Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MafK mediates chromatin remodeling to silence IRF8 expression in non-immune cells in a lineage-specific manner

ABSTRACT: The regulation of gene expression is a result of a complex interplay between chromatin remodeling, transcription factors (TFs) and signaling molecules. Cell differentiation is accompanied by chromatin remodeling of specific loci to permanently silence genes that are not essential for the differentiated cell activity. The molecular cues that recruit the chromatin remodeling machinery are not well characterized. IRF8 is an immune-cell specific TF, and thus, serves as a model gene to elucidate the molecular mechanisms governing its silencing in non-immune cells. A high-throughput shRNA library screen in IRF8 expression-restrictive cells enabled the identification of MafK as modulator of IRF8 silencing, affecting chromatin architecture. ChIP-seq analysis revealed three MafK binding-regions (-25kb, -20kb and IRF8 6th intron) in the IRF8 locus. These MafK binding-sites are sufficient to repress a reporter-gene when cloned in genome-integrated lentiviral reporter constructs in expression-restrictive cells only, while plasmid-based constructs do not demonstrate such repressive effect. Furthermore, removal of MafK-int6 binding-region from BAC-IRF8 reporter construct was sufficient to promote accessible chromatin conformation. Taken together, we identified and characterized several MafK binding elements within the IRF8 locus that mediate repressive chromatin conformation resulting in the silencing of IRF8 expression only in non-immune cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE113145 | GEO | 2018/10/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from myelo-dendritic progenitors as well as from mature myeloid and dendritic cells

Project description:Dendritic cells (DCs) are essential regulators of immune responses; however, transcriptional mechanisms establishing DC lineage commitment are poorly defined. Here we report that the PU.1 transcription factor induces specific remodeling of the higher-order chromatin structure at the Interferon Regulatory Factor-8 (Irf8) gene to initiate DC fate choice. Generation of an Irf8 reporter mouse enabled us to pinpoint an initial progenitor stage at which DCs separate from other myeloid lineages in the bone marrow. In the absence of Irf8, this progenitor undergoes DC-to-neutrophil reprogramming, indicating that DC commitment requires an active, Irf8-dependent escape from alternative myeloid lineage potential. Mechanistically, myeloid Irf8 expression depends on high PU.1 levels, resulting in local chromosomal looping and activation of a lineage- and developmental stage-specific cis-enhancer. These data delineate PU.1 as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements, and suggest that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation. Mature macrophages, Granulocytes and DCs were isolated from wildtype mouse spleens for successive RNA extraction and hybridization on Affymetrix microarrays. 3 different pools, each consisting of splenic cells from 5 mice were prepared. Cell populations were isolated by flow cytometry. MDPs were isolated from Wildtype and IRF8 deficient bonemarrow by flowcytometry, again creating 3 biological replicates, each consisting of pooled cells from 5 mice. Differential gene expression between wildtype and IRF8 deficient MDPs was subgrouped into macrophage, granuloctic and DC signatures, derived from expression data of these cell populations.

2013-04-27 | E-GEOD-45467 | biostudies-arrayexpress

MafK mediates chromatin remodeling to silence IRF8 expression in non-immune cells in a lineage-specific manner

Project description:MafK mediates chromatin remodeling to silence IRF8 expression in non-immune cells in a lineage-specific manner

| PRJNA450258 | ENA

Expression data from myelo-dendritic progenitors as well as from mature myeloid and dendritic cells

2013-04-27 | GSE45467 | GEO

4C-Seq identify the interaction between IRF8 promoter and rs2280381-containing region

Project description:To test if there is a physical interaction between the IRF8 promoter and the rs2280381-containing region, we conducted circular chromatin conformation capture assay in the U937 cell. For the IRF8 viewpoint group, we used CSP6I as the first digested enzyme and NlaIII as the second enzyme. For the rs2280381-containing region, we used MboI as the first digested enzyme and NlaIII as the second enzyme. We use 4C-PCR primer to construct IRF8 point view and rs2280381-containing region 4C library.

