Similar Datasets
Project description:We find that the myeloid master regulatory transcription factor, PU.1, binds to >16,000 sites in both normal and leukemic erythroid cells. Of these bound sites, ~7,000 lie within 2kb of TSS of a gene, suggesting PU.1 may regulate a large number of genes in erythroid cells. Coupling this data with gene expression analysis, we show PU.1 directly regulates several critical signaling pathways in erythroid cells. Assaying PU.1 occupancy in normal and leukemic erythroid cells
2011-06-23 | E-GEOD-21950 | biostudies-arrayexpress
Project description:"Master" transcription factors are the gatekeepers of lineage identity. As such, they have been a major focus of efforts to manipulate cell fate for therapeutic purposes. The ETS transcription factor PU.1 has a potent ability to confer macrophage phenotypes on cells already committed to a different lineage, but how it overcomes the presence of other master regulators is not known. The nuclear receptor PPARM-NM-3 is the master regulator of the adipose lineage, and its genomic binding pattern is well characterized in adipocytes. Here, we show that when expressed at macrophage levels in mature adipocytes, PU.1 bound a large fraction of its macrophage sites, where it induced chromatin opening and the expression of macrophage target genes. Strikingly, PU.1 markedly reduced the genomic binding of PPARM-NM-3 without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARM-NM-3 binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARM-NM-3 cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator. ChIP-seq was performed on 3T3-L1 adipocytes from two treatment groups: (1) adipocytes transduced with a control adenovirus expressing beta-galactosidase (LACZ-Ads) and (2) adipocytes transduced with an adenovirus expressing full-length murine PU.1 cDNA (PU.1-Ads). Nuclear lysates from each group were used for PPARg ChIP. For PU.1-Ads, PU.1 ChIP was also performed. To generate chromatin for ChIP-seq, DNA from three immunoprecipitations per condition was pooled. This process was repreated from a second set of L1 adipocytes to generate two biological replicates for sequencing. Genomic input DNA was sequenced from the first biological replicate only.
2013-06-27 | E-GEOD-48343 | biostudies-arrayexpress
Project description:PU.1 is a prototype master transcription factor (TF) of hematopoietic cell differentiation with diverse roles in different lineages. Analysis of its genome-wide binding pattern across PU.1 expressing cell types revealed manifold cell type-specific binding patterns. They are not consistent with the epigenetic and chromatin constraints to PU.1 binding observed in vitro, suggesting that PU.1 requires auxiliary factors to access DNA in vivo. Using a model of transient mRNA expression we show that PU.1 induction leads to the extensive remodeling of chromatin, redistribution of partner transcription factors and rapid initiation of a myeloid gene expression program in heterologous cell types. By probing PU.1 mutants for defects in chromatin access and screening for PU.1 proximal proteins in vivo, we found that its N-terminal acidic domain was required for the recruitment of SWI/SNF remodeling complexes, de novo chromatin access and stable binding as well as the redistribution of partner TFs.
2019-11-20 | PXD013167 | Pride
Project description:PU.1 is an Ets family transcription factor that is essential for the differentiation of both myeloid and lymphoid cells. PU.1 is down-regulated in classical Hodgkin lymphoma cells via methylation of the PU.1 promoter. To evaluate whether down-regulation of PU.1 is essential for the growth of cHL cells, we generated L428 derived cell lines conditionally express PU.1 by tet-off system (designated L428tetPU.1). Conditonally expressed PU.1 by tetracycline removal induced complete growth arrest and apoptosis in L428 cells. To elucidate the mechanisms underlying cell cycle arrest and apoptosis induced by PU.1, we compared gene expression profiles of L428tetPU.1 cells 0, 1 and 3 days after PU.1 induction, by DNA microarray. We extracted total RNA from L428tetPU.1 cells 0, 1 and 3 days after PU.1 induction by tetracycline removal. We compared gene expression profiles of KL428tetPU.1 cells 0, 1 and 3 days after PU.1 induction using DNA microarray analysis. 4 independent experiments were performed with each RNA samples.
