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Identification of PU.1 target genes by expression profiling of PUER cells

ABSTRACT: PU.1 is a key transcription factor for macrophage differentiation. Novel PU.1 target genes were identified by mRNA profiling of PU.1-deficient progenitor cells (PUER) before and after PU.1 activation. We used two different types of Affymetrix DNA-microarrays (430 2.0 arrays and ST 1.0 exon arrays) to characterize the global PU.1-regulated transcriptional program underlying the early processes of macrophage differentiation. Keywords: time course

ORGANISM(S): Mus musculus

PROVIDER: GSE13125 | GEO | 2008/10/11

SECONDARY ACCESSION(S): PRJNA109667

REPOSITORIES: GEO

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Identification of PU.1 target genes by expression profiling of PUER cells

Project description:PU.1 is a key transcription factor for macrophage differentiation. Novel PU.1 target genes were identified by mRNA profiling of PU.1-deficient progenitor cells (PUER) before and after PU.1 activation. We used two different types of Affymetrix DNA-microarrays (430 2.0 arrays and ST 1.0 exon arrays) to characterize the global PU.1-regulated transcriptional program underlying the early processes of macrophage differentiation. Keywords: time course Uninduced and 24h 4-hydroxy-tamoxifen (OHT) induced PUER cells were cultured before RNA extraction and hybridization on Affymetrix Mouse Genome 430 2.0 and Mouse Exon ST 1.0 microarrays. Triplicates before (0h) and after (24h) induction of PU.1 were analyzed.

2008-10-11 | E-GEOD-13125 | biostudies-arrayexpress

Activation of Wnt/Î²-catenin Signaling Blocks Monocyte-Macrophage Differentiation Through Antagonizing PU.1-Targeted Gene Transcription

Project description:We have shown that Î²-catenin overexpression induced blockage of monocyte-macrophage differentiation by inhibiting PU.1-targeted gene transcription including Egr2 expression in myeloid progenitor cells. Our results suggest that compromised PU.1-targeted gene transcription induced by Î²-catenin overexpression, at least partially, may mediate a pathogenic role of Î²-catenin in myeloid leukemia. PUER cells were infected with retrovirus expressing beta-catenin-S33Y or control vector MIGR1. Five days after infection, the GFP positive cells were sorted by flow cytometry, and were treated with 4-OHT to induce the expression of PU.1. Total RNA was exacted from cell samples and purified by RNeasy Micro kit (Qiagen). cRNAs were generated and hybridized to the mouse whole genome 4Ã44K arrays according to manufacturerâs instructions (Agilent Technologies).

2016-04-06 | E-GEOD-79932 | biostudies-arrayexpress

Genome-wide ChIP-seq binding profiles and linked gene expression arrays [array]

Project description:Pu.1-mutated murine AML cell line X18.1.1 transfected with inducible Pu.1 (PuER) or empty vector (EV) and clonal lines selected. Cells were induced with OHT for 2 hours prior to collection for ChIPSeq and expression arrays.

2015-12-08 | GSE64068 | GEO

Genome-wide ChIP-seq binding profiles and linked gene expression arrays [ChIP-seq]

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Comparisons of Affymetrix Whole-Transcript Human Gene 1.0 ST array with standard 3' expression arrays

Project description:The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array. Keywords: Cross-platform comparison

2008-02-01 | GSE9819 | GEO

Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1 (expression)

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 PPARγ 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 PPARγ without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARγ binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARγ cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator. Microarray expression profiling 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). Each sample group consists of four biological replicates which are here defined as separate differentiations of mature 3T3-L1 adipocytes and adenoviral infections. Each replicate was hybridized to an individual array for a total of eight arrays.

2013-06-27 | E-GEOD-48344 | biostudies-arrayexpress

Transcription profiling of hematopoietic stem cells in the preleukemic phase from wiltype mice and mice deficient in transcription factor PU.1 to identify transcriptional changes preceding malignant transformation

Project description:Knockdown of the transcription factor PU.1 (Spi1) leads to acute myeloid leukemia (AML) in mice. We examined the transcriptome of PU.1 knockdown hematopoietic stem cells (HSC) in the preleukemic phase by linear amplification and genome-wide array analysis to identify transcriptional changes preceding malignant transformation. Hierarchical cluster analysis and principal component analysis clearly distinguished PU.1 knockdown from wildtype HSC. Jun family transcription factors c-Jun and JunB were among the top downregulated targets. Retroviral restoration of c-Jun expression in bone marrow cells of preleukemic mice partially rescued the PU.1-initiated myelomonocytic differentiation block. Lentiviral restoration of JunB at the leukemic stage led to reduced clonogenic growth, loss of leukemic self-renewal capacity, and prevented leukemia in transplanted NOD-SCID mice. Examination of 305 AML patients confirmed the correlation between PU.1 and JunB downregulation and suggests its relevance in human disease. These results delineate a transcriptional pattern that precedes the leukemic transformation in PU.1 knockdown HSC and demonstrate that decreased levels of c-Jun and JunB contribute to the development of PU.1-induced AML by blocking differentiation (c-Jun) and increasing self-renewal (JunB). Therefore, examination of disturbed gene expression in HSC can identify genes whose dysregulation is essential for leukemic stem cell function and are targets for therapeutic interventions. Experiment Overall Design: Total RNA of HSC of PU.1 knockdown or wildtype animals (3 pools of 3 animals each) was amplified by two rounds of RT and T7 promoter-based in-vitro transcription and the resultant biotinylated cRNA was then hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

2007-11-22 | E-GEOD-5654 | biostudies-arrayexpress

Genome-wide ChIP-seq binding profiles and linked gene expression arrays [array]

2015-12-08 | E-GEOD-64068 | biostudies-arrayexpress

Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1 (ChIP-seq)

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

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Project description:The aim of this study is to survey global gene expression across a range of mouse tissues. Biotinylated cRNA was synthesized from total RNA, then fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays at the Siteman Cancer Center Gene Chip Core Facility (Washington University, St Louis, Missouri) according to manufacturer's protocols. Image files were generated using MicroArray Suite 5.0 (Affymetrix). Keywords: other

2007-02-23 | GSE1986 | GEO

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