2021-07-01 | E-MTAB-10120 | biostudies-arrayexpress

4C-Seq identify the interaction between IRF8 promoter and rs2280381-containing region in human primary monocyte

Project description:To test if lncRNA AC092723.1 play a role in physical interaction between the IRF8 promoter and the rs2280381-containing region, we conducted circular chromatin conformation capture assay in the human primary monocyte. We knock down lncRNA AC092723.1 by electro-transfecting ASOs, the control group is transfected negtive ASOs with no impact on lncRNA AC092723.1.We used CSP6I as the first digested enzyme and NlaIII as the second enzyme. After constructing 4C library,we then utilize 4C-PCR primer to construct IRF8 point view 4C library.

2022-02-25 | E-MTAB-11175 | biostudies-arrayexpress

Gene Expression of Small Cell Carcinoma of the Ovary-Hypercalcemic Type

Project description:<p>Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer afflicting young women at a median age of 24 years. SCCOHTs are characterized by loss of protein expression of SWI/SNF chromatin remodeling ATPases SMARCA4 and SMARCA2 through mutation and epigenetic silencing, respectively. This study aims to establish gene expression profiles of this cancer through RNA-Seq of four pathologically confirmed cases of SCCOHT tumors.</p>

| phs001528 | dbGaP

Factors for Epigenetic Silencing of Lung Cancer Genes

Project description:To test the hypothesis that the propensity for silencing of tumor suppressor genes in the respiratory epithelium of chronic smokers by promoter hypermethylation is influenced by sequence variations that modify the activity of genes and microRNAÕs that directly or indirectly influence de novo methylation and chromatin remodeling.

2014-09-29 | ST000104 | MetabolomicsWorkbench

The nucleoporin Nup170p is required for subtelomeric chromatin structure and gene silencing. [MNase-Seq]

Project description:Transcriptionally silent heterochromatin preferentially localizes at the nuclear periphery, but, despite this, certain budding yeast genes relocate to the nuclear periphery following gene activation, implicating the nuclear envelope in both transcriptional activation and silencing. It is unclear how these distinct chromatin domains are established, maintained and distinguished from one another at the nuclear envelope. Here we report that nuclear pore complexes (NPCs) facilitate the transition between chromatin states by providing a platform to which chromatin-remodeling and chromatin-modifying complexes bind. In particular, we show that the RSC chromatin-remodeling complex associates with NPCs and that the nucleoporin Nup170p nucleates heterochromatin formation at telomeres through recruitment of Sir4p. Deletion of NUP170 altered subtelomeric chromatin structure, reduced SIR complex binding at telomeres, impaired telomeric silencing and abated telomere tethering. These results support a model in which telomeric heterochromatin formation occurs through telomere-NPC interactions that both promote Sir4p binding at telomeres and permit chromatin-remodeling complexes to mediate the transition between chromatin states. Examination of genome-wide nucleosome positions in WT and nup170∆ cells via next-generation sequencing of mononucleosomal DNA.

2013-02-28 | E-GEOD-36792 | biostudies-arrayexpress

Gene expression change after inactivation of IRF8

Project description:Cancer cell type-selective addiction of transcription-chromatin regulatory program provides opportunities for therapeutic interventions. Here, we uncovered an IRF8-MEF2D transcription factor (TF) regulatory circuit as an acute myeloid leukemia (AML)-biased dependency. Combining CRISPR-based genetic screens, transcriptional analysis, and chromatin profiling, we demonstrated that a chromatin regulator, ZMYND8, directly regulates IRF8 and MYC expression through occupying AML-specific enhancer regions. ZMYND8 was essential for AML proliferation both in vitro and in vivo. The ZMYND8-occupied IRF8 enhancer was further characterized using Circular Chromosome Conformation Capture and CRISPRi-based perturbation assays and was observed in primary patient cells. Importantly, mutagenesis experiments revealed that the PHD/Bromodomain/PWWP reader module is required for ZMYND8 tethering to leukemia-essential co-activator BRD4 for enhancer-mediated gene regulation. Our results rationalize ZMYND8 as a potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML.

2021-08-04 | GSE157249 | GEO