2012-11-22 | E-GEOD-42437 | biostudies-arrayexpress
Project description:miR-155 inhibits PU.1 expression, leading to the initiation of the initiation of plasma cell differentiation pathway. Additional PU.1 targets include a network of genes whose products are involved in adhesion, with direct links to B:T interactions. Sequencing analysis of PU.1 binding in B cells using Illumina ChIP-seq sample prep kit and Illumina platform. Cells were from ex-vivo LPS and IL-4 activated (96h) splenic B cells from wild type, PU.1[155-/155-] and miR-155[-/-] mice.
2014-09-26 | E-GEOD-61424 | biostudies-arrayexpress
Project description:The transcription factor PU.1 occupies a central role in controlling myeloid and early B cell development and its correct lineage-specific expression is critical for the differentiation choice of hematopoietic progenitors. However, little is known of how this tissue-specific pattern is established. We previously identified an upstream regulatory cis-element (URE) whose targeted deletion in mice decreases PU.1 expression and causes leukemia. We show here that the URE alone is insufficient to confer physiological PU.1 expression, but requires the cooperation with other, previously unidentified elements. Using a combination of transgenic studies, global chromatin assays and detailed molecular analyses we present evidence that Pu.1 is regulated by a novel mechanism involving cross-talk between different cis-elements together with lineage-restricted autoregulation. In this model, PU.1 regulates its expression in B cells and macrophages by differentially associating with cell-type specific transcription factors at one of its cis-regulatory elements to establish differential activity patterns at other elements. Two DNaseI hypersensitivity datasets; bone marrow derived-macrophages and Splenic CD19+IgM+ B cells were used to study PU.1 regulatory elements
2011-02-21 | E-GEOD-26550 | biostudies-arrayexpress
Project description:PU.1 is an Ets family transcription factor that is essential for the differentiation of both myeloid and lymphoid cells. PU.1 is down-regulated in classical Hodgkin lymphoma cells via methylation of the PU.1 promoter. To evaluate whether down-regulation of PU.1 is essential for the growth of cHL cells, we generated KM-H2 derived cell lines conditionally express PU.1 by tet-off system (designated KM-H2tetPU.1). Conditonally expressed PU.1 by tetracycline removal induced complete growth arrest and apoptosis in KM-H2 cells. To elucidate the mechanisms underlying cell cycle arrest and apoptosis induced by PU.1, we compared gene expression profiles of KM-H2tetPU.1 cells 0, 1 and 3 days after PU.1 induction, by DNA microarray. We extracted total RNA from KM-H2tetPU.1 cells 0, 1 and 3 days after PU.1 induction by tetracycline removal. We compared gene expression profiles of KM-H2tetPU.1 cells 0, 1 and 3 days after PU.1 induction using DNA microarray analysis. 4 independent experiments were performed with each RNA samples.
2012-11-22 | E-GEOD-42440 | biostudies-arrayexpress
Project description:The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 in-vivo and in-vitro to unveil basic features of occupied vs. non-occupied consensus sites. In addition to published PU.1 ChIP-seq data we mapped CTCF binding sites in monocytes and macrophages to determine chromatin domain boundaries and performed MCIp-seq in monocytes to reveal DNA methylation patterns across the genome. ChIP-seq of CTCF in human monocytes and human monocyte-derived macrophages as well as MCIp-seq in human monocytes
2013-05-15 | E-GEOD-43098 | biostudies-arrayexpress
Project description:We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression and perform PU.1 ChIP-seq in p53-deficient shPU.1 AML cells in vivo. This causes rapid cell cycle shutdown and myeloid differentiation. PU.1 restoration results in regression and clearance and prolongs survival.
2019-05-13 | GSE76933 | GEO
Project description:Downregulation of the hematopoietic transcription factor PU.1 in PU.1 low acute myeloid leukemia cells (AML) by novel heterocyclic diamidines or PU.1 inhibitors leads to decrease cell proliferation and apoptosis, representing a new therapeutic strategy for AML treatment. These inhibitors induces decreased PU.1 binding on its target sites, as well as deregulation in PU.1 canonical target genes We used microarray to identify the pathways deregulated after drug treatment.
2017-12-07 | GSE77651 | GEO