT1/PU.1) were found to have a major role in controlling macrophage transcriptional programs both at basal level and following IFNγ activation. They direct expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and anti-microbial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immuno-deficiencies, and with loci associated for several inflammatory diseases in humans.
2016-03-07 | GSE77884 | GEO
Project description:The Akirin (AKR) family of transcription cofactors are involved in the regulation of different biological processes such as immunity, interdigital regression, muscle and neural development throughout the metazoan. This model regulatory proteins do not have catalytic or DNA-binding capability and exert its regulatory function primarily through interacting proteins such as transcription factors, chromatin remodelers, and RNA-associated proteins. The application of regulomics and interactomics to key transcriptional regulators such as AKR is important to better understand their role in cell biology and epigenetic regulation of gene expression. In this study, we focused on the human AKR2 regulome and interactome to advance the knowledge on the function of this highly conserved regulatory cofactor. Based on the key function of AKR2 in cell interactome, regulome and epigenetic gene regulation, herein we hypothesized that metazoan evolved to have AKR2 functional complements and different mechanisms for AKR2-mediated epigenetic regulation of gene expression. To address this hypothesis, experiments were conducted to identify AKR2 gene/protein targets, functional complements after akr2 knockdown in human cells and to provide evidence of different mechanisms that may be involved in AKR2-mediated chromatin remodeling. The results revealed multiple AKR2 gene/protein targets, identified immune response genes as candidate AKR2 functional complements and showed that AKR2 is not only a link with chromatin remodelers, but also directly interacts with histone H3, thus providing new information on the function of this protein
2021-09-09 | PXD022073 | Pride
Project description:We applied a global approach using broad-range, next-generation sequecing to identify a repertoire of eosinophil-specific enhancers. H3K4me1, H3K4me3, H3K27ac and PU.1 ChIPseq data was paired with ATAC and gene expression data from bmEos. Transcription factor motif analysis revealed enrichment for PU.1 in eosinophil enhancers, and ChIP-seq confirmed PU.1 binding in enhancer of genes highly expressed in eosinophils. Comparison of identified PU.1-bound enhancers with 3 publically available myeloid datasets (neutrophils, bone marrow derived macrophages and immature granulocytes) revealed 25% of PU.1-bound enhancers were unique to eosinophils - an eosinophil-specific PU.1 regulome. GO analysis of eosinophil-specific PU.1-bound enhancers revealed enrichmend for genes involved in migration, proliferation, degranulation and survival. Collectively, our data identify eosinophil-specific enhancers regulating key eosinophil genes through epigenetic mechanisms and TF binding. These findings are supportive of a dynamic, epigenetic eosinophil regulome underlying eosinophil function and diversity.